From gordonp at pub.open-bio.org Fri Sep 3 16:28:16 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Fri Sep 3 16:04:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409032028.i83KSGf5010451@pub.open-bio.org> gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv10407/src/main/org/biomoby/client Modified Files: MobyRequest.java Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/07/07 16:02:47 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/09/03 20:28:16 1.5 @@ -506,6 +506,24 @@ throw new MobyException("The MOBY payload has no text contents at all"); } + // Check if the payload is an XML document. If not, try a last ditch effort + // by base64 decoding the contents. This is technically not allowable in the + // MOBY spec, but we are being lenient. + if(!responseString.startsWith(" gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv10407/docs Modified Files: ChangeLog Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/docs ChangeLog,1.16,1.17 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/07/07 16:07:46 1.16 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/03 20:28:16 1.17 @@ -1,3 +1,11 @@ +2004-09-03 Paul Gordon + + * First commit of data instance classes for base objects (Floats, Integers, Strings), + and updates to Simple and Service Associated Instance objects to deal with the new + object types. You can now create these objects (no XML knowledge required) for + use in services, and you can create complex Moby objects using DOM fragments. + Aggregation of base objects to create complex objects still needs to be implemented. + 2004-07-07 Paul Gordon * Modifications to MobyRequest to handle Axis 1.1beta, and a variety of From gordonp at pub.open-bio.org Fri Sep 3 16:28:16 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Fri Sep 3 16:05:54 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409032028.i83KSGmd010476@pub.open-bio.org> gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv10407/src/main/org/biomoby/shared Modified Files: MobyDataServiceAssocInstance.java MobyDataSimpleInstance.java Added Files: MobyDataFloat.java MobyDataInt.java MobyDataString.java Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/src/main/org/biomoby/shared MobyDataFloat.java,NONE,1.1 MobyDataInt.java,NONE,1.1 MobyDataString.java,NONE,1.1 MobyDataServiceAssocInstance.java,1.1,1.2 MobyDataSimpleInstance.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java 2004/09/03 20:28:16 1.2 @@ -3,30 +3,92 @@ import org.w3c.dom.Element; /** - * A convenience class that just associates a set of possible services to run with a data instance + * A convenience class that just associates a set of possible services to run with a data instance. */ public class MobyDataServiceAssocInstance extends MobyDataSimpleInstance{ + protected MobyDataSimpleInstance dataInstance; protected MobyService[] mobyServices; - public MobyDataServiceAssocInstance(MobyDataType type, String name, String value, MobyService[] services){ - super(type, name, value); + public MobyDataServiceAssocInstance(MobyDataType type, String name, String id, MobyService[] services){ + super(type, name, id); mobyServices = services; + dataInstance = this; } public MobyDataServiceAssocInstance(Central central, Element simple, MobyService[] services) throws MobyException{ super(central, simple); mobyServices = services; + dataInstance = this; } public MobyDataServiceAssocInstance(MobyDataSimpleInstance mdsi, MobyService[] services){ - super(mdsi.getDataType(), mdsi.getName(), mdsi.getId()); - setValue(mdsi.getValue()); + super(mdsi.getName()); + dataInstance = (MobyDataSimpleInstance) mdsi.clone(); mobyServices = services; } + public Object clone(){ + if(dataInstance == this){ + // Avoid recursion, we're using the simple instance base behaviours + return super.clone(); + } + else{ + // Clone according to the base instance's subclass specific methods + return new MobyDataServiceAssocInstance(dataInstance, mobyServices); + } + } + public MobyService[] getServices(){ return mobyServices; } + + public MobyDataType getDataType(){ + return dataInstance.getDataType(); + } + + public void setServices(MobyService[] services){ + mobyServices = services; + } + + public void setXmlMode(int mode) throws IllegalArgumentException{ + dataInstance.setXmlMode(mode); + } + + public String getValue(){ + return dataInstance.getValue(); + } + + public void setId(String value){ + dataInstance.setId(value); + } + + public String getId(){ + return dataInstance.getId(); + } + + public void addNamespace(MobyNamespace ns){ + dataInstance.addNamespace(ns); + } + + public MobyNamespace[] getNamespaces(){ + return dataInstance.getNamespaces(); + } + + public void setValue(Element simple) throws javax.xml.transform.TransformerException{ + dataInstance.setValue(simple); + } + + public void setValue(String value){ + dataInstance.setValue(value); + } + + public String toString(){ + return dataInstance.toString(); + } + + public String toXML(){ + return dataInstance.toXML(); + } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/03 20:28:16 1.2 @@ -24,7 +24,7 @@ * SERVICE_XML_MODE. */ -public class MobyDataSimpleInstance extends MobyPrimaryDataSimple implements MobyDataInstance{ +public class MobyDataSimpleInstance extends MobyPrimaryDataSimple implements MobyDataInstance, Cloneable{ public static final int CENTRAL_XML_MODE = 124; public static final int SERVICE_XML_MODE = 891; protected int xmlMode = SERVICE_XML_MODE; @@ -36,10 +36,10 @@ * If you're looking to pass in an XML string for the constructor, you can't. You can use * the one argument constructor or this one, then use setValue(String). */ - public MobyDataSimpleInstance(MobyDataType dataType, String name, String value){ + public MobyDataSimpleInstance(MobyDataType dataType, String name, String id){ super(name); setDataType(dataType); - setId(value); + setId(id); } /** @@ -51,11 +51,27 @@ } /** + * Creates a simple object from the input instance, as opposed to clone, which creates + * an exact copy. + */ + public MobyDataSimpleInstance(MobyDataSimpleInstance mdsi){ + super(mdsi.getName()); + } + + /** * Standard constructor, build the object value using a DOM element. * @throws MobyException if the XML passed in does not have a moby:Simple root node */ public MobyDataSimpleInstance(Central mobyCentral, Element simple) throws MobyException{ super(MobyPrefixResolver.getAttr(simple, "articleName")); + + if(!simple.getLocalName().equals("Simple") || !(simple.getNamespaceURI() == null || + simple.getNamespaceURI().length() == 0 || + simple.getNamespaceURI().equals(MobyPrefixResolver.MOBY_XML_NAMESPACE))){ + throw new MobyException("Element passed to MobyDataSimpleInstance was not a moby:Simple, but " + + simple.getNodeName()); + } + NodeList children = simple.getElementsByTagName("*"); if(children == null || children.getLength() == 0){ throw new MobyException("Simple element (" + simple + @@ -172,6 +188,26 @@ public String toString(){ return dataValue; } + + /** + * Simply calls new constructor with object's existing data type, name and value. + * Subclasses should override this method if more datafields need to be copied for + * an accurate clone of the Moby Data Instance (i.e. anything but a base object). The + * subclasses should ensure that they also return a MobyDataSimpleInstance + * + * @return an object of class MobyDataSimpleInstance + */ + public Object clone(){ + MobyDataSimpleInstance copy = null; + copy = new MobyDataSimpleInstance(getName()); + copy.setDataType(getDataType()); + copy.setNamespaces(getNamespaces()); + copy.setId(getId()); + if(!isObject){ // Complex object that has its own XML representation we'll just copy over + copy.setValue(getValue()); + } + return copy; + } /** * Produces a full-blown XML fragment that depending on the value of getXmlMode() is either From mwilkinson at pub.open-bio.org Fri Sep 10 19:34:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Fri Sep 10 19:09:32 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409102334.i8ANYbGt014004@pub.open-bio.org> mwilkinson Fri Sep 10 19:34:37 EDT 2004 Update of /home/repository/moby/moby-live/Accessories In directory pub.open-bio.org:/tmp/cvs-serv13986/Accessories Log Message: Directory /home/repository/moby/moby-live/Accessories added to the repository moby-live/Accessories - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 12:58:56 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:30:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131658.i8DGwulk031796@pub.open-bio.org> kawas Mon Sep 13 12:58:55 EDT 2004 Update of /home/repository/moby/Accessories In directory pub.open-bio.org:/tmp/cvs-serv31772 Log Message: Create module Status: Vendor Tag: vendor-tag Release Tags: release-tag No conflicts created by this import Accessories - Imported sources rcsdiff: /home/repository/moby/Accessories/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/Accessories/RCS/Imported,v: No such file or directory rcsdiff: /home/repository/moby/Accessories/RCS/sources,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:11:43 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:46:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131811.i8DIBhls032217@pub.open-bio.org> kawas Mon Sep 13 14:11:43 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv32193/ObjectCreationTool Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool added to the repository moby-live/Accessories/ObjectCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:29 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrgX032309@pub.open-bio.org> kawas Mon Sep 13 14:13:52 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv32284/img Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img added to the repository moby-live/Accessories/ObjectCreationTool/img - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDr3F032345@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrhb032327@pub.open-bio.org> kawas Mon Sep 13 14:13:52 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:34 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrZm032404@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrwf032386@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDswG032453@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:35 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrtB032365@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsIE032517@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby/client Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby/client - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDslx032428@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsib032493@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsW0032475@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org In directory pub.open-bio.org:/tmp/cvs-serv32284/org Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org added to the repository moby-live/Accessories/ObjectCreationTool/org - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtnW032535@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby/shared Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtJG032635@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/util Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/util - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtTf032574@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDt5r032556@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtMo032617@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object/creation/applet Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:43 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtJD032597@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object/creation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEA1W032718@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/text Added Files: AlignCenter16.gif AlignLeft16.gif AlignJustify16.gif AlignRight16.gif Bold16.gif Bold24.gif Italic24.gif AlignCenter24.gif Normal24.gif AlignRight24.gif AlignJustify24.gif Italic16.gif Normal16.gif AlignLeft24.gif Underline16.gif Underline24.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text AlignCenter16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Bold16.gif,NONE,1.1 Bold24.gif,NONE,1.1 Italic24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Normal24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Italic16.gif,NONE,1.1 Normal16.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Underline16.gif,NONE,1.1 Underline24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEAut032687@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/general Added Files: SaveAs24.gif Redo16.gif About24.gif Bookmarks24.gif Paste16.gif AlignRight24.gif Cut24.gif Delete16.gif PageSetup16.gif AlignLeft24.gif Replace24.gif FindAgain16.gif Edit16.gif Save24.gif Export24.gif AlignBottom24.gif SaveAs16.gif Save16.gif AlignTop16.gif Export16.gif Paste24.gif History16.gif Print24.gif Help16.gif PageSetup24.gif AlignTop24.gif AlignBottom16.gif Bookmarks16.gif Import16.gif PrintPreview24.gif Information16.gif SendMail16.gif SendMail24.gif SaveAll24.gif Replace16.gif ZoomOut16.gif ZoomIn24.gif Add24.gif Copy24.gif ComposeMail16.gif Import24.gif Remove24.gif FindAgain24.gif ContextualHelp24.gif SaveAll16.gif History24.gif Stop24.gif Redo24.gif Print16.gif Edit24.gif ComposeMail24.gif Open16.gif AlignJustifyVertical24.gif Help24.gif Find24.gif New24.gif TipOfTheDay16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif About16.gif Add16.gif Copy16.gif PrintPreview16.gif ZoomOut24.gif New16.gif Open24.gif Remove16.gif AlignLeft16.gif ContextualHelp16.gif Preferences16.gif AlignJustifyHorizontal16.gif Cut16.gif Refresh24.gif AlignCenter24.gif Search24.gif Zoom24.gif Delete24.gif Properties24.gif ZoomIn16.gif TipOfTheDay24.gif Zoom16.gif Refresh16.gif Information24.gif Undo16.gif Search16.gif Preferences24.gif Properties16.gif Undo24.gif Stop16.gif AlignCenter16.gif Find16.gif AlignRight16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general SaveAs24.gif,NONE,1.1 Redo16.gif,NONE,1.1 About24.gif,NONE,1.1 Bookmarks24.gif,NONE,1.1 Paste16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Cut24.gif,NONE,1.1 Delete16.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Replace24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Edit16.gif,NONE,1.1 Save24.gif,NONE,1.1 Export24.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 Save16.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Export16.gif,NONE,1.1 Paste24.gif,NONE,1.1 History16.gif,NONE,1.1 Print24.gif,NONE,1.1 Help16.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignBottom16.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 Import16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Information16.gif,NONE,1.1 SendMail16.gif,NONE,1.1 SendMail24.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 Replace16.gif,NONE,1.1 ZoomOut16.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 Add24.gif,NONE,1.1 Copy24.gif,NONE,1.1 ComposeMail16.gif,NONE! ,1.1 Import24.gif,NONE,1.1 Remove24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 History24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Redo24.gif,NONE,1.1 Print16.gif,NONE,1.1 Edit24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 Open16.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Help24.gif,NONE,1.1 Find24.gif,NONE,1.1 New24.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 About16.gif,NONE,1.1 Add16.gif,NONE,1.1 Copy16.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 New16.gif,NONE,1.1 Open24.gif,NONE,1.1 Remove16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 ContextualHelp16.gif,NONE,1.1 Preferences16.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 Cut16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Search24.gif,NONE,1.1 Zoom24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Properties24.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 Zoom16.gif,NONE! ,1.1 Refresh16.gif,NONE,1.1 Information24.gif,NONE,1.1 Undo16! .gif,NONE,1.1 Search16.gif,NONE,1.1 Preferences24.gif,NONE,1.1 Properties16.gif,NONE,1.1 Undo24.gif,NONE,1.1 Stop16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Find16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEADs032702@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32666/org/biomoby/shared Added Files: PendingCurationException.java MobyObject.java MobyDataType.java MobyDataInstance.java MobyDataSetInstance.java MobyDataSimpleInstance.java MobyDataSecondaryInstance.java MobyPrimaryDataSet.java NoSuccessException.java MobyNamespace.java MobyException.java Central.java MobyServiceType.java MobySecondaryData.java MobyNativeService.java MobyData.java MobyPrefixResolver.java SOAPException.java MobyService.java MobyDataServiceAssocInstance.java MobyPrimaryDataSimple.java Utils.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/biomoby/shared PendingCurationException.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyDataType.java,NONE,1.1 MobyDataInstance.java,NONE,1.1 MobyDataSetInstance.java,NONE,1.1 MobyDataSimpleInstance.java,NONE,1.1 MobyDataSecondaryInstance.java,NONE,1.1 MobyPrimaryDataSet.java,NONE,1.1 NoSuccessException.java,NONE,1.1 MobyNamespace.java,NONE,1.1 MobyException.java,NONE,1.1 Central.java,NONE,1.1 MobyServiceType.java,NONE,1.1 MobySecondaryData.java,NONE,1.1 MobyNativeService.java,NONE,1.1 MobyData.java,NONE,1.1 MobyPrefixResolver.java,NONE,1.1 SOAPException.java,NONE,1.1 MobyService.java,NONE,1.1 MobyDataServiceAssocInstance.java,NONE,1.1 MobyPrimaryDataSimple.java,NONE,1.1 Utils.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:51 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBmj032734@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv32666/org/mobycentral/util Added Files: MobyXML.java TreeLoaderThread.java Registration.java MobyUtilities.java MobyPlainText.java Household.java Pair.java Construct.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/mobycentral/util MobyXML.java,NONE,1.1 TreeLoaderThread.java,NONE,1.1 Registration.java,NONE,1.1 MobyUtilities.java,NONE,1.1 MobyPlainText.java,NONE,1.1 Household.java,NONE,1.1 Pair.java,NONE,1.1 Construct.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDKl000389@pub.open-bio.org> kawas Mon Sep 13 14:14:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/media Added Files: Play24.gif Pause24.gif Pause16.gif Rewind24.gif Stop24.gif StepForward24.gif Volume24.gif Movie24.gif Volume16.gif FastForward16.gif StepBack24.gif Movie16.gif StepForward16.gif Play16.gif FastForward24.gif StepBack16.gif Rewind16.gif Stop16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media Play24.gif,NONE,1.1 Pause24.gif,NONE,1.1 Pause16.gif,NONE,1.1 Rewind24.gif,NONE,1.1 Stop24.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Volume24.gif,NONE,1.1 Movie24.gif,NONE,1.1 Volume16.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Movie16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Play16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 Rewind16.gif,NONE,1.1 Stop16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEB4Z032752@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/development Added Files: Application16.gif Bean16.gif Application24.gif J2EEApplicationClientAdd24.gif J2EEServer24.gif WebComponent24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBean16.gif Host24.gif EnterpriseJavaBean24.gif ApplicationDeploy16.gif BeanAdd16.gif Jar16.gif BeanAdd24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClient16.gif Bean24.gif War24.gif WebComponentAdd16.gif J2EEApplicationClient24.gif Host16.gif J2EEServer16.gif JarAdd24.gif WarAdd16.gif ApplicationDeploy24.gif WebComponentAdd24.gif J2EEApplication24.gif Jar24.gif JarAdd16.gif Applet16.gif WebComponent16.gif War16.gif Server24.gif EnterpriseJavaBeanJar24.gif WarAdd24.gif Server16.gif Applet24.gif J2EEApplication16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development Application16.gif,NONE,1.1 Bean16.gif,NONE,1.1 Application24.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Host24.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 Jar16.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 Bean24.gif,NONE,1.1 War24.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 Host16.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 JarAdd24.gif,NONE,1.1 WarAdd16.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 Jar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 Applet16.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 War16.gif,NONE,1.1 Server24.gif,NONE,1.1 EnterpriseJavaBean! Jar24.gif,NONE,1.1 WarAdd24.gif,NONE,1.1 Server16.gif,NONE,1.1 Applet24.gif,NONE,1.1 J2EEApplication16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDSe000371@pub.open-bio.org> kawas Mon Sep 13 14:14:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/table Added Files: ColumnDelete16.gif RowDelete16.gif RowInsertAfter16.gif ColumnInsertAfter24.gif RowInsertBefore24.gif ColumnInsertBefore24.gif ColumnInsertAfter16.gif RowInsertAfter24.gif ColumnDelete24.gif RowInsertBefore16.gif ColumnInsertBefore16.gif RowDelete24.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table ColumnDelete16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 ColumnInsertAfter16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBBa000338@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv32666/img Added Files: LICENSE bio.gif moby.gif MOBY-S.jpeg java.gif moby1.gif left.gif moby_small.gif middle.gif right.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img LICENSE,NONE,1.1 bio.gif,NONE,1.1 moby.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 java.gif,NONE,1.1 moby1.gif,NONE,1.1 left.gif,NONE,1.1 moby_small.gif,NONE,1.1 middle.gif,NONE,1.1 right.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBZk000304@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/navigation Added Files: Home16.gif Up24.gif Down16.gif Up16.gif Forward24.gif Home24.gif Forward16.gif Back24.gif Down24.gif Back16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation Home16.gif,NONE,1.1 Up24.gif,NONE,1.1 Down16.gif,NONE,1.1 Up16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Home24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Back24.gif,NONE,1.1 Down24.gif,NONE,1.1 Back16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:57 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBLc000322@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32666/org/biomoby/client Added Files: ServletFileCache.java MobyRequest.java SimpleCache.java FilterServices.java ServiceConnections.java GraphsServlet.java RDF.java Graphviz.java ServicesEdge.java FileCache.java CentralImpl.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/biomoby/client ServletFileCache.java,NONE,1.1 MobyRequest.java,NONE,1.1 SimpleCache.java,NONE,1.1 FilterServices.java,NONE,1.1 ServiceConnections.java,NONE,1.1 GraphsServlet.java,NONE,1.1 RDF.java,NONE,1.1 Graphviz.java,NONE,1.1 ServicesEdge.java,NONE,1.1 FileCache.java,NONE,1.1 CentralImpl.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIECTo000353@pub.open-bio.org> kawas Mon Sep 13 14:14:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv32666/org/mobycentral/object/creation/applet Added Files: ObjectCreationTool.java MobyTree.java ButtonActions.java FieldFocusListeners.java MobyUserPanel.java ButtonBeautifier.java FieldKeyListener.java TreeListener.java PanelFactory.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet ObjectCreationTool.java,NONE,1.1 MobyTree.java,NONE,1.1 ButtonActions.java,NONE,1.1 FieldFocusListeners.java,NONE,1.1 MobyUserPanel.java,NONE,1.1 ButtonBeautifier.java,NONE,1.1 FieldKeyListener.java,NONE,1.1 TreeListener.java,NONE,1.1 PanelFactory.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 13:48:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDcg000410@pub.open-bio.org> kawas Mon Sep 13 14:14:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv32666 Added Files: .project .classpath Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool .project,NONE,1.1 .classpath,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWQs001120@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWA8001084@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets added to the repository moby-live/Accessories/ObjectCreationTool/Applets - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWTb001102@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/Demo Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo added to the repository moby-live/Accessories/ObjectCreationTool/Applets/Demo - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXCP001159@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXUl001265@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXx9001182@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXP9001139@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXqa001202@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXKK001286@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/lib Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib added to the repository moby-live/Accessories/ObjectCreationTool/Applets/lib - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXZX001306@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/offline Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline added to the repository moby-live/Accessories/ObjectCreationTool/Applets/offline - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCX76001247@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:47:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCX3Q001226@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJV8W001373@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/general Added Files: ZoomOut16.gif Add16.gif Copy16.gif AlignRight16.gif PrintPreview16.gif AlignLeft16.gif Add24.gif Import16.gif Redo16.gif Import24.gif Edit16.gif Refresh24.gif Export24.gif Stop24.gif About16.gif Remove16.gif Undo16.gif AlignCenter16.gif Find16.gif Undo24.gif Remove24.gif ZoomIn24.gif Search16.gif History16.gif Copy24.gif ComposeMail16.gif Help16.gif History24.gif Cut16.gif Paste24.gif Refresh16.gif Replace16.gif Properties16.gif Replace24.gif About24.gif AlignTop24.gif AlignRight24.gif Print16.gif Paste16.gif ContextualHelp24.gif Information16.gif Save16.gif ContextualHelp16.gif AlignTop16.gif Information24.gif SaveAll16.gif Properties24.gif SaveAs16.gif Find24.gif AlignJustifyHorizontal24.gif Zoom24.gif Preferences16.gif Edit24.gif SendMail16.gif PageSetup24.gif AlignBottom24.gif PageSetup16.gif TipOfTheDay16.gif AlignJustifyVertical16.gif Search24.gif ZoomOut24.gif Print24.gif Delete16.gif Export16.gif SendMail24.gif SaveAll24.gif AlignLeft24.gif Help24.gif FindAgain24.gif Zoom16.gif Open24.gif SaveAs24.gif Preferences24.gif Save24.gif New24.gif AlignJustifyVertical24.gif Delete24.gif Redo24.gif Bookmarks24.gif FindAgain16.gif Stop16.gif AlignBottom16.gif AlignJustifyHorizontal16.gif AlignCenter24.gif ComposeMail24.gif ZoomIn16.gif PrintPreview24.gif Open16.gif Bookmarks16.gif New16.gif Cut24.gif TipOfTheDay24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general ZoomOut16.gif,NONE,1.1 Add16.gif,NONE,1.1 Copy16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Add24.gif,NONE,1.1 Import16.gif,NONE,1.1 Redo16.gif,NONE,1.1 Import24.gif,NONE,1.1 Edit16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 Export24.gif,NONE,1.1 Stop24.gif,NONE,1.1 About16.gif,NONE,1.1 Remove16.gif,NONE,1.1 Undo16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Find16.gif,NONE,1.1 Undo24.gif,NONE,1.1 Remove24.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 Search16.gif,NONE,1.1 History16.gif,NONE,1.1 Copy24.gif,NONE,1.1 ComposeMail16.gif,NONE,1.1 Help16.gif,NONE,1.1 History24.gif,NONE,1.1 Cut16.gif,NONE,1.1 Paste24.gif,NONE,1.1 Refresh16.gif,NONE,1.1 Replace16.gif,NONE,1.1 Properties16.gif,NONE,1.1 Replace24.gif,NONE,1.1 About24.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Print16.gif,NONE,1.1 Paste16.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 Informatio! n16.gif,NONE,1.1 Save16.gif,NONE,1.1 ContextualHelp16.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Information24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 Properties24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 Find24.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 Zoom24.gif,NONE,1.1 Preferences16.gif,NONE,1.1 Edit24.gif,NONE,1.1 SendMail16.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 Search24.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 Print24.gif,NONE,1.1 Delete16.gif,NONE,1.1 Export16.gif,NONE,1.1 SendMail24.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Help24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 Zoom16.gif,NONE,1.1 Open24.gif,NONE,1.1 SaveAs24.gif,NONE,1.1 Preferences24.gif,NONE,1.1 Save24.gif,NONE,1.1 New24.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Redo24.gif,NONE,1.1 Bookmarks24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Stop16.gif,NONE,1.1 AlignBot! tom16.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 Alig! nCenter24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Open16.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 New16.gif,NONE,1.1 Cut24.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJVOl001388@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/navigation Added Files: Down16.gif Forward24.gif Up24.gif Home16.gif Down24.gif Forward16.gif Up16.gif Back24.gif Home24.gif Back16.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Down16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Up24.gif,NONE,1.1 Home16.gif,NONE,1.1 Down24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Up16.gif,NONE,1.1 Back24.gif,NONE,1.1 Home24.gif,NONE,1.1 Back16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWNX001456@pub.open-bio.org> kawas Mon Sep 13 16:19:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/media Added Files: Pause24.gif Rewind24.gif StepForward24.gif Movie16.gif Stop16.gif FastForward24.gif Pause16.gif Volume16.gif Volume24.gif Play16.gif Movie24.gif FastForward16.gif StepBack24.gif Stop24.gif Play24.gif StepBack16.gif StepForward16.gif Rewind16.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media Pause24.gif,NONE,1.1 Rewind24.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Movie16.gif,NONE,1.1 Stop16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 Pause16.gif,NONE,1.1 Volume16.gif,NONE,1.1 Volume24.gif,NONE,1.1 Play16.gif,NONE,1.1 Movie24.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Play24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Rewind16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJVuk001404@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/table Added Files: ColumnDelete16.gif ColumnInsertBefore16.gif RowInsertAfter24.gif ColumnInsertAfter16.gif RowDelete16.gif RowInsertBefore16.gif ColumnDelete24.gif RowDelete24.gif RowInsertBefore24.gif RowInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 ColumnInsertAfter16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:11 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWvL001439@pub.open-bio.org> kawas Mon Sep 13 16:19:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/development Added Files: J2EEApplication16.gif WebComponent24.gif J2EEServer16.gif JarAdd24.gif J2EEApplicationClient16.gif J2EEApplicationClientAdd16.gif ApplicationDeploy16.gif J2EEApplicationClientAdd24.gif BeanAdd16.gif Application24.gif EnterpriseJavaBean16.gif Applet24.gif War24.gif BeanAdd24.gif Host24.gif Jar24.gif J2EEApplicationClient24.gif WebComponent16.gif Application16.gif WarAdd16.gif J2EEApplication24.gif Server16.gif Jar16.gif Bean16.gif WebComponentAdd24.gif EnterpriseJavaBeanJar24.gif JarAdd16.gif EnterpriseJavaBean24.gif Server24.gif ApplicationDeploy24.gif War16.gif Applet16.gif EnterpriseJavaBeanJar16.gif WarAdd24.gif Bean24.gif Host16.gif WebComponentAdd16.gif J2EEServer24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development J2EEApplication16.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 JarAdd24.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 Application24.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Applet24.gif,NONE,1.1 War24.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 Host24.gif,NONE,1.1 Jar24.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 Application16.gif,NONE,1.1 WarAdd16.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 Server16.gif,NONE,1.1 Jar16.gif,NONE,1.1 Bean16.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 EnterpriseJavaBeanJar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 Server24.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 War16.gif,NONE,1.1 Applet16.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE! ,1.1 WarAdd24.gif,NONE,1.1 Bean24.gif,NONE,1.1 Host16.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWWl001420@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/text Added Files: AlignLeft24.gif Underline16.gif Bold24.gif Bold16.gif AlignRight16.gif Underline24.gif AlignJustify16.gif AlignJustify24.gif Normal24.gif AlignCenter24.gif AlignCenter16.gif Italic24.gif AlignLeft16.gif Italic16.gif Normal16.gif AlignRight24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text AlignLeft24.gif,NONE,1.1 Underline16.gif,NONE,1.1 Bold24.gif,NONE,1.1 Bold16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Underline24.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Normal24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Italic24.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Italic16.gif,NONE,1.1 Normal16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJaa0001535@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/Demo Added Files: jena.jar icu4j.jar xercesImpl.jar index.htm Demo.jar commons-logging.jar demo2.htm Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/Demo jena.jar,NONE,1.1 icu4j.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 index.htm,NONE,1.1 Demo.jar,NONE,1.1 commons-logging.jar,NONE,1.1 demo2.htm,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:35 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJZbq001481@pub.open-bio.org> kawas Mon Sep 13 16:19:35 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/lib Added Files: antlr.jar xalan.jar log4j-1.2.7.jar jdom.jar jaxrpc.jar jaxen-core.jar commons-discovery.jar wsdl4j.jar saaj.jar axis.jar adenine.jar activation.jar concurrent.jar jena.jar junit.jar servlet.jar xercesImpl.jar jakarta-oro-2.0.5.jar saxpath.jar xml-apis.jar rdf-api-2001-01-19.jar icu4j.jar jaxen-jdom.jar commons-logging.jar alltools.jar axis-ant.jar Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/lib antlr.jar,NONE,1.1 xalan.jar,NONE,1.1 log4j-1.2.7.jar,NONE,1.1 jdom.jar,NONE,1.1 jaxrpc.jar,NONE,1.1 jaxen-core.jar,NONE,1.1 commons-discovery.jar,NONE,1.1 wsdl4j.jar,NONE,1.1 saaj.jar,NONE,1.1 axis.jar,NONE,1.1 adenine.jar,NONE,1.1 activation.jar,NONE,1.1 concurrent.jar,NONE,1.1 jena.jar,NONE,1.1 junit.jar,NONE,1.1 servlet.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 jakarta-oro-2.0.5.jar,NONE,1.1 saxpath.jar,NONE,1.1 xml-apis.jar,NONE,1.1 rdf-api-2001-01-19.jar,NONE,1.1 icu4j.jar,NONE,1.1 jaxen-jdom.jar,NONE,1.1 commons-logging.jar,NONE,1.1 alltools.jar,NONE,1.1 axis-ant.jar,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJaC1001513@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets Added Files: Untitled-2.htm tree-app.jar index-old.html service.jar service.html service-app.jar index.htm tree.jar Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets Untitled-2.htm,NONE,1.1 tree-app.jar,NONE,1.1 index-old.html,NONE,1.1 service.jar,NONE,1.1 service.html,NONE,1.1 service-app.jar,NONE,1.1 index.htm,NONE,1.1 tree.jar,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJa9U001496@pub.open-bio.org> kawas Mon Sep 13 16:19:35 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img Added Files: moby_small.gif left.gif LICENSE java.gif MOBY-S.jpeg middle.gif right.gif moby1.gif moby.gif bio.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img moby_small.gif,NONE,1.1 left.gif,NONE,1.1 LICENSE,NONE,1.1 java.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 middle.gif,NONE,1.1 right.gif,NONE,1.1 moby1.gif,NONE,1.1 moby.gif,NONE,1.1 bio.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:54:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJalF001550@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/offline Added Files: Namespaces Services Objects Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/offline Namespaces,NONE,1.1 Services,NONE,1.1 Objects,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:21:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 15:55:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132021.i8DKL3wf001599@pub.open-bio.org> kawas Mon Sep 13 16:21:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1578 Added Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:28:00 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 16:02:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132028.i8DKS0PM001776@pub.open-bio.org> kawas Mon Sep 13 16:28:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1751 Modified Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:21:03 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:28:00 1.2 @@ -34,7 +34,7 @@ There are also many various DEBUG flags that when enabled print out various pieces of information. - 3. There is a runnable version of the code located in the /moby-live/Accessories/ObjectToolApplet + 3. There is a runnable version of the code located in the /moby-live/Accessories/Applets To notify me of bugs or if you have comments please email me at the address below Eddie Kawas From kawas at pub.open-bio.org Mon Sep 13 16:30:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 16:04:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132030.i8DKUCRc001903@pub.open-bio.org> kawas Mon Sep 13 16:30:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1878 Modified Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:28:00 1.2 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:30:12 1.3 @@ -34,7 +34,7 @@ There are also many various DEBUG flags that when enabled print out various pieces of information. - 3. There is a runnable version of the code located in the /moby-live/Accessories/Applets + 3. There is a runnable version of the code located in the /moby-live/Accessories/ObjectCreationTool/Applets To notify me of bugs or if you have comments please email me at the address below Eddie Kawas From kawas at pub.open-bio.org Mon Sep 13 16:51:51 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 13 16:26:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132051.i8DKpp3m002023@pub.open-bio.org> kawas Mon Sep 13 16:51:51 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1990/Applets Modified Files: index.htm tree.jar tree-app.jar Log Message: Recreated the jar files and modified the applet page html moby-live/Accessories/ObjectCreationTool/Applets index.htm,1.1,1.2 tree.jar,1.1,1.2 tree-app.jar,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm 2004/09/13 20:19:36 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm 2004/09/13 20:51:50 1.2 @@ -10,7 +10,13 @@ Moby Object Creation Tool - +

=================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar 2004/09/13 20:19:36 1.1 and /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar 2004/09/13 20:51:50 1.2 differ rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar 2004/09/13 20:19:36 1.1 and /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar 2004/09/13 20:51:51 1.2 differ rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar: diff failed From mwilkinson at pub.open-bio.org Tue Sep 14 17:32:35 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Sep 14 17:07:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142132.i8ELWZGP006220@pub.open-bio.org> mwilkinson Tue Sep 14 17:32:35 EDT 2004 Update of /home/repository/moby/moby-live/Database In directory pub.open-bio.org:/tmp/cvs-serv6201 Modified Files: mobycentral.mysql Log Message: updating empty database schema moby-live/Database mobycentral.mysql,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Database/mobycentral.mysql,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Database/mobycentral.mysql 2003/05/24 20:22:15 1.3 +++ /home/repository/moby/moby-live/Database/mobycentral.mysql 2004/09/14 21:32:35 1.4 @@ -92,6 +92,7 @@ authoritative enum('1','0') NOT NULL default '0', description text NOT NULL, service_instance_id int(10) unsigned NOT NULL auto_increment, + signatureURL varchar(255), PRIMARY KEY (service_instance_id), UNIQUE KEY servicename (servicename,authority_id) ) TYPE=MyISAM; From mwilkinson at pub.open-bio.org Tue Sep 14 17:36:20 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Sep 14 17:10:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142136.i8ELaK7G006269@pub.open-bio.org> mwilkinson Tue Sep 14 17:36:20 EDT 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv6250 Modified Files: INSTALL Log Message: typos moby-live/Perl INSTALL,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/INSTALL 2004/07/28 23:00:09 1.2 +++ /home/repository/moby/moby-live/Perl/INSTALL 2004/09/14 21:36:20 1.3 @@ -8,7 +8,7 @@ For details on how to configure your own MOBY Central registry, should you want to set one up (you DO NOT -need to set up a registry to acess nor service MOBY-S +need to set up a registry to access nor serve MOBY-S Services) please visit the "Installing a Local Registy" link on the biomoby.org homepage. From mwilkinson at pub.open-bio.org Tue Sep 14 18:05:04 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue Sep 14 17:39:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142205.i8EM54PZ006416@pub.open-bio.org> mwilkinson Tue Sep 14 18:05:04 EDT 2004 Update of /home/repository/moby/moby-live/Database In directory pub.open-bio.org:/tmp/cvs-serv6401 Added Files: mobycentral.config Log Message: adding a template mobycentral.config file moby-live/Database mobycentral.config,NONE,1.1 From kawas at pub.open-bio.org Thu Sep 16 10:22:56 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu Sep 16 09:57:12 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409161422.i8GEMut9014234@pub.open-bio.org> kawas Thu Sep 16 10:22:56 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv14209/org/biomoby/client Modified Files: CentralImpl.java Log Message: fixed buf2->buf3 bug. moby-live/Accessories/ObjectCreationTool/org/biomoby/client CentralImpl.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java 2004/09/13 18:14:11 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java 2004/09/16 14:22:56 1.2 @@ -956,11 +956,11 @@ Hashtable childrenHAS = dataType.getHASChildren(); for (Enumeration en = childrenHAS.keys(); en.hasMoreElements();) { String name = (String) en.nextElement(); - buf2.append(""); - buf2.append(children.get(name)); - buf2.append(""); + buf3.append(""); + buf3.append(children.get(name)); + buf3.append(""); } // done addition From mwilkinson at pub.open-bio.org Thu Sep 16 18:21:02 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Sep 16 17:55:20 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409162221.i8GML2lO015538@pub.open-bio.org> mwilkinson Thu Sep 16 18:21:02 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv15519/MOBY Modified Files: Central.pm Log Message: as per Martin's observation, there is no need to pass the RDF as CDATA. This required changes in both the client and server libraries. Everyone needs to do a CVS update to use it moby-live/Perl/MOBY Central.pm,1.140,1.141 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.140 retrieving revision 1.141 diff -u -r1.140 -r1.141 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/26 20:52:28 1.140 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/09/16 22:21:01 1.141 @@ -165,11 +165,17 @@ $RDF = $details->{RDF}; +# return " +# $id +# $success +# +# +# "; return " $id $success - + $RDF "; } From mwilkinson at pub.open-bio.org Thu Sep 16 18:21:02 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu Sep 16 17:55:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409162221.i8GML2oV015557@pub.open-bio.org> mwilkinson Thu Sep 16 18:21:02 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv15519/MOBY/Client Modified Files: Central.pm Log Message: as per Martin's observation, there is no need to pass the RDF as CDATA. This required changes in both the client and server libraries. Everyone needs to do a CVS update to use it moby-live/Perl/MOBY/Client Central.pm,1.79,1.80 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.79 retrieving revision 1.80 diff -u -r1.79 -r1.80 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/08/11 16:27:48 1.79 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/09/16 22:21:02 1.80 @@ -1656,7 +1656,7 @@ my $id = &_nodeTextContent($Object, 'id'); my $success = &_nodeTextContent($Object, 'success'); my $message = &_nodeTextContent($Object, 'message'); - my $RDF = &_nodeTextContent($Object, 'RDF'); + my $RDF = &_nodeRawContent($Object, 'RDF'); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, @@ -1691,6 +1691,22 @@ return $content; } +sub _nodeRawContent { + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ($DOM, $node) = @_; + my $x = $DOM->getElementsByTagName($node); + unless ($x->item(0)){return}; + my @child = $x->item(0)->getChildNodes; + my $content; + foreach (@child){ + #print $_->getNodeTypeName, "\t", $_->toString,"\n"; +# next unless $_->getNodeType == TEXT_NODE; + $content .= $_->toString; + } + return $content; +} + sub _nodeArrayContent { # will get array content of all child $node from given $DOM From gss at pub.open-bio.org Tue Sep 21 11:36:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Sep 21 11:09:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409211536.i8LFa62b009514@pub.open-bio.org> gss Tue Sep 21 11:36:06 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv9492/WebRoot/images Removed Files: rdf-logo.PNG Log Message: Changed size; stored as different name moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images rdf-logo.PNG,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/rdf-logo.PNG,v: No such file or directory From gss at pub.open-bio.org Tue Sep 21 11:36:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue Sep 21 11:10:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409211536.i8LFaZ0c009550@pub.open-bio.org> gss Tue Sep 21 11:36:35 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv9529/WebRoot/images Added Files: rdf-logo.png Log Message: Added "RDF" to image moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images rdf-logo.png,NONE,1.1 From kawas at pub.open-bio.org Tue Sep 21 21:49:59 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:23:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220149.i8M1nxbi011675@pub.open-bio.org> kawas Tue Sep 21 21:49:58 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool Removed Files: .classpath .project README.TXT Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool .classpath,1.1,NONE .project,1.1,NONE README.TXT,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/.classpath,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/.project,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/README.TXT,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:00 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:23:47 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o0nX011705@pub.open-bio.org> kawas Tue Sep 21 21:50:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/Demo Removed Files: Demo.jar commons-logging.jar demo2.htm icu4j.jar index.htm jena.jar xercesImpl.jar Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/Demo Demo.jar,1.1,NONE commons-logging.jar,1.1,NONE demo2.htm,1.1,NONE icu4j.jar,1.1,NONE index.htm,1.1,NONE jena.jar,1.1,NONE xercesImpl.jar,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/Demo.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/demo2.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/icu4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/index.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/jena.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/xercesImpl.jar,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:01 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:23:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o1pf011789@pub.open-bio.org> kawas Tue Sep 21 21:50:01 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1! ,NONE WebComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE 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rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:01 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:23:48 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o1WM011731@pub.open-bio.org> kawas Tue Sep 21 21:50:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img Removed Files: LICENSE MOBY-S.jpeg bio.gif java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: 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directory From kawas at pub.open-bio.org Tue Sep 21 21:50:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:23:55 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o3al011899@pub.open-bio.org> kawas Tue Sep 21 21:50:01 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif ZoomOut16.gif ZoomOut24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE AlignJustifyHorizontal24.gif,1.1,NONE AlignJustifyVertical16.gif,1.1,NONE AlignJustifyVertical24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE AlignTop16.gif,1.1,NONE AlignTop24.gif,1.1,NONE Bookmarks16.gif,1.1,NONE Bookmarks24.gif,1.1,NONE ComposeMail16.gif,1.1,NONE ComposeMail24.gif,1.1,NONE ContextualHelp16.gif,1.1,NONE ContextualHelp24.gif,1.1,NONE Copy16.gif,1.1,NONE Copy24.gif,1.1,NONE Cut16.gif,1.1,NONE Cut24.gif,1.1,NONE Delete16.gif,1.1,NONE Delete24.gif,1.1,NONE Edit16.gif,1.1,NONE Edit24.gif,1.1,NONE Export16.gif,1.1,NONE Export24.gif,1.1,NONE Find16.gif,1.1,NONE Find24.gif,1.1,NONE FindAgain1! 6.gif,1.1,NONE FindAgain24.gif,1.1,NONE Help16.gif,1.1,NONE Help24.gif,1.1,NONE History16.gif,1.1,NONE History24.gif,1.1,NONE Import16.gif,1.1,NONE Import24.gif,1.1,NONE Information16.gif,1.1,NONE Information24.gif,1.1,NONE New16.gif,1.1,NONE New24.gif,1.1,NONE Open16.gif,1.1,NONE Open24.gif,1.1,NONE PageSetup16.gif,1.1,NONE PageSetup24.gif,1.1,NONE Paste16.gif,1.1,NONE Paste24.gif,1.1,NONE Preferences16.gif,1.1,NONE Preferences24.gif,1.1,NONE Print16.gif,1.1,NONE Print24.gif,1.1,NONE PrintPreview16.gif,1.1,NONE PrintPreview24.gif,1.1,NONE Properties16.gif,1.1,NONE Properties24.gif,1.1,NONE Redo16.gif,1.1,NONE Redo24.gif,1.1,NONE Refresh16.gif,1.1,NONE Refresh24.gif,1.1,NONE Remove16.gif,1.1,NONE Remove24.gif,1.1,NONE Replace16.gif,1.1,NONE Replace24.gif,1.1,NONE Save16.gif,1.1,NONE Save24.gif,1.1,NONE SaveAll16.gif,1.1,NONE SaveAll24.gif,1.1,NONE SaveAs16.gif,1.1,NONE SaveAs24.gif,1.1,NONE Search16.gif,1.1,NONE Search24.gif,1.1,NONE SendMail16.gif,1.1,NONE SendMail24.gif,1.! 1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE TipOfTheDay16.! gif,1.1,NONE TipOfTheDay24.gif,1.1,NONE Undo16.gif,1.1,NONE Undo24.gif,1.1,NONE Zoom16.gif,1.1,NONE Zoom24.gif,1.1,NONE ZoomIn16.gif,1.1,NONE ZoomIn24.gif,1.1,NONE ZoomOut16.gif,1.1,NONE ZoomOut24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/About16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/About24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/Add16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/Add24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:23:56 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o4gF011988@pub.open-bio.org> kawas Tue Sep 21 21:50:04 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowInsertBefore24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE 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From kawas at pub.open-bio.org Tue Sep 21 21:50:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:00 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o3PN011933@pub.open-bio.org> kawas Tue Sep 21 21:50:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o46J011958@pub.open-bio.org> kawas Tue Sep 21 21:50:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o4BG012022@pub.open-bio.org> kawas Tue Sep 21 21:50:04 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignLeft24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignRight16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignRight24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Bold16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Bold24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o9KA012089@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/offline Removed Files: Namespaces Objects Services Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/offline Namespaces,1.1,NONE Objects,1.1,NONE Services,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Namespaces,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Objects,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Services,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oA15012115@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img Removed Files: LICENSE MOBY-S.jpeg bio.gif java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/bio.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/java.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/left.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/middle.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby1.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby_small.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/right.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oARW012176@pub.open-bio.org> kawas Tue Sep 21 21:50:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1,NONE We! bComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE WebComponentAdd24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Applet16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Applet24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Application16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Application24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/ApplicationDeploy16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/ApplicationDeploy24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Bean16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Bean24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/BeanAdd16.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEApplicationClientAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEServer16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEServer24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Jar16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Jar24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/JarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBGQ012378@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowInsertBefore24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertBefore24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBqD012348@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBQ5012286@pub.open-bio.org> kawas Tue Sep 21 21:50:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif ZoomOut16.gif ZoomOut24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE AlignJustifyHorizontal24.gif,1.1,NONE AlignJustifyVertical16.gif,1.1,NONE AlignJustifyVertical24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE AlignTop16.gif,1.1,NONE AlignTop24.gif,1.1,NONE Bookmarks16.gif,1.1,NONE Bookmarks24.gif,1.1,NONE ComposeMail16.gif,1.1,NONE ComposeMail24.gif,1.1,NONE ContextualHelp16.gif,1.1,NONE ContextualHelp24.gif,1.1,NONE Copy16.gif,1.1,NONE Copy24.gif,1.1,NONE Cut16.gif,1.1,NONE Cut24.gif,1.1,NONE Delete16.gif,1.1,NONE Delete24.gif,1.1,NONE Edit16.gif,1.1,NONE Edit24.gif,1.1,NONE Export16.gif,1.1,NONE Export24.gif,1.1,NONE Find16.gif,1.1,NONE Find24.gif,1.1,NONE FindAgain16.gif,1.! 1,NONE FindAgain24.gif,1.1,NONE Help16.gif,1.1,NONE Help24.gif,1.1,NONE History16.gif,1.1,NONE History24.gif,1.1,NONE Import16.gif,1.1,NONE Import24.gif,1.1,NONE Information16.gif,1.1,NONE Information24.gif,1.1,NONE New16.gif,1.1,NONE New24.gif,1.1,NONE Open16.gif,1.1,NONE Open24.gif,1.1,NONE PageSetup16.gif,1.1,NONE PageSetup24.gif,1.1,NONE Paste16.gif,1.1,NONE Paste24.gif,1.1,NONE Preferences16.gif,1.1,NONE Preferences24.gif,1.1,NONE Print16.gif,1.1,NONE Print24.gif,1.1,NONE PrintPreview16.gif,1.1,NONE PrintPreview24.gif,1.1,NONE Properties16.gif,1.1,NONE Properties24.gif,1.1,NONE Redo16.gif,1.1,NONE Redo24.gif,1.1,NONE Refresh16.gif,1.1,NONE Refresh24.gif,1.1,NONE Remove16.gif,1.1,NONE Remove24.gif,1.1,NONE Replace16.gif,1.1,NONE Replace24.gif,1.1,NONE Save16.gif,1.1,NONE Save24.gif,1.1,NONE SaveAll16.gif,1.1,NONE SaveAll24.gif,1.1,NONE SaveAs16.gif,1.1,NONE SaveAs24.gif,1.1,NONE Search16.gif,1.1,NONE Search24.gif,1.1,NONE SendMail16.gif,1.1,NONE SendMail24.gif,1.1,NONE S! top16.gif,1.1,NONE Stop24.gif,1.1,NONE TipOfTheDay16.gif,1.1,! NONE TipOfTheDay24.gif,1.1,NONE Undo16.gif,1.1,NONE Undo24.gif,1.1,NONE Zoom16.gif,1.1,NONE Zoom24.gif,1.1,NONE ZoomIn16.gif,1.1,NONE ZoomIn24.gif,1.1,NONE ZoomOut16.gif,1.1,NONE ZoomOut24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/About16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/About24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Add16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Add24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/AlignBottom16.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Search24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/SendMail16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/SendMail24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/TipOfTheDay16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/TipOfTheDay24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Undo16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Undo24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Zoom16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Zoom24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:23 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oDnV012478@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/biomoby/shared Removed Files: Central.java MobyData.java MobyDataInstance.java MobyDataSecondaryInstance.java MobyDataServiceAssocInstance.java MobyDataSetInstance.java MobyDataSimpleInstance.java MobyDataType.java MobyException.java MobyNamespace.java MobyNativeService.java MobyObject.java MobyPrefixResolver.java MobyPrimaryDataSet.java MobyPrimaryDataSimple.java MobySecondaryData.java MobyService.java MobyServiceType.java NoSuccessException.java PendingCurationException.java SOAPException.java Utils.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/biomoby/shared Central.java,1.1,NONE MobyData.java,1.1,NONE MobyDataInstance.java,1.1,NONE MobyDataSecondaryInstance.java,1.1,NONE MobyDataServiceAssocInstance.java,1.1,NONE MobyDataSetInstance.java,1.1,NONE MobyDataSimpleInstance.java,1.1,NONE MobyDataType.java,1.1,NONE MobyException.java,1.1,NONE MobyNamespace.java,1.1,NONE MobyNativeService.java,1.1,NONE MobyObject.java,1.1,NONE MobyPrefixResolver.java,1.1,NONE MobyPrimaryDataSet.java,1.1,NONE MobyPrimaryDataSimple.java,1.1,NONE MobySecondaryData.java,1.1,NONE MobyService.java,1.1,NONE MobyServiceType.java,1.1,NONE NoSuccessException.java,1.1,NONE PendingCurationException.java,1.1,NONE SOAPException.java,1.1,NONE Utils.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/Central.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSecondaryInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataServiceAssocInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSetInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSimpleInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyNamespace.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyNativeService.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrefixResolver.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrimaryDataSet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrimaryDataSimple.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobySecondaryData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyService.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyServiceType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/NoSuccessException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/PendingCurationException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/SOAPException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/Utils.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:14 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oEFE012532@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/mobycentral/util Removed Files: Construct.java Household.java MobyPlainText.java MobyUtilities.java MobyXML.java Pair.java Registration.java TreeLoaderThread.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/mobycentral/util Construct.java,1.1,NONE Household.java,1.1,NONE MobyPlainText.java,1.1,NONE MobyUtilities.java,1.1,NONE MobyXML.java,1.1,NONE Pair.java,1.1,NONE Registration.java,1.1,NONE TreeLoaderThread.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Construct.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Household.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyPlainText.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyUtilities.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyXML.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Pair.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Registration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/TreeLoaderThread.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oC8s012441@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/biomoby/client Removed Files: CentralImpl.java FileCache.java FilterServices.java GraphsServlet.java Graphviz.java MobyRequest.java RDF.java ServiceConnections.java ServicesEdge.java ServletFileCache.java SimpleCache.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/biomoby/client CentralImpl.java,1.2,NONE FileCache.java,1.1,NONE FilterServices.java,1.1,NONE GraphsServlet.java,1.1,NONE Graphviz.java,1.1,NONE MobyRequest.java,1.1,NONE RDF.java,1.1,NONE ServiceConnections.java,1.1,NONE ServicesEdge.java,1.1,NONE ServletFileCache.java,1.1,NONE SimpleCache.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/CentralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/FileCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/FilterServices.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/GraphsServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/Graphviz.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/MobyRequest.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/RDF.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServiceConnections.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServicesEdge.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServletFileCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/SimpleCache.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o9i4012071@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/lib Removed Files: activation.jar adenine.jar alltools.jar antlr.jar axis-ant.jar axis.jar commons-discovery.jar commons-logging.jar concurrent.jar icu4j.jar jakarta-oro-2.0.5.jar jaxen-core.jar jaxen-jdom.jar jaxrpc.jar jdom.jar jena.jar junit.jar log4j-1.2.7.jar rdf-api-2001-01-19.jar saaj.jar saxpath.jar servlet.jar wsdl4j.jar xalan.jar xercesImpl.jar xml-apis.jar Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/lib activation.jar,1.1,NONE adenine.jar,1.1,NONE alltools.jar,1.1,NONE antlr.jar,1.1,NONE axis-ant.jar,1.1,NONE axis.jar,1.1,NONE commons-discovery.jar,1.1,NONE commons-logging.jar,1.1,NONE concurrent.jar,1.1,NONE icu4j.jar,1.1,NONE jakarta-oro-2.0.5.jar,1.1,NONE jaxen-core.jar,1.1,NONE jaxen-jdom.jar,1.1,NONE jaxrpc.jar,1.1,NONE jdom.jar,1.1,NONE jena.jar,1.1,NONE junit.jar,1.1,NONE log4j-1.2.7.jar,1.1,NONE rdf-api-2001-01-19.jar,1.1,NONE saaj.jar,1.1,NONE saxpath.jar,1.1,NONE servlet.jar,1.1,NONE wsdl4j.jar,1.1,NONE xalan.jar,1.1,NONE xercesImpl.jar,1.1,NONE xml-apis.jar,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/activation.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/adenine.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/alltools.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/antlr.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/axis-ant.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/axis.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/commons-discovery.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/concurrent.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/icu4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jakarta-oro-2.0.5.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxen-core.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxen-jdom.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxrpc.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jdom.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jena.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/junit.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/log4j-1.2.7.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/rdf-api-2001-01-19.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/saaj.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/saxpath.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/servlet.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/wsdl4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xalan.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xercesImpl.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xml-apis.jar,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBSb012412@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignLeft24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignRight16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignRight24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Bold16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Bold24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:30 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oDVb012505@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/mobycentral/object/creation/applet Removed Files: ButtonActions.java ButtonBeautifier.java FieldFocusListeners.java FieldKeyListener.java MobyTree.java MobyUserPanel.java ObjectCreationTool.java PanelFactory.java TreeListener.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet ButtonActions.java,1.1,NONE ButtonBeautifier.java,1.1,NONE FieldFocusListeners.java,1.1,NONE FieldKeyListener.java,1.1,NONE MobyTree.java,1.1,NONE MobyUserPanel.java,1.1,NONE ObjectCreationTool.java,1.1,NONE PanelFactory.java,1.1,NONE TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ButtonActions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/FieldFocusListeners.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/FieldKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/MobyTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/MobyUserPanel.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ObjectCreationTool.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/PanelFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/TreeListener.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue Sep 21 21:24:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oB40012320@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Pause16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Pause24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Play16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Play24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Rewind16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Rewind24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 16:44:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHiW015522@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv15476/src/Clients Modified Files: MobyCmdLineClient.java PopulateLocalCentralForTesting.java TestingCentral.java Log Message: new registration procedure, etc. moby-live/Java/src/Clients MobyCmdLineClient.java,1.4,1.5 PopulateLocalCentralForTesting.java,1.1,1.2 TestingCentral.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/05/18 10:13:16 1.4 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/22 21:11:17 1.5 @@ -221,11 +221,24 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i]); + data.addChild (null, hasas [i], MobyRelationship.HASA); } else if (pos == hasas[i].length() - 1) { - data.addChild (null, hasas [i].substring (0, pos)); + data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HASA); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1)); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HASA); + } + } + } + if ((param = cmd.getParam ("-rd-has")) != null ) { + String[] hasas = StringUtils.split (param, ","); + for (int i = 0; i < hasas.length; i++) { + int pos = hasas[i].indexOf (":"); + if (pos == -1) { + data.addChild (null, hasas [i], MobyRelationship.HAS); + } else if (pos == hasas[i].length() - 1) { + data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HAS); + } else { + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HAS); } } } @@ -273,7 +286,15 @@ service.setAuthoritative (param.equals ("1") ? true : false); } service.setURL (cmd.getParam ("-rs-url")); - if ((param = cmd.getParam ("-rs-in")) != null ) { + service.setSignatureURL (cmd.getParam ("-rs-rdf")); + if ( (param = cmd.getParam ("-rs-rdfpath")) != null ) { + service.setPathToRDF (param); + } else { + File tmpFile = File.createTempFile ("Moby-RDF." + service.getName() + ".", ".xml"); + service.setPathToRDF (tmpFile.getAbsolutePath()); + } + + if ( (param = cmd.getParam ("-rs-in")) != null ) { String[] inputs = StringUtils.split (param, ","); for (int i = 0; i < inputs.length; i++) { String[] parts = StringUtils.split (inputs[i], "="); @@ -346,7 +367,9 @@ if ((param = cmd.getParam ("-rs-out")) != null ) { String[] outs = StringUtils.split (param, ","); for (int i = 0; i < outs.length; i++) { - service.addOutput (new MobyPrimaryDataSimple (outs[i])); + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (outs[i])); + service.addOutput (data); } } if ((param = cmd.getParam ("-rs-ofile")) != null ) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2003/10/17 13:13:34 1.1 +++ /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/22 21:11:17 1.2 @@ -240,10 +240,10 @@ protected MobyDataType[] createAllDataTypes() { MobyDataType data1 = createDataType (dataType_1); data1.addParentName ("Object"); - data1.addChild ("address", "string"); - data1.addChild ("age", "integer"); - data1.addChild ("salary", "float"); - data1.addChild ("born", "datetime"); + data1.addChild ("address", "string", MobyRelationship.HASA); + data1.addChild ("age", "integer", MobyRelationship.HASA); + data1.addChild ("salary", "float", MobyRelationship.HASA); + data1.addChild ("born", "datetime", MobyRelationship.HASA); MobyDataType data2 = createDataType (dataType_2); data2.addParentName ("Object"); MobyDataType data3 = createDataType (dataType_3); @@ -253,8 +253,8 @@ MobyDataType data5 = createDataType (dataType_5); data5.addParentName (dataType_3); data5.addParentName (dataType_2); - data5.addChild ("range_min", "integer"); - data5.addChild ("range_max", "integer"); + data5.addChild ("range_min", "integer", MobyRelationship.HAS); + data5.addChild ("range_max", "integer", MobyRelationship.HAS); return new MobyDataType [] { data1, data2, data3, data4, data5 }; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2003/10/17 13:13:34 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/22 21:11:17 1.3 @@ -122,7 +122,7 @@ // command-line parameters int i = 0; while (i < args.length) { - if (args[i].equals ("-help") || args[i].equals ("-")) { + if (args[i].equals ("-help") || args[i].equals ("-h")) { System.out.println ("Usage: java TestingCentral [-e ] [-u ] [-debug]"); System.exit (0); @@ -160,6 +160,7 @@ // create service proxy... TestingCentral helper = new TestingCentral(); Central worker = new CentralImpl (endpoint, uri); + worker.setDebug (debug); // ...and call other methods: String result; @@ -246,9 +247,9 @@ try { start ("registerDataType - 2"); data2.addParentName (data1.getName()); - data2.addChild ("len", "Integer"); - data2.addChild ("sub", "String"); - data2.addChild ("real_type", data3.getName()); + data2.addChild ("len", "Integer", MobyRelationship.HASA); + data2.addChild ("sub", "String", MobyRelationship.HAS); + data2.addChild ("real_type", data3.getName(), MobyRelationship.HASA); worker.registerDataType (data2); ok(); } catch (MobyException e) { error (e); @@ -283,7 +284,8 @@ MobySecondaryData secData1 = helper.createSecondaryData ("Secondary_A", "Integer"); MobySecondaryData secData2 = helper.createSecondaryData ("Secondary_B", "String"); - MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", name3); +// MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", name3); + MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", "DateTime"); MobyService service = helper.createService ("MyTestingService_" + new Date().getTime()); service.setType (stype.getName()); From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 16:44:59 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHwP015495@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv15476/docs Modified Files: ChangeLog Log Message: new registration procedure, etc. moby-live/Java/docs ChangeLog,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/03 20:28:16 1.17 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/22 21:11:17 1.18 @@ -1,3 +1,27 @@ +2004-09-22 Martin Senger + + * Fixed option -rs-out in MobyCmdLineClient. + + * Added a -debug option to the TestingCentral client. + + * Fixed TestingCentral client - it used incorectly user-defined + data type in the output secondary article. + + * Added HAS relationship type for children of MobyDataType + objects. It uses a new class MobyRelationship (meaning that + methods returning children in MobyDataType got new signatures). + + * Changes reflecting new service registration procedure: + - MobyService has new members with corresponding set/get methods + for storing 'signatureURL' and a fully qualified path to the + place where the service signature (an RDF document) can be + stored). + - CentralImpl stores retrieved RDF in a local file (read API for + MobyService class, it explains what CentralImpl is doing). + - command-line program MobyCmdLineClient got few new options in + order to deal with 'signatureURL' (see its new help). + + 2004-09-03 Paul Gordon * First commit of data instance classes for base objects (Floats, Integers, Strings), From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 16:45:04 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHCA015542@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv15476/src/Clients/help Modified Files: MobyCmdLineClient_usage.txt Log Message: new registration procedure, etc. moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/05/18 10:13:16 1.4 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/09/22 21:11:17 1.5 @@ -88,12 +88,13 @@ -rd-email -rd-isa this should be a comma-delimited list of names of the - parent data types (but Moby accept now only one parent) + parent data types (but Moby accepts now only one parent) -rd-hasa - this should be a comma-delimited list of names of the + -rd-has + these should be comma-delimited lists of names of the data types referred from this data type; every element of this list may have two parts - separated by a colon: : + separated by a colon: : To register a service type: @@ -123,6 +124,19 @@ -rs-url -rs-main use: 1 or 0 + -rs-rdf + points to your HTTP space + to a place where an RDF describing this service will be + -rs-rdfpath + if the service registration is succesful, the returned + RDF is copied to a file given by + (which completes the registration process); + use it, however, with caution because this client + overwrites a possibly existing document (it does not + merge the new RDF with the possibly existing one); + Default: it creates a temporary file where the + returned RDF is stored + -rs-in are comma-delimited names of inputs; each of them is a pair of an input type and a namespace From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 16:45:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBH3G015567@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv15476/src/main/org/biomoby/client Modified Files: CentralImpl.java Graphviz.java Log Message: new registration procedure, etc. moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.13,1.14 Graphviz.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/05/18 10:13:17 1.13 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/22 21:11:17 1.14 @@ -178,30 +178,37 @@ * Parse the given XML sniplet to find tag 'success'. If it has value '1' * look further for tag 'id' and return it back (or return an empty string * if ID is not there). Otherwise raise an exception with the 'culprit' - * and with the message from the tag 'message'. + * and with the message from the tag 'message'.

+ * + * The return value is a two-element long array. The first element + * is the ID (given by BioMobe registry), and the second element + * is RDF corresponding with the registered object (BioMoby + * returns this only for service instances, so for other objects + * this will be null).

* * This is how the XML is supposed to look: * * * * + * * * * Success takes the value "1" to indicate success, "0" to * indicate failure, and "-1" to indicate "Pending Curation". - * - * I keep 'id' in but it does not seem to be used anymore by the current - * Moby Central. *************************************************************************/ - protected String checkRegistration (String xml, Object culprit) + protected String[] checkRegistration (String xml, Object culprit) throws MobyException, NoSuccessException, PendingCurationException { - String id = "", success = "0", message = ""; + String id = "", success = "0", message = "", rdf = ""; // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(xml));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document=docBuilder.parse(new StringBufferInputStream(xml)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } Element root = document.getDocumentElement(); NodeList children = root.getChildNodes(); @@ -212,12 +219,23 @@ if (elem.getNodeName().equals ("id")) { if (elem.getFirstChild() != null) id = elem.getFirstChild().getNodeValue(); - } else if (elem.getNodeName().equals ("success")) { + } else if (elem.getNodeName().equals("success")) { if (elem.getFirstChild() != null) success = elem.getFirstChild().getNodeValue(); } else if (elem.getNodeName().equals ("message")) { if (elem.getFirstChild() != null) message = elem.getFirstChild().getNodeValue(); + } else if (elem.getNodeName().equals ("RDF")) { + // well, this is a simple, but most time working, + // hack... I actually do not know how to extract the + // whole subtree from a Document (without using XPath, + // XSLT or similar) ... let me know please if you know + int fromPos = xml.indexOf (""); + int toPos = xml.indexOf (""); + if (fromPos > -1 && toPos > fromPos) + rdf = xml.substring (fromPos, toPos + 6); +// if (elem.getFirstChild() != null) +// rdf = elem.getFirstChild().getNodeValue(); } } @@ -225,7 +243,7 @@ throw new NoSuccessException (message, culprit); else if (success.equals ("-1")) throw new PendingCurationException(); - return id; + return new String[] { id, rdf }; } /************************************************************************** @@ -414,8 +432,11 @@ throws MobyException { Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(xml));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(xml)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("Service"); MobyService[] results = new MobyService [list.getLength()]; @@ -506,7 +527,7 @@ // First, check to se if we have the values cached from a previous call // in this instance - if(useCache && cache.containsKey("retrieveServiceNames")) + if (useCache && cache.containsKey("retrieveServiceNames")) return (Map) cache.get("retrieveServiceNames"); String result = (String)doCall ("retrieveServiceNames", @@ -515,8 +536,11 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("serviceName"); for (int i = 0; i < list.getLength(); i++) { @@ -526,7 +550,7 @@ } // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveServiceNames", results); return results; } @@ -543,16 +567,19 @@ throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveServiceProviders")) - return (String[]) cache.get("retrieveServiceProviders"); + if (useCache && cache.containsKey ("retrieveServiceProviders")) + return (String[]) cache.get ("retrieveServiceProviders"); String result = (String)doCall ("retrieveServiceProviders", new Object[] {}); // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("serviceProvider"); String[] results = new String [list.getLength()]; @@ -560,7 +587,7 @@ results[i] = ((Element)list.item (i)).getAttribute ("name"); // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveServiceProviders", results); return results; } @@ -579,7 +606,7 @@ public Map getServiceTypes() throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveServiceTypes")) + if (useCache && cache.containsKey ("retrieveServiceTypes")) return (Map) cache.get("retrieveServiceTypes"); String result = (String)doCall ("retrieveServiceTypes", @@ -588,7 +615,8 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} + try { + document = docBuilder.parse(new StringBufferInputStream(result));} catch(Exception e){throw new MobyException(e.toString());} NodeList list = document.getElementsByTagName ("serviceType"); @@ -634,31 +662,33 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace"); - if(list == null || list.getLength() == 0){ - throw new MobyException("Could not find Namespace children of response root node " + - document.getDocumentElement()); + if (list == null || list.getLength() == 0) { + throw new MobyException ("Could not find Namespace children of response root node " + + document.getDocumentElement()); } int length = list.getLength(); for (int i = 0; i < length; i++) { Element elem = (Element)list.item (i); NodeList children = elem.getElementsByTagName("Description"); - if(children.item(0).hasChildNodes()){ + if (children.item(0).hasChildNodes()) { children.item(0).normalize(); results.put (elem.getAttribute ("name"), children.item(0).getFirstChild().getNodeValue()); - } - else{ + } else { // No description provided results.put (elem.getAttribute ("name"), ""); } } - + // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveNamespaces", results); return results; } @@ -677,7 +707,7 @@ public Map getDataTypeNames() throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveObjectNames")) + if (useCache && cache.containsKey("retrieveObjectNames")) return (Map) cache.get("retrieveObjectNames"); String result = (String)doCall ("retrieveObjectNames", @@ -686,8 +716,11 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("Object"); for (int i = 0; i < list.getLength(); i++) { @@ -702,7 +735,7 @@ } } - if(useCache) + if (useCache) cache.put("retrieveObjectNames", results); return results; } @@ -723,6 +756,10 @@ * urn:lsid:biomoby.org:objectclass:string * urn:lsid:biomoby.org:objectclass:string * + * + * urn:lsid:biomoby.org:objectclass:string + * urn:lsid:biomoby.org:objectclass:string + * * * *************************************************************************/ @@ -730,9 +767,9 @@ throws MobyException, NoSuccessException { // See if we've already retrieved the DataType and cached it - if(cache.containsKey("retrieveObjectDefinition"+dataTypeName)) - return (MobyDataType) cache.get("retrieveObjectDefinition"+dataTypeName); - + if (cache.containsKey("retrieveObjectDefinition" + dataTypeName)) + return (MobyDataType) cache.get("retrieveObjectDefinition" + dataTypeName); + String result = (String)doCall ("retrieveObjectDefinition", new Object[] { @@ -743,18 +780,21 @@ // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("retrieveObjectDefinition"); if (list == null || list.getLength() == 0) - throw new NoSuccessException ("Data Type name was not founnd.", + throw new NoSuccessException ("Data Type name was not found.", dataTypeName); MobyDataType data = null; Element elem = (Element)list.item (0); NodeList children = elem.getChildNodes(); - // first find the "real" data type name + // first find the "real" (LSID-ized) data type name for (int j = 0; j < children.getLength(); j++) { String nodeName = children.item (j).getNodeName(); if (nodeName.equals ("objectType")) { @@ -792,7 +832,18 @@ for (int k = 0; k < belows.getLength(); k++) { if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), - belows.item (k).getFirstChild().getNodeValue() ); + belows.item (k).getFirstChild().getNodeValue(), + MobyRelationship.HASA ); + } + } + } else if (relationshipType.endsWith ("has")) { + + NodeList belows = children.item (j).getChildNodes(); + for (int k = 0; k < belows.getLength(); k++) { + if (belows.item (k).getNodeName().equals ("objectType")) { + data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), + belows.item (k).getFirstChild().getNodeValue(), + MobyRelationship.HAS ); } } } @@ -804,42 +855,6 @@ /************************************************************************** * B - * - * - * ]]> - * - * - * ... - * ... - * - * - *************************************************************************/ -// public String getDataType (String dataTypeName) -// throws MobyException, NoSuccessException { -// String result = -// (String)doCall ("retrieveObjectSchema", -// new Object[] { -// "" + -// "" + dataTypeName + "" + -// "" -// }); - -// // parse returned XML (hack: taking blindly everything in the Schema tag) -// String xsd = ""; -// int pos = result.indexOf (""); -// if (pos == 1) -// throw new NoSuccessException ("Data Type name was not founnd.", -// dataTypeName); -// int pos2 = result.indexOf (""); -// if (pos2 < pos) -// throw new NoSuccessException ("Something wrong with the returned XML.", -// result); -// return result.substring (pos + 8, pos2); -// } - - /************************************************************************** - * B *************************************************************************/ public String getServiceWSDL (String serviceName) throws MobyException, NoSuccessException { @@ -889,7 +904,7 @@ } /************************************************************************* - * B + * *************************************************************************/ public void registerDataType (MobyDataType dataType) throws MobyException, NoSuccessException, PendingCurationException { @@ -904,16 +919,24 @@ buf.append ("\n"); } - // build the HASA tag (expressing containment of data types) - Hashtable children = dataType.getChildren(); - StringBuffer buf2 = new StringBuffer(); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { - String name = (String)en.nextElement(); - buf2.append (""); - buf2.append (children.get (name)); - buf2.append (""); + // build the HASA/HAS tags (expressing containments of data types) + MobyRelationship[] children = dataType.getChildren(); + StringBuffer buf2 = new StringBuffer(); // for HASA + StringBuffer buf3 = new StringBuffer(); // for HAS + for (int i = 0; i < children.length; i++) { + if (children[i].getRelationshipType() == MobyRelationship.HASA) { + buf2.append (""); + buf2.append (children[i].getDataTypeName()); + buf2.append (""); + } else if (children[i].getRelationshipType() == MobyRelationship.HAS) { + buf3.append (""); + buf3.append (children[i].getDataTypeName()); + buf3.append (""); + } } String result = @@ -927,30 +950,15 @@ "" + "" + new String (buf2) + "" + + "" + new String (buf3) + + "" + "" + dataType.getAuthority() + "" + "" + dataType.getEmailContact() + "" + "" }); - dataType.setId (checkRegistration (result, dataType)); + dataType.setId (checkRegistration (result, dataType)[0]); } -// -// NewObjectType -// -// -// -// ExistingObjectType -// ... -// ... -// -// ... -// ... -// Your.URI.here -// You@your.address.com -// - /************************************************************************* * B *************************************************************************/ @@ -995,7 +1003,7 @@ "" + "" }); - serviceType.setId (checkRegistration (result, serviceType)); + serviceType.setId (checkRegistration (result, serviceType)[0]); } // @@ -1042,7 +1050,7 @@ "" + "" }); - namespace.setId (checkRegistration (result, namespace)); + namespace.setId (checkRegistration (result, namespace)[0]); } /************************************************************************* @@ -1074,6 +1082,7 @@ "" + service.getName() + "" + "" + service.getType() + "" + "" + service.getAuthority() + "" + + "" + service.getSignatureURL() + "" + "" + service.getURL() + "" + "" + service.getEmailContact() + "" + "" + (service.isAuthoritative() ? "1" : "0") + "" + @@ -1084,7 +1093,22 @@ buildOutputTag (service) + "" }); - service.setId (checkRegistration (result, service)); + String[] registered = checkRegistration (result, service); + service.setId (registered [0]); + service.setRDF (registered [1]); + String pathToRDF = service.getPathToRDF(); + if ( ! pathToRDF.equals ("") ) { + File fileRDF = new File (pathToRDF); + try { + PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF)); + fileout.println (registered [1]); + fileout.close(); + } catch (IOException e) { + throw new MobyException ("Failed to save RDF in '" + fileRDF.getAbsolutePath() + "'. " + + e.toString() + + "\nReturned RDF:\n" + registered [1]); + } + } } /************************************************************************* @@ -1390,11 +1414,13 @@ } /** - * By default, caching is enabled to reduce network traffic and XML parsing. Setting - * this to false will clear the cache, and not cache any further calls unless it is - * set to true again. - * - * @param shouldCache whether retrieveXXX call results should be cached in case they are called again (i.e. don't requery MobyCentral every time) + * By default, caching is enabled to reduce network traffic. + * Setting this to false will clear the cache, and not cache any + * further calls unless it is set to true again.

+ * + * @param shouldCache whether retrieveXXX call results should be + * cached in case they are called again (i.e. don't requery + * MobyCentral every time) */ public void setCacheMode(boolean shouldCache){ useCache = shouldCache; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2003/11/25 13:18:10 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/22 21:11:17 1.3 @@ -6,11 +6,14 @@ package org.biomoby.client; -import org.biomoby.shared.*; - -import java.net.*; -import java.util.*; -import java.io.*; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Properties; + +import org.biomoby.shared.MobyDataType; +import org.biomoby.shared.MobyRelationship; +import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.Utils; /** * A utility class that understands how to create @@ -134,15 +137,15 @@ buf.append (trName (name)); buf.append (";\n"); } - Hashtable children = type.getChildren(); - if (children.size() > 0) { + MobyRelationship[] children = type.getChildren(); + if (children.length > 0) { String dummyName = trName (name) + "_HASA"; buf.append ("\t" + trName (name) + " -> " + dummyName); buf.append (" [style=dotted,dir=forward,arrowhead=none,arrowtail=ediamond];\n"); StringBuffer hasaBuf = new StringBuffer(); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { - String childName = (String)en.nextElement(); - String childType = Utils.pureName ((String)children.get (childName)); + for (int i = 0; i < children.length; i++) { + String childName = Utils.pureName (children[i].getName()); + String childType = Utils.pureName (children[i].getDataTypeName()); if (childType == null) childType = "n/a"; // should not happen I guess hasaBuf.append (" | {" + childType + "|" + childName + "}"); From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 16:45:05 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBH8l015617@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv15476/src/support Modified Files: README _README.FIRST_ Log Message: new registration procedure, etc. moby-live/Java/src/support README,1.3,1.4 _README.FIRST_,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/support/README 2003/11/08 00:27:24 1.3 +++ /home/repository/moby/moby-live/Java/src/support/README 2004/09/22 21:11:17 1.4 @@ -1,5 +1,5 @@ This directory contains Moby clients in Java, ready to be used and to -communicate with a real Moby server. More documentation is available +communicate with a real Moby registry. More documentation is available in the 'docs' directory. A full distribution with sources is available from the BioMoby home page http://biomoby.org. @@ -8,9 +8,10 @@ Invoke available clients using provided (and very simple) scripts (use those ending with '.bat' for Windows OS): - sh ./run-cmdline-client -help - sh ./run-testing-central - sh ./run-graphs-client -help + sh ./run/run-cmdline-client -help + sh ./run/run-testing-central + sh ./run/run-graphs-client -help + etc. Or, on Unix platforms, use chmod to make the scripts above executable and call them without 'sh' (note that this small inconvenience is due =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/_README.FIRST_,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/support/_README.FIRST_ 2003/09/25 02:35:02 1.1 +++ /home/repository/moby/moby-live/Java/src/support/_README.FIRST_ 2004/09/22 21:11:17 1.2 @@ -1,6 +1,6 @@ Files in this directory are used as templates when creating a binary distribution. They are not intended to be used per se. For invoking -various clients, use scripts available in the main directory above. +various clients, use scripts available in the build/run directory. -------------------------------------------------------------------- Comments to the biomoby mailing lists, or directly to Martin Senger From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 16:45:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHe1015594@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv15476/src/main/org/biomoby/shared Modified Files: MobyDataType.java MobyPrimaryDataSimple.java MobyService.java Added Files: MobyRelationship.java Log Message: new registration procedure, etc. moby-live/Java/src/main/org/biomoby/shared MobyRelationship.java,NONE,1.1 MobyDataType.java,1.2,1.3 MobyPrimaryDataSimple.java,1.1,1.2 MobyService.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/03/09 00:20:13 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/22 21:11:17 1.3 @@ -11,15 +11,14 @@ /** - * A container representing a data type used in the Moby registry. - * The Moby data types are used to specify what types of inputs and - * outputs are needed or produced by Moby services. - *

+ * A container representing a data type used in the Moby registry (in + * the BioMoby speak it is called "Object Class"). The Moby data + * types are used to specify what types of inputs and outputs are + * needed or produced by Moby services.

* - * This container is used mainly to register a new data type in a + * This container is used mainly to register a new data type into a * Moby registry, and to find services with this particular input or - * output data type. - *

+ * output data type.

* * @author Martin Senger * @version $Id$ @@ -32,12 +31,18 @@ protected String emailContact = ""; protected String description = ""; protected String[] parentNames = new String[] { }; - protected Hashtable children = new Hashtable(); + protected MobyRelationship[] children = new MobyRelationship[] { }; protected String id = null; /************************************************************************** - * Default constructor. Other characteristics are empty - which is usually - * wrong - therefore use 'set' method to fill them. + * Default constructor. Other characteristics are empty - which is + * usually wrong - you should use 'set' methods to fill them + * before using this instance.

+ * + * @param name of this data type (e.g. GenericSequence, or + * String). The name can be either a simple string (e.g. Object), + * or a full-blown LSID + * (e.g. urn:lsid:biomoby.org:objectclass:Object). *************************************************************************/ public MobyDataType (String name) { this.name = name; @@ -47,34 +52,76 @@ return name; } + /** + * Return an ID that is given to this data type during its + * registration. The ID seems to be used only for de-registration + * of this data type; you are not supposed to fill it when you + * create an instance of this object. + */ public String getId() { return id; } + + /** + * @see #getId + */ public void setId (String value) { id = value; } + /** + * Return an authority for this data type. The authority is an URI + * of this data type provider. Very often empty. + */ public String getAuthority() { return authority; } + /** + * @see #getAuthority + */ public void setAuthority (String value) { authority = (value == null ? "" : value); } + /** + * Return a contact email. The purpose of this field is still a + * bit obscure - but I think that the intention is to use it in + * the process of de-registration of this data type. + */ public String getEmailContact() { return emailContact; } + /** + * @see #getEmailContact + */ public void setEmailContact (String value) { emailContact = (value == null ? "" : value); } + /** + * Return a (usually) human readable description of this data + * type. + */ public String getDescription() { return description; } + /** + * @see #getDescription + */ public void setDescription (String value) { description = (value == null ? "" : value); } + /** + * Return names of all parental data types (as stored in the + * BioMoby class ontology). Note, however, that the current + * BioMoby API (0.8) does not expect (probably even does not + * allow) multiple-inheritance.

+ * + * @return (at the moment) none (for the root data type) or one + * name. The name is an LSID + * (e.g. urn:lsid:biomoby.org:objectclass:Object). + */ public String[] getParentNames() { synchronized (parentNames) { String[] names = new String [parentNames.length]; @@ -82,6 +129,12 @@ return names; } } + /** + * @see #getParentNames + * @param value is a set of parent names (usually just one name, + * however). If it is null all parents set previously are + * forgotten. + */ public void setParentNames (String[] value) { synchronized (parentNames) { if (value == null) @@ -92,6 +145,13 @@ } } } + /** + * Add one parent of this data type.

+ * + * @see #getParentNames + * @param value is a name of a parental data type. A null value is + * ignored. + */ public void addParentName (String value) { if (value != null) { synchronized (parentNames) { @@ -105,53 +165,90 @@ } /** - * Describes what children this data type has (expressing ontology - * term HAS-A). The returned value is a hashtable with: - *

+ * Return children of this data type, and the way how they are + * ontologically related to this data type. The returned elements + * are containers, each of them defining the child data type, + * under what name it is used here (the BioMoby API calls this + * name an "article name"), and what relationship it has to this + * data type (HAS, HASA).

+ * + * Note that it does not return children that belong to the parent + * types - in other words it does not go up through the whole + * ontology tree to find all children.

+ * + * @see MobyRelationship.HAS + * @see MobyRelationship.HASA */ - public Hashtable getChildren() { + public MobyRelationship[] getChildren() { return children; } - public void setChildren (Hashtable value) { - children = (value == null ? new Hashtable() : value); + /** + * @see #getChildren + * @param value is an array of children. If it is null all + * children set previously are forgotten. + */ + public void setChildren (MobyRelationship[] value) { + children = (value == null ? new MobyRelationship[] {} : value); } /** - * 'name' is a name given to this child (attribute) - * 'typeName' is a name of a type represented by this child + * @see #getChildren + * @param child a new child to be added. If null it is ignored. */ - public void addChild (String name, String typeName) { + public void addChild (MobyRelationship child) { + if (child != null) { + synchronized (children) { + int len = children.length + 1; + MobyRelationship[] newChildren = new MobyRelationship [len]; + System.arraycopy (children, 0, newChildren, 0, len-1); + newChildren [len - 1] = child; + setChildren (newChildren); + } + } + } + /** + * Create a {@link MobyRelationship MobyRelationship} object from + * given parameters and add it as a new child.

+ * + * @see #getChildren + * @param name is a name how the new child is known to this data + * type (an "article name" in the BioMoby speak), + * e.g. 'length'. Because of the backward compatibility it accepts + * also a null or empty string here - but according to the BioMoby + * API (0.8) this name should be always given. + * @param typeName is a name of the child data type, + * e.g. 'Integer'. If null it is ignored. + * @param relationshipType is either {@link MobyRelationship.HASA + * HASA} or {@link MobyRelationship.HAS HAS}. If it is something + * else it is silenty changed to {@link MobyRelationship.HASA + * HASA}. + */ + public void addChild (String name, String typeName, int relationshipType) { if (typeName != null) { - if (name == null || name.equals ("")) - name = typeName; -// children.put (typeName, name); - children.put (name, typeName); + if (name == null) name = ""; + if (relationshipType != MobyRelationship.HASA && + relationshipType != MobyRelationship.HAS) + relationshipType = MobyRelationship.HASA; + addChild (new MobyRelationship (name, typeName, relationshipType)); } } - public String toString() { StringBuffer buf = new StringBuffer(); buf.append ("Name: " + name + "\n"); buf.append ("Auth: " + authority + "\n"); buf.append ("Desc: " + description + "\n"); buf.append ("Contact: " + emailContact + "\n"); - buf.append ("ID: " + id + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); buf.append ("Parents:\n"); for (int i = 0 ; i < parentNames.length; i++) { buf.append (Utils.format (null, 1)); buf.append (parentNames [i]); buf.append ("\n"); } - buf.append ("Children:\n"); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { + buf.append ("Children (only those registered here):\n"); + for (int i = 0 ; i < children.length; i++) { buf.append (Utils.format (null, 1)); - String key = (String)en.nextElement(); - buf.append (key); - buf.append (" => "); - buf.append (children.get (key)); + buf.append (children[i].toString()); buf.append ("\n"); } return new String (buf); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2003/09/24 14:33:37 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2004/09/22 21:11:17 1.2 @@ -104,7 +104,7 @@ buf.append (name); buf.append ("\">\n"); buf.append (""); - buf.append (dataType.getName()); + if (dataType != null) buf.append (dataType.getName()); buf.append ("\n"); if (namespaces.size() > 0) { for (Enumeration en = namespaces.elements(); en.hasMoreElements(); ) { @@ -121,7 +121,7 @@ public String toString() { StringBuffer buf = new StringBuffer(); buf.append ("Name: " + name + "\n"); - buf.append ("ID: " + id + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); if (dataType != null) buf.append ("Data Type:\n" + dataType.format (1)); buf.append ("Namespaces:\n"); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2004/04/01 23:24:27 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2004/09/22 21:11:17 1.3 @@ -10,12 +10,12 @@ import java.util.*; /** - * A container representing a service. - *

+ * A container representing a service. But do not be too excited - + * this is not a real service but only its definition as it appears in + * the BioMoby regustry.

* * This container is used mainly to register a new service in a - * Moby registry, and to find registered services later. - *

+ * Moby registry, and to find registered services later.

* * @author Martin Senger * @version $Id$ @@ -30,6 +30,9 @@ protected String type = ""; protected String description = ""; protected String url = ""; + protected String signatureURL = ""; + protected String rdf = ""; + protected String pathToRDF = ""; protected boolean authoritativeService = true; protected String id = null; @@ -39,8 +42,9 @@ protected Vector primaryOutputs = new Vector(); /************************************************************************** - * Default constructor. Other characteristics are empty - which is usually - * wrong - therefore use 'set' method to fill them. + * Default constructor. Other characteristics are empty - which is + * usually wrong - therefore use 'set' methods to fill them before + * using this instance. *************************************************************************/ public MobyService (String name) { this.name = name; @@ -50,9 +54,21 @@ return name; } + /** + * Return an ID that is given to this service instance during its + * registration. The ID is used only for de-registration of this + * service instance (you are not supposed to fill it when you + * create an instance of this object). But it soon becomes + * obsolete anyway because of the new way of registering services + * (see {@link #getSignatureURL}).

+ */ public String getId() { return id; } + /** + * Don't use it. + * @see #getId + */ public void setId (String value) { id = value; } @@ -99,13 +115,89 @@ type = (value == null ? "" : value); } + /** + * Return a URL where this service is being served from. It is a + * URL where the clients of this service are going when they want + * to use it.

+ * + * Note that there is nothing in the BioMoby registry remembering + * (registering) a namespace of your service. Therefore, your + * service is supposed to use always the namespace + * http://biomoby.org.

+ */ public String getURL() { return url; } + /** + * @see #getURL + */ public void setURL (String value) { url = (value == null ? "" : value); } + /** + * Return a URL pointing to an RDF document that contains this + * service description (signature). Note that this RDF document + * can include also other things, such as other service + * signatures.

+ * + * This is how it works: + *

    + * + *
  1. When you register a service (using an instance of this + * class) you put here (by calling {@link #setSignatureURL}) a + * URL pointing to your HTTP space, to an RDF + * document. But this document does not need to exist yet. + * + *
  2. After a successful registration this instance will have + * an RDF document with this service signature. You can obtain + * it by calling {@link #getRDF}. + * + *
  3. You are expected to copy this RDF document to the place + * that you had suggested in step 1. Failing to do it will + * result in de-registrating your service automatically + * sometimes later. Therefore, if your service is only a testing + * one, do not copy RDF anywhere and the service will disappear. + * + *
  4. Some implementations of the {@link Central} interface + * (such as its default implementation {@link + * org.biomoby.client.CentralImpl CentralImpl} can copy the RDF + * document for you if you put here a fully qualified path to + * the file where the RDF document should be put (by calling + * {@link #setPathToRDF}). + * + *
+ */ + public String getSignatureURL() { + return signatureURL; + } + /** + * @see #getSignatureURL + */ + public void setSignatureURL (String value) { + signatureURL = (value == null ? "" : value); + } + + /** + * @see #getSignatureURL + */ + public String getPathToRDF() { + return pathToRDF; + } + public void setPathToRDF (String value) { + pathToRDF = (value == null ? "" : value); + } + + /** + * @see #getSignatureURL + */ + public String getRDF() { + return rdf; + } + public void setRDF (String value) { + rdf = (value == null ? "" : value); + } + public void setInputs (MobyData[] value) { if (value == null) { primaryInputs.clear(); @@ -176,14 +268,16 @@ public String toString() { StringBuffer buf = new StringBuffer(); - buf.append ("Name: " + name + "\n"); - buf.append ("Type: " + type + "\n"); - buf.append ("Category: " + category + "\n"); - buf.append ("Auth: " + authority + "\n"); - buf.append ("Desc: " + description + "\n"); - buf.append ("URL: " + url + "\n"); - buf.append ("Contact: " + emailContact + "\n"); - buf.append ("ID: " + id + "\n"); + buf.append ("Name: " + name + "\n"); + buf.append ("Type: " + type + "\n"); + buf.append ("Category: " + category + "\n"); + buf.append ("Auth: " + authority + "\n"); + buf.append ("Desc: " + description + "\n"); + buf.append ("URL: " + url + "\n"); + buf.append ("Contact: " + emailContact + "\n"); + buf.append ("Signature URL: " + signatureURL + "\n"); + buf.append ("Path to RDF: " + pathToRDF + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); buf.append ("\nPrimary inputs:\n"); for (Enumeration en = primaryInputs.elements(); en.hasMoreElements(); ) From senger at pub.open-bio.org Wed Sep 22 19:20:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 18:53:52 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222320.i8MNKHtJ015938@pub.open-bio.org> senger Wed Sep 22 19:20:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv15920/src/config Log Message: Directory /home/repository/moby/moby-live/Java/src/config added to the repository moby-live/Java/src/config - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/directory,v: No such file or directory From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 19:51:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1B1016161@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs/API In directory pub.open-bio.org:/tmp/cvs-serv16113/docs/API Modified Files: .cvsignore.template Log Message: enhanced build.xml to support other subprojects moby-live/Java/docs/API .cvsignore.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2003/09/25 12:27:47 1.2 +++ /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2004/09/23 00:18:01 1.3 @@ -4,4 +4,4 @@ *-list class-use org - +resources From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 19:51:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1dB016176@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv16113/src/config Added Files: run-any-client run-any-client.bat run-cmdline-client run-cmdline-client.bat run-graphs-client run-graphs-client.bat run-testing-central run-testing-central.bat source.me.csh source.me.sh Log Message: enhanced build.xml to support other subprojects moby-live/Java/src/config run-any-client,NONE,1.1 run-any-client.bat,NONE,1.1 run-cmdline-client,NONE,1.1 run-cmdline-client.bat,NONE,1.1 run-graphs-client,NONE,1.1 run-graphs-client.bat,NONE,1.1 run-testing-central,NONE,1.1 run-testing-central.bat,NONE,1.1 source.me.csh,NONE,1.1 source.me.sh,NONE,1.1 From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 19:51:40 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1gA016142@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java In directory pub.open-bio.org:/tmp/cvs-serv16113 Modified Files: build.xml Removed Files: run-any-client run-any-client.bat run-cmdline-client run-cmdline-client.bat run-graphs-client run-graphs-client.bat run-testing-central run-testing-central.bat Log Message: enhanced build.xml to support other subprojects moby-live/Java build.xml,1.6,1.7 run-any-client,1.1,NONE run-any-client.bat,1.1,NONE run-cmdline-client,1.2,NONE run-cmdline-client.bat,1.2,NONE run-graphs-client,1.1,NONE run-graphs-client.bat,1.1,NONE run-testing-central,1.2,NONE run-testing-central.bat,1.2,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/build.xml 2003/11/09 01:05:02 1.6 +++ /home/repository/moby/moby-live/Java/build.xml 2004/09/23 00:18:00 1.7 @@ -22,6 +22,7 @@ + @@ -43,6 +44,7 @@ + @@ -79,6 +81,18 @@ + + + + + + + + + + + + @@ -115,6 +129,20 @@ + + + + + + + + + + + + + + @@ -135,6 +163,7 @@ + @@ -156,6 +185,19 @@ + + + + + + + + + + + + + @@ -209,12 +251,24 @@ + + + + + + + + + + + + - Missing one or more third-party libraries. @@ -240,6 +294,18 @@ + + + + + + + + + + + @@ -407,6 +473,20 @@ + + + + + + + + + + + + + + rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-any-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-any-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-cmdline-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-cmdline-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-graphs-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-graphs-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-testing-central,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-testing-central.bat,v: No such file or directory From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed Sep 22 19:51:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I15k016197@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv16113/src/support Modified Files: README Log Message: enhanced build.xml to support other subprojects moby-live/Java/src/support README,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/README,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/support/README 2004/09/22 21:11:17 1.4 +++ /home/repository/moby/moby-live/Java/src/support/README 2004/09/23 00:18:01 1.5 @@ -8,9 +8,9 @@ Invoke available clients using provided (and very simple) scripts (use those ending with '.bat' for Windows OS): - sh ./run/run-cmdline-client -help - sh ./run/run-testing-central - sh ./run/run-graphs-client -help + sh ./run-cmdline-client -help + sh ./run-testing-central + sh ./run-graphs-client -help etc. Or, on Unix platforms, use chmod to make the scripts above executable From senger at pub.open-bio.org Thu Sep 23 06:20:29 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu Sep 23 05:54:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKTMn017972@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv17926/src/Clients Modified Files: MobyCmdLineClient.java PopulateLocalCentralForTesting.java TestingCentral.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/Clients MobyCmdLineClient.java,1.5,1.6 PopulateLocalCentralForTesting.java,1.2,1.3 TestingCentral.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/22 21:11:17 1.5 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/23 10:20:29 1.6 @@ -221,11 +221,11 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i], MobyRelationship.HASA); + data.addChild (null, hasas [i], Central.iHASA); } else if (pos == hasas[i].length() - 1) { - data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HASA); + data.addChild (hasas [i].substring (0, pos), null, Central.iHASA); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HASA); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), Central.iHASA); } } } @@ -234,11 +234,11 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i], MobyRelationship.HAS); + data.addChild (null, hasas [i], Central.iHAS); } else if (pos == hasas[i].length() - 1) { - data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HAS); + data.addChild (hasas [i].substring (0, pos), null, Central.iHAS); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HAS); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), Central.iHAS); } } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/22 21:11:17 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/23 10:20:29 1.3 @@ -240,10 +240,10 @@ protected MobyDataType[] createAllDataTypes() { MobyDataType data1 = createDataType (dataType_1); data1.addParentName ("Object"); - data1.addChild ("address", "string", MobyRelationship.HASA); - data1.addChild ("age", "integer", MobyRelationship.HASA); - data1.addChild ("salary", "float", MobyRelationship.HASA); - data1.addChild ("born", "datetime", MobyRelationship.HASA); + data1.addChild ("address", "string", Central.iHASA); + data1.addChild ("age", "integer", Central.iHASA); + data1.addChild ("salary", "float", Central.iHASA); + data1.addChild ("born", "datetime", Central.iHASA); MobyDataType data2 = createDataType (dataType_2); data2.addParentName ("Object"); MobyDataType data3 = createDataType (dataType_3); @@ -253,8 +253,8 @@ MobyDataType data5 = createDataType (dataType_5); data5.addParentName (dataType_3); data5.addParentName (dataType_2); - data5.addChild ("range_min", "integer", MobyRelationship.HAS); - data5.addChild ("range_max", "integer", MobyRelationship.HAS); + data5.addChild ("range_min", "integer", Central.iHAS); + data5.addChild ("range_max", "integer", Central.iHAS); return new MobyDataType [] { data1, data2, data3, data4, data5 }; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/23 10:20:29 1.4 @@ -247,9 +247,9 @@ try { start ("registerDataType - 2"); data2.addParentName (data1.getName()); - data2.addChild ("len", "Integer", MobyRelationship.HASA); - data2.addChild ("sub", "String", MobyRelationship.HAS); - data2.addChild ("real_type", data3.getName(), MobyRelationship.HASA); + data2.addChild ("len", "Integer", Central.iHASA); + data2.addChild ("sub", "String", Central.iHAS); + data2.addChild ("real_type", data3.getName(), Central.iHASA); worker.registerDataType (data2); ok(); } catch (MobyException e) { error (e); From senger at pub.open-bio.org Thu Sep 23 06:20:29 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu Sep 23 05:54:41 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKT07017945@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv17926/docs Modified Files: ChangeLog Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/docs ChangeLog,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/22 21:11:17 1.18 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/23 10:20:29 1.19 @@ -1,3 +1,8 @@ +2004-09-23 Martin Senger + + * Moved constants ISA, HAS, HASA from MobyRelationship to Central + (as iHAS, iHASA and iISA). + 2004-09-22 Martin Senger * Fixed option -rs-out in MobyCmdLineClient. From senger at pub.open-bio.org Thu Sep 23 06:20:30 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu Sep 23 05:54:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKUR8017992@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv17926/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/22 21:11:17 1.14 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/23 10:20:29 1.15 @@ -833,7 +833,7 @@ if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), belows.item (k).getFirstChild().getNodeValue(), - MobyRelationship.HASA ); + Central.iHASA ); } } } else if (relationshipType.endsWith ("has")) { @@ -843,7 +843,7 @@ if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), belows.item (k).getFirstChild().getNodeValue(), - MobyRelationship.HAS ); + Central.iHAS ); } } } @@ -924,13 +924,13 @@ StringBuffer buf2 = new StringBuffer(); // for HASA StringBuffer buf3 = new StringBuffer(); // for HAS for (int i = 0; i < children.length; i++) { - if (children[i].getRelationshipType() == MobyRelationship.HASA) { + if (children[i].getRelationshipType() == Central.iHASA) { buf2.append (""); buf2.append (children[i].getDataTypeName()); buf2.append (""); - } else if (children[i].getRelationshipType() == MobyRelationship.HAS) { + } else if (children[i].getRelationshipType() == Central.iHAS) { buf3.append (""); From senger at pub.open-bio.org Thu Sep 23 06:20:30 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu Sep 23 05:54:45 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKUIn018025@pub.open-bio.org> senger Thu Sep 23 06:20:30 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv17926/src/main/org/biomoby/shared Modified Files: Central.java MobyDataSimpleInstance.java MobyDataType.java MobyRelationship.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/main/org/biomoby/shared Central.java,1.5,1.6 MobyDataSimpleInstance.java,1.2,1.3 MobyDataType.java,1.3,1.4 MobyRelationship.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/05/18 10:13:17 1.5 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/23 10:20:29 1.6 @@ -48,15 +48,38 @@ public interface Central { - /** A name for the relationship type "is a". */ + /** A relationship type expressing a straight inheritance (as + * string). If Object_A ISA Object_B then all attributes of + * Object_B are guaranteed to be present in Object_A. + */ static final String ISA = "ISA"; - /** A name for the relationship type "has a". */ + /** A relationship type expressing a contaiment (as string). If + * Object_A HASA Object_B then Object_B is an object inside of + * Object_A in one copy only. */ static final String HASA = "HASA"; - /** A name for the relationship type "has". */ + /** A relationship type expressing a contaiment (as string). If + * Object_A HAS Object_B then Object_B is an object inside of + * Object_A in one or more copies. */ static final String HAS = "HAS"; + /** A relationship type expressing a straight inheritance (as + * integer). If Object_A ISA Object_B then all attributes of + * Object_B are guaranteed to be present in Object_A. + */ + static final int iISA = 1; + + /** A relationship type expressing a contaiment (as integer). If + * Object_A HASA Object_B then Object_B is an object inside of + * Object_A in one copy only. */ + static final int iHASA = 2; + + /** A relationship type expressing a contaiment (as integer). If + * Object_A HAS Object_B then Object_B is an object inside of + * Object_A in one or more copies. */ + static final int iHAS = 3; + /************************************************************************** * Get a (redundant) list of all registered service names. *

@@ -309,7 +332,7 @@ /************************************************************************** * Find service matching both all non-empty fields in the 'pattern' and - * the 'keywords', and take into account also the whole ontology tree: + * the 'keywords', and take into account also the whole ontology tree. *

* @param includeChildrenServiceTypes - if true (which is default) * then it discovers also services that are child types (more @@ -351,4 +374,12 @@ * Reports whether server responses are being cached or not. *************************************************************************/ boolean getCacheMode(); + + + // Work in progress: +// http://biomoby.org/RESOURCES/MOBY-S/Objects +// http://biomoby.org/RESOURCES/MOBY-S/Services +// http://biomoby.org/RESOURCES/MOBY-S/Namespaces +// http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances + } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/03 20:28:16 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/23 10:20:29 1.3 @@ -140,7 +140,7 @@ } /** - * Used to set the data instance value based on a ID string (i.e. just an Object) + * Used to set the data instance value based on an ID string. E.i. just an Object. */ public void setId(String value){ super.setId(value); @@ -214,7 +214,7 @@ * a template for use in MOBY Central services, or a Simple element for use in calling a service * instance. * - * @returns the MOBY XML representation of the data instance + * @return the MOBY XML representation of the data instance */ public String toXML(){ if(xmlMode == SERVICE_XML_MODE) =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/23 10:20:29 1.4 @@ -176,8 +176,8 @@ * types - in other words it does not go up through the whole * ontology tree to find all children.

* - * @see MobyRelationship.HAS - * @see MobyRelationship.HASA + * @see Central#iHAS + * @see Central#iHASA */ public MobyRelationship[] getChildren() { return children; @@ -216,18 +216,18 @@ * also a null or empty string here - but according to the BioMoby * API (0.8) this name should be always given. * @param typeName is a name of the child data type, - * e.g. 'Integer'. If null it is ignored. - * @param relationshipType is either {@link MobyRelationship.HASA - * HASA} or {@link MobyRelationship.HAS HAS}. If it is something - * else it is silenty changed to {@link MobyRelationship.HASA + * e.g. 'Integer'. If it is null it is ignored. + * @param relationshipType is either {@link Central#iHASA + * HASA} or {@link Central#iHAS HAS}. If it is something + * else it is silenty changed to {@link Central#iHASA * HASA}. */ public void addChild (String name, String typeName, int relationshipType) { if (typeName != null) { if (name == null) name = ""; - if (relationshipType != MobyRelationship.HASA && - relationshipType != MobyRelationship.HAS) - relationshipType = MobyRelationship.HASA; + if (relationshipType != Central.iHASA && + relationshipType != Central.iHAS) + relationshipType = Central.iHASA; addChild (new MobyRelationship (name, typeName, relationshipType)); } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java 2004/09/22 21:11:17 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java 2004/09/23 10:20:29 1.2 @@ -20,25 +20,9 @@ public class MobyRelationship { - /** A relationship type expressing a straight inheritance. If - * Object_A ISA Object_B then all attributes of Object_B are - * guaranteed to be present in Object_A. - */ - public static final int ISA = 1; - - /** A relationship type expressing a contaiment. If Object_A HASA - * Object_B then Object_B is an object inside of Object_A in one - * copy only. */ - public static final int HASA = 2; - - /** A relationship type expressing a contaiment. If Object_A HAS - * Object_B then Object_B is an object inside of Object_A in one - * or more copies. */ - public static final int HAS = 3; - protected String name; // articleName protected String dataTypeName; - protected int relationshipType = HASA; + protected int relationshipType = Central.iHASA; /************************************************************************** * Default (and only) constructor.

@@ -50,15 +34,15 @@ * should be always given. * @param dataTypeName is a name of a data type that is defined by * this relationship, e.g. 'Integer'. - * @param relationshipType is either {@link #HASA} or {@link - * #HAS}. If it is something else it is silently changed to {@link - * #HASA}. + * @param relationshipType is either {@link Central#iHASA HASA} or {@link + * Central#iHAS HAS}. If it is something else it is silently changed to {@link + * Central#iHASA HASA}. *************************************************************************/ public MobyRelationship (String name, String dataTypeName, int relationshipType) { this.name = name; this.dataTypeName = dataTypeName; - if (relationshipType != HASA && relationshipType != HAS) - relationshipType = HASA; + if (relationshipType != Central.iHASA && relationshipType != Central.iHAS) + relationshipType = Central.iHASA; this.relationshipType = relationshipType; } @@ -78,8 +62,8 @@ } /** - * Return type of this relationship. It is either {@link #HASA} or - * {@link #HAS}. + * Return type of this relationship. It is either {@link Central#iHASA HASA} or + * {@link Central#iHAS HAS}. */ public int getRelationshipType() { return relationshipType; @@ -93,9 +77,9 @@ */ public static String type2str (int relationshipType) { switch (relationshipType) { - case HASA: return "HASA"; - case HAS: return "HAS"; - case ISA: return "ISA"; + case Central.iHASA: return Central.HASA; + case Central.iHAS: return Central.HAS; + case Central.iISA: return Central.ISA; default: return "unknown"; } } From kawas at pub.open-bio.org Thu Sep 23 10:27:08 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu Sep 23 10:00:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231427.i8NER8aO019251@pub.open-bio.org> kawas Thu Sep 23 10:27:08 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv19222 Removed Files: Untitled-2.htm index-old.html index.htm service-app.jar service.html service.jar tree-app.jar tree.jar Log Message: removed the files and will commit them to their proper packages. part 3 (i missed a few) moby-live/Accessories/ObjectCreationTool/Applets Untitled-2.htm,1.1,NONE index-old.html,1.1,NONE index.htm,1.2,NONE service-app.jar,1.1,NONE service.html,1.1,NONE service.jar,1.1,NONE tree-app.jar,1.2,NONE tree.jar,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/Untitled-2.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/index-old.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/index.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service-app.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/tree-app.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/tree.jar,v: No such file or directory From senger at pub.open-bio.org Fri Sep 24 15:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri Sep 24 15:26:22 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquZ7032093@pub.open-bio.org> senger Fri Sep 24 15:52:55 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv32055/src/Clients/help Modified Files: MobyGraphs_usage.txt Log Message: signatureURL was missing in service response object moby-live/Java/src/Clients/help MobyGraphs_usage.txt,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2003/11/25 13:18:10 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2004/09/24 19:52:55 1.4 @@ -1,12 +1,23 @@ Usage: java MobyGraphs -h[elp] - java MobyGraphs + java MobyGraphs [] - -q ... quiet mode +where specify what Moby registry to connect to: - -d ... graph showing data types - -s ... graph showing service instances - -t ... graph showing service types + -e + ia an endpoint of a Moby registry + (default: http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY-Central.pl) + -uri + is a URI defining Moby registry's namespace + (default: http://mobycentral.cbr.nrc.ca/MOBY/Central) + +where are: + + -q ... quiet mode + + -d ... make graph showing data types + -s ... make graph showing service instances + -t ... make graph showing service types output format: -dot ... (this is default) From senger at pub.open-bio.org Fri Sep 24 15:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri Sep 24 15:26:25 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquwd032118@pub.open-bio.org> senger Fri Sep 24 15:52:56 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32055/src/main/org/biomoby/client Modified Files: CentralImpl.java Graphviz.java Log Message: signatureURL was missing in service response object moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.15,1.16 Graphviz.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/23 10:20:29 1.15 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/24 19:52:55 1.16 @@ -407,8 +407,9 @@ * * Service_Ontology_Term * moby - * http://service.endpoint.here/scriptname * your@email.addy.here + * http://service.RDF.here + * http://service.endpoint.here/scriptname * 1 * * @@ -453,6 +454,8 @@ service.setCategory (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("URL")) { service.setURL (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("signatureURL")) { + service.setSignatureURL (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("contactEmail")) { service.setEmailContact (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("serviceType")) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/24 19:52:56 1.4 @@ -93,8 +93,8 @@ edgeAttrs.append ("]"); } buf.append ("\t" + - edge.sourceService.getName() + " -> " + - edge.targetService.getName() + + quoteIt (edge.sourceService.getName()) + " -> " + + quoteIt (edge.targetService.getName()) + new String (edgeAttrs) + "\n"); } } @@ -132,15 +132,15 @@ String[] parents = type.getParentNames(); for (int i = 0; i < parents.length; i++) { buf.append ("\t"); - buf.append (trName (Utils.pureName (parents[i]))); + buf.append (quoteIt (trName (Utils.pureName (parents[i])))); buf.append (" -> "); - buf.append (trName (name)); + buf.append (quoteIt (trName (name))); buf.append (";\n"); } MobyRelationship[] children = type.getChildren(); if (children.length > 0) { String dummyName = trName (name) + "_HASA"; - buf.append ("\t" + trName (name) + " -> " + dummyName); + buf.append ("\t" + quoteIt (trName (name)) + " -> " + quoteIt (dummyName)); buf.append (" [style=dotted,dir=forward,arrowhead=none,arrowtail=ediamond];\n"); StringBuffer hasaBuf = new StringBuffer(); for (int i = 0; i < children.length; i++) { @@ -150,7 +150,7 @@ childType = "n/a"; // should not happen I guess hasaBuf.append (" | {" + childType + "|" + childName + "}"); } - buf.append ("\t" + dummyName + " [shape=record, label=\"HAS[A]"); + buf.append ("\t" + quoteIt (dummyName) + " [shape=record, label=\"HAS[A]"); buf.append (hasaBuf); buf.append ("\"];\n"); } @@ -187,9 +187,9 @@ String[] parents = type.getParentNames(); for (int i = 0; i < parents.length; i++) { buf.append ("\t"); - buf.append (trName (Utils.pureName (parents[i])).toLowerCase()); + buf.append (quoteIt (trName (Utils.pureName (parents[i])).toLowerCase())); buf.append (" -> "); - buf.append (trName (name).toLowerCase()); + buf.append (quoteIt (trName (name).toLowerCase())); buf.append (";\n"); } } @@ -219,4 +219,16 @@ return name.replace ('-', '_'); } + /************************************************************************* + * Surround given text by quotes. This will prevent errors + * encoutered by 'dot' when names have whitespaces or when they + * are identical to the 'dot's keywords (such as 'edge'). + * + * @param name to be quoted + * @return changed 'name' + *************************************************************************/ + public static String quoteIt (String name) { + return "\"" + name + "\""; + } + } From senger at pub.open-bio.org Fri Sep 24 15:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri Sep 24 15:26:26 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquf9032137@pub.open-bio.org> senger Fri Sep 24 15:52:56 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32055/src/main/org/biomoby/shared Modified Files: Central.java Log Message: signatureURL was missing in service response object moby-live/Java/src/main/org/biomoby/shared Central.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/23 10:20:29 1.6 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/24 19:52:56 1.7 @@ -381,5 +381,6 @@ // http://biomoby.org/RESOURCES/MOBY-S/Services // http://biomoby.org/RESOURCES/MOBY-S/Namespaces // http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances +// http://biomoby.org/RESOURCES/MOBY-S/FULL } From senger at pub.open-bio.org Fri Sep 24 15:52:55 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri Sep 24 15:26:27 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJqt8S032074@pub.open-bio.org> senger Fri Sep 24 15:52:55 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv32055/docs Modified Files: ChangeLog Log Message: signatureURL was missing in service response object moby-live/Java/docs ChangeLog,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/23 10:20:29 1.19 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/24 19:52:55 1.20 @@ -1,3 +1,7 @@ +2004-09-24 Martin Senger + + * Fixed signatureURL in service response object. + 2004-09-23 Martin Senger * Moved constants ISA, HAS, HASA from MobyRelationship to Central From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:31 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPQa019481@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:32 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIP3o019502@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:33 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIP4h019445@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui added to the repository moby-live/Java/src/main/org/biomoby/client/gui - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:36 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPR2019463@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:37 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPCb019520@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:38 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPO0019539@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:39 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQo0019584@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:42 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQsK019606@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:44 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQqn019624@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/serviceTypeCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:46 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQhh019647@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/util Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util added to the repository moby-live/Java/src/main/org/biomoby/client/util - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:49 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQ9d019557@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:37 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:51:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIbV7019697@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/general Added Files: Remove24.gif Save16.gif SaveAs24.gif AlignTop16.gif Refresh24.gif TipOfTheDay24.gif Paste24.gif PageSetup24.gif Export24.gif Import24.gif AlignBottom16.gif Stop24.gif FindAgain16.gif Stop16.gif ZoomIn16.gif AlignRight16.gif SaveAll24.gif Delete16.gif Zoom24.gif SaveAll16.gif Properties24.gif SendMail24.gif Paste16.gif Refresh16.gif Open16.gif Cut24.gif PrintPreview16.gif ComposeMail16.gif History16.gif About24.gif Edit24.gif SaveAs16.gif AlignCenter24.gif Search16.gif AlignTop24.gif AlignJustifyHorizontal24.gif Information24.gif Copy16.gif Help16.gif ZoomOut16.gif PageSetup16.gif AlignJustifyVertical24.gif Import16.gif AlignRight24.gif Redo16.gif Save24.gif Add16.gif AlignJustifyVertical16.gif Cut16.gif Find24.gif Remove16.gif Properties16.gif Undo16.gif TipOfTheDay16.gif History24.gif ZoomIn24.gif AlignJustifyHorizontal16.gif About16.gif Undo24.gif ContextualHelp24.gif Export16.gif Print24.gif Redo24.gif SendMail16.gif Add24.gif ComposeMail24.gif ZoomOut24.gif Replace16.gif Help24.gif Delete24.gif Edit16.gif New24.gif Preferences16.gif Zoom16.gif Find16.gif AlignCenter16.gif New16.gif AlignBottom24.gif Copy24.gif AlignLeft16.gif Information16.gif Bookmarks24.gif Preferences24.gif ContextualHelp16.gif Open24.gif FindAgain24.gif Bookmarks16.gif PrintPreview24.gif Replace24.gif AlignLeft24.gif Print16.gif Search24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general Remove24.gif,NONE,1.1 Save16.gif,NONE,1.1 SaveAs24.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 Paste24.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 Export24.gif,NONE,1.1 Import24.gif,NONE,1.1 AlignBottom16.gif,NONE,1.1 Stop24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Stop16.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 Delete16.gif,NONE,1.1 Zoom24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 Properties24.gif,NONE,1.1 SendMail24.gif,NONE,1.1 Paste16.gif,NONE,1.1 Refresh16.gif,NONE,1.1 Open16.gif,NONE,1.1 Cut24.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 ComposeMail16.gif,NONE,1.1 History16.gif,NONE,1.1 About24.gif,NONE,1.1 Edit24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Search16.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 Information24.gif,NONE,1.1 Copy16.gif,NONE,1.1 Help16.gif,NONE,1.1 ! ZoomOut16.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Import16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Redo16.gif,NONE,1.1 Save24.gif,NONE,1.1 Add16.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 Cut16.gif,NONE,1.1 Find24.gif,NONE,1.1 Remove16.gif,NONE,1.1 Properties16.gif,NONE,1.1 Undo16.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 History24.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 About16.gif,NONE,1.1 Undo24.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 Export16.gif,NONE,1.1 Print24.gif,NONE,1.1 Redo24.gif,NONE,1.1 SendMail16.gif,NONE,1.1 Add24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 Replace16.gif,NONE,1.1 Help24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Edit16.gif,NONE,1.1 New24.gif,NONE,1.1 Preferences16.gif,NONE,1.1 Zoom16.gif,NONE,1.1 Find16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 New16.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 Copy24.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Information16.gif,NONE,1.1 Bo! okmarks24.gif,NONE,1.1 Preferences24.gif,NONE,1.1 ContextualH! elp16.gif,NONE,1.1 Open24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Replace24.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Print16.gif,NONE,1.1 Search24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:01 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcvj019800@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Added Files: Back24.gif Back16.gif Down16.gif Home24.gif Up24.gif Forward16.gif Up16.gif Home16.gif Forward24.gif Down24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Back24.gif,NONE,1.1 Back16.gif,NONE,1.1 Down16.gif,NONE,1.1 Home24.gif,NONE,1.1 Up24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Up16.gif,NONE,1.1 Home16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Down24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:09 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIc6e019818@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img Added Files: LICENSE moby_small.gif middle.gif java.gif MOBY-S.jpeg left.gif bio.gif moby1.gif moby.gif right.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img LICENSE,NONE,1.1 moby_small.gif,NONE,1.1 middle.gif,NONE,1.1 java.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 left.gif,NONE,1.1 bio.gif,NONE,1.1 moby1.gif,NONE,1.1 moby.gif,NONE,1.1 right.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:10 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcS2019782@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/table Added Files: ColumnInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif ColumnInsertAfter24.gif ColumnDelete16.gif ColumnInsertBefore16.gif RowInsertBefore24.gif ColumnInsertBefore24.gif ColumnDelete24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table ColumnInsertAfter16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 ColumnDelete16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:13 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcsS019834@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/text Added Files: AlignLeft24.gif AlignCenter16.gif Underline16.gif AlignLeft16.gif Normal16.gif Bold24.gif AlignRight24.gif Normal24.gif Italic24.gif Underline24.gif AlignRight16.gif Italic16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif Bold16.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text AlignLeft24.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Underline16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Normal16.gif,NONE,1.1 Bold24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Normal24.gif,NONE,1.1 Italic24.gif,NONE,1.1 Underline24.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Italic16.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Bold16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcru019764@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/serviceTypeCreationTool Added Files: ServiceTypeApplet.java README Household.java Construct.java MobyTree.java Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,NONE,1.1 README,NONE,1.1 Household.java,NONE,1.1 Construct.java,NONE,1.1 MobyTree.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIct2019729@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/development Added Files: JarAdd24.gif War16.gif EnterpriseJavaBeanJar16.gif WebComponentAdd16.gif WebComponent24.gif Host24.gif J2EEApplicationClient16.gif EnterpriseJavaBean24.gif J2EEServer16.gif Server16.gif J2EEApplicationClientAdd16.gif J2EEApplication24.gif War24.gif ApplicationDeploy16.gif Host16.gif Application16.gif J2EEApplication16.gif J2EEServer24.gif ApplicationDeploy24.gif Server24.gif BeanAdd24.gif Bean24.gif Jar24.gif Applet24.gif Jar16.gif BeanAdd16.gif WebComponent16.gif EnterpriseJavaBean16.gif Bean16.gif Applet16.gif Application24.gif J2EEApplicationClientAdd24.gif J2EEApplicationClient24.gif WarAdd24.gif WarAdd16.gif EnterpriseJavaBeanJar24.gif JarAdd16.gif WebComponentAdd24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development JarAdd24.gif,NONE,1.1 War16.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 Host24.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 Server16.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 War24.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 Host16.gif,NONE,1.1 Application16.gif,NONE,1.1 J2EEApplication16.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 Server24.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 Bean24.gif,NONE,1.1 Jar24.gif,NONE,1.1 Applet24.gif,NONE,1.1 Jar16.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Bean16.gif,NONE,1.1 Applet16.gif,NONE,1.1 Application24.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 WarAdd24.gif! ,NONE,1.1 WarAdd16.gif,NONE,1.1 EnterpriseJavaBeanJar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:17 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcg6019746@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/util Added Files: TreeLoaderThread.java REGEXP.java Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/util TreeLoaderThread.java,NONE,1.1 REGEXP.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:37 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 15:52:24 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIbgL019712@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/media Added Files: Play16.gif StepForward16.gif Movie16.gif StepBack24.gif Rewind16.gif Volume24.gif Stop16.gif Pause16.gif Play24.gif Volume16.gif FastForward24.gif FastForward16.gif StepForward24.gif Pause24.gif StepBack16.gif Rewind24.gif Stop24.gif Movie24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media Play16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Movie16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Rewind16.gif,NONE,1.1 Volume24.gif,NONE,1.1 Stop16.gif,NONE,1.1 Pause16.gif,NONE,1.1 Play24.gif,NONE,1.1 Volume16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Pause24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 Rewind24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Movie24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 17:02:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 16:35:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272102.i8RL26T2020147@pub.open-bio.org> kawas Mon Sep 27 17:02:06 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20123/org/biomoby/client/gui/util Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util added to the repository moby-live/Java/src/main/org/biomoby/client/gui/util - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 17:02:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 16:35:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272102.i8RL29Ak020181@pub.open-bio.org> kawas Mon Sep 27 17:02:09 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20160/org/biomoby/client/gui/util Added Files: REGEXP.java TreeLoaderThread.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,NONE,1.1 TreeLoaderThread.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 17:06:17 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 16:39:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272106.i8RL6HA6020232@pub.open-bio.org> kawas Mon Sep 27 17:06:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20203/org/biomoby/client/gui/util Modified Files: REGEXP.java TreeLoaderThread.java Log Message: fixed some imports and ensured that code is in the gui package moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.1,1.2 TreeLoaderThread.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:02:09 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:06:17 1.2 @@ -1,4 +1,4 @@ -package org.biomoby.client.util; +package org.biomoby.client.gui.util; import java.util.regex.Matcher; import java.util.regex.Pattern; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:02:09 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:06:17 1.2 @@ -1,4 +1,4 @@ -package org.biomoby.client.util; +package org.biomoby.client.gui.util; import javax.swing.SwingUtilities; /** From kawas at pub.open-bio.org Mon Sep 27 17:06:17 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 16:39:21 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272106.i8RL6HGO020251@pub.open-bio.org> kawas Mon Sep 27 17:06:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20203/org/biomoby/client/gui/serviceTypeCreationTool Modified Files: ServiceTypeApplet.java Log Message: fixed some imports and ensured that code is in the gui package moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 20:18:38 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 21:06:17 1.2 @@ -26,8 +26,8 @@ import javax.swing.tree.TreePath; import org.biomoby.client.CentralImpl; -import org.biomoby.client.util.REGEXP; -import org.biomoby.client.util.TreeLoaderThread; +import org.biomoby.client.gui.util.REGEXP; +import org.biomoby.client.gui.util.TreeLoaderThread; import org.biomoby.shared.Central; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyServiceType; From kawas at pub.open-bio.org Mon Sep 27 17:26:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 16:59:58 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272126.i8RLQsHn020435@pub.open-bio.org> kawas Mon Sep 27 17:26:54 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20410/org/biomoby/client/gui/util Modified Files: REGEXP.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:26:54 1.3 @@ -5,62 +5,56 @@ /** * - * @author Edward Kawas - *

- * This class provides the methods necessary to validate email - * addresses, - *

- * URLs, and URIs. + * @author Eddie Kawas + *

Created for the Biomoby Project + *

This class was created to provide the necessary methods to validate email addresses + *

URLs, and URIs. + *

For questions, comments, or bugs + *

email me at edward.kawas@gmail.com */ - public class REGEXP { - /* - * regular expressions used for validation. - */ - private final static String EMAIL = "(^[\\w]+\\+?\\w*(\\.[\\w]+)*@[\\w]{2,}\\.[\\w]{2,}(\\.[\\w]{2,})*$)"; - - private final static String URI = - //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; - //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per - // rfc 2396 appendix a. - "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; - - private final static String URL = "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; - - /** - * - * @param address - - * the string to validate. - * @return true is address is a valid email address, false otherwise. - */ - public static boolean isValidEmailAddress(String address) { - Pattern p = Pattern.compile(EMAIL); - Matcher m = p.matcher(address); - return m.matches(); - } - - /** - * - * @param uri - - * the string to validate. - * @return true if the uri is a valid uri, false otherwise. - */ - public static boolean isValidURI(String uri) { - Pattern p = Pattern.compile(URI); - Matcher m = p.matcher(uri); - return m.matches(); - } - - /** - * - * @param url - - * the string to validate. - * @return true if url is a valid URL, false otherwise. - */ - public static boolean isValidURL(String url) { - Pattern p = Pattern.compile(URL); - Matcher m = p.matcher(url); - return m.matches(); - } + /* + * regular expressions used for validation. + */ + private final static String EMAIL = "(^[\\w]+\\+?\\w*(\\.[\\w]+)*@[\\w]{2,}\\.[\\w]{2,}(\\.[\\w]{2,})*$)"; + private final static String URI = + //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; + //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per rfc 2396 appendix a. + "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; + private final static String URL = + "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; + + /** + * + * @param address - the string to validate. + * @return true is address is a valid email address, false otherwise. + */ + public static boolean isValidEmailAddress(String address) { + Pattern p = Pattern.compile(EMAIL); + Matcher m = p.matcher(address); + return m.matches(); + } + + /** + * + * @param uri - the string to validate. + * @return true if the uri is a valid uri, false otherwise. + */ + public static boolean isValidURI(String uri) { + Pattern p = Pattern.compile(URI); + Matcher m = p.matcher(uri); + return m.matches(); + } + + /** + * + * @param url - the string to validate. + * @return true if url is a valid URL, false otherwise. + */ + public static boolean isValidURL(String url) { + Pattern p = Pattern.compile(URL); + Matcher m = p.matcher(url); + return m.matches(); + } } \ No newline at end of file From kawas at pub.open-bio.org Mon Sep 27 17:27:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 17:00:06 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272127.i8RLR4J3020465@pub.open-bio.org> kawas Mon Sep 27 17:27:04 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20440/org/biomoby/client/gui/util Modified Files: TreeLoaderThread.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util TreeLoaderThread.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:27:04 1.3 @@ -2,17 +2,14 @@ import javax.swing.SwingUtilities; /** - * This is the 3rd version of SwingWorker (also known as - * SwingWorker 3), an abstract class that you subclass to - * perform GUI-related work in a dedicated thread. For - * instructions on and examples of using this class, see: - * - * http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html - * - * Note that the API changed slightly in the 3rd version: - * You must now invoke start() on the SwingWorker after - * creating it. + * @author Sun Micro Systems + *

This class was created to provide an abstract class that you subclass to + *

perform GUI-related work in a dedicated thread. + * @see http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html + *

For questions, comments, or bugs + *

email me at edward.kawas@gmail.com */ + public abstract class TreeLoaderThread { private Object value; // see getValue(), setValue() From kawas at pub.open-bio.org Mon Sep 27 17:29:08 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 17:02:14 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLT8YU020499@pub.open-bio.org> kawas Mon Sep 27 17:29:08 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20475/org/biomoby/client/gui/serviceInstanceCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 17:29:15 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 17:02:18 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLTFxU020541@pub.open-bio.org> kawas Mon Sep 27 17:29:15 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20520/org/biomoby/client/gui/serviceInstanceCreationTool Added Files: MobyCollection.java MobyUtilities.java NamespaceListener.java Construct.java NamespaceTree.java Pair.java MobyTree.java README Household.java TreeListener.java HelpActionListener.java ServiceCreationTool.java InputOutputActionListener.java ServiceInstancePanelFactory.java Service.java ButtonBeautifier.java ServiceActionListener.java InputOutputFocusListener.java MobyInputOutputData.java ServiceFocusListener.java ServiceTypeTree.java Log Message: ServiceInstanceBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyCollection.java,NONE,1.1 MobyUtilities.java,NONE,1.1 NamespaceListener.java,NONE,1.1 Construct.java,NONE,1.1 NamespaceTree.java,NONE,1.1 Pair.java,NONE,1.1 MobyTree.java,NONE,1.1 README,NONE,1.1 Household.java,NONE,1.1 TreeListener.java,NONE,1.1 HelpActionListener.java,NONE,1.1 ServiceCreationTool.java,NONE,1.1 InputOutputActionListener.java,NONE,1.1 ServiceInstancePanelFactory.java,NONE,1.1 Service.java,NONE,1.1 ButtonBeautifier.java,NONE,1.1 ServiceActionListener.java,NONE,1.1 InputOutputFocusListener.java,NONE,1.1 MobyInputOutputData.java,NONE,1.1 ServiceFocusListener.java,NONE,1.1 ServiceTypeTree.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 17:29:15 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 17:02:19 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLTFwG020556@pub.open-bio.org> kawas Mon Sep 27 17:29:15 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv20520 Added Files: .cvsignore Log Message: ServiceInstanceBuilder initial commit moby-live/Java/src/main .cvsignore,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 18:07:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 17:40:15 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272207.i8RM7Ctp021120@pub.open-bio.org> kawas Mon Sep 27 18:07:12 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv21097 Removed Files: REGEXP.java TreeLoaderThread.java Log Message: no message moby-live/Java/src/main/org/biomoby/client/util REGEXP.java,1.1,NONE TreeLoaderThread.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/REGEXP.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/TreeLoaderThread.java,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 18:10:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 17:43:08 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272210.i8RMA6nZ021205@pub.open-bio.org> kawas Mon Sep 27 18:10:06 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv21181/org/biomoby/client/gui/objectCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 18:15:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon Sep 27 17:48:16 2004 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272215.i8RMFDkX021327@pub.open-bio.org> kawas Mon Sep 27 18:15:13 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv21306/org/biomoby/client/gui/objectCreationTool Added Files: ButtonBeautifier.java MobyUtilities.java TreeListener.java MobyUserPanel.java Construct.java FieldFocusListeners.java FieldKeyListener.java Pair.java MobyXML.java ButtonActions.java PanelFactory.java MobyTree.java Household.java Registration.java ObjectCreationTool.java MobyPlainText.java Log Message: ObjectCreationTool initial commit moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool ButtonBeautifier.java,NONE,1.1 MobyUtilities.java,NONE,1.1 TreeListener.java,NONE,1.1 MobyUserPanel.java,NONE,1.1 Construct.java,NONE,1.1 FieldFocusListeners.java,NONE,1.1 FieldKeyListener.java,NONE,1.1 Pair.java,NONE,1.1 MobyXML.java,NONE,1.1 ButtonActions.java,NONE,1.1 PanelFactory.java,NONE,1.1 MobyTree.java,NONE,1.1 Household.java,NONE,1.1 Registration.java,NONE,1.1 ObjectCreationTool.java,NONE,1.1 MobyPlainText.java,NONE,1.1 From gordonp at pub.open-bio.org Fri Sep 3 16:28:16 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Fri, 3 Sep 2004 16:28:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409032028.i83KSGf5010451@pub.open-bio.org> gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv10407/src/main/org/biomoby/client Modified Files: MobyRequest.java Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/07/07 16:02:47 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/09/03 20:28:16 1.5 @@ -506,6 +506,24 @@ throw new MobyException("The MOBY payload has no text contents at all"); } + // Check if the payload is an XML document. If not, try a last ditch effort + // by base64 decoding the contents. This is technically not allowable in the + // MOBY spec, but we are being lenient. + if(!responseString.startsWith(" gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv10407/docs Modified Files: ChangeLog Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/docs ChangeLog,1.16,1.17 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/07/07 16:07:46 1.16 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/03 20:28:16 1.17 @@ -1,3 +1,11 @@ +2004-09-03 Paul Gordon + + * First commit of data instance classes for base objects (Floats, Integers, Strings), + and updates to Simple and Service Associated Instance objects to deal with the new + object types. You can now create these objects (no XML knowledge required) for + use in services, and you can create complex Moby objects using DOM fragments. + Aggregation of base objects to create complex objects still needs to be implemented. + 2004-07-07 Paul Gordon * Modifications to MobyRequest to handle Axis 1.1beta, and a variety of From gordonp at pub.open-bio.org Fri Sep 3 16:28:16 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Fri, 3 Sep 2004 16:28:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409032028.i83KSGmd010476@pub.open-bio.org> gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv10407/src/main/org/biomoby/shared Modified Files: MobyDataServiceAssocInstance.java MobyDataSimpleInstance.java Added Files: MobyDataFloat.java MobyDataInt.java MobyDataString.java Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/src/main/org/biomoby/shared MobyDataFloat.java,NONE,1.1 MobyDataInt.java,NONE,1.1 MobyDataString.java,NONE,1.1 MobyDataServiceAssocInstance.java,1.1,1.2 MobyDataSimpleInstance.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java 2004/09/03 20:28:16 1.2 @@ -3,30 +3,92 @@ import org.w3c.dom.Element; /** - * A convenience class that just associates a set of possible services to run with a data instance + * A convenience class that just associates a set of possible services to run with a data instance. */ public class MobyDataServiceAssocInstance extends MobyDataSimpleInstance{ + protected MobyDataSimpleInstance dataInstance; protected MobyService[] mobyServices; - public MobyDataServiceAssocInstance(MobyDataType type, String name, String value, MobyService[] services){ - super(type, name, value); + public MobyDataServiceAssocInstance(MobyDataType type, String name, String id, MobyService[] services){ + super(type, name, id); mobyServices = services; + dataInstance = this; } public MobyDataServiceAssocInstance(Central central, Element simple, MobyService[] services) throws MobyException{ super(central, simple); mobyServices = services; + dataInstance = this; } public MobyDataServiceAssocInstance(MobyDataSimpleInstance mdsi, MobyService[] services){ - super(mdsi.getDataType(), mdsi.getName(), mdsi.getId()); - setValue(mdsi.getValue()); + super(mdsi.getName()); + dataInstance = (MobyDataSimpleInstance) mdsi.clone(); mobyServices = services; } + public Object clone(){ + if(dataInstance == this){ + // Avoid recursion, we're using the simple instance base behaviours + return super.clone(); + } + else{ + // Clone according to the base instance's subclass specific methods + return new MobyDataServiceAssocInstance(dataInstance, mobyServices); + } + } + public MobyService[] getServices(){ return mobyServices; } + + public MobyDataType getDataType(){ + return dataInstance.getDataType(); + } + + public void setServices(MobyService[] services){ + mobyServices = services; + } + + public void setXmlMode(int mode) throws IllegalArgumentException{ + dataInstance.setXmlMode(mode); + } + + public String getValue(){ + return dataInstance.getValue(); + } + + public void setId(String value){ + dataInstance.setId(value); + } + + public String getId(){ + return dataInstance.getId(); + } + + public void addNamespace(MobyNamespace ns){ + dataInstance.addNamespace(ns); + } + + public MobyNamespace[] getNamespaces(){ + return dataInstance.getNamespaces(); + } + + public void setValue(Element simple) throws javax.xml.transform.TransformerException{ + dataInstance.setValue(simple); + } + + public void setValue(String value){ + dataInstance.setValue(value); + } + + public String toString(){ + return dataInstance.toString(); + } + + public String toXML(){ + return dataInstance.toXML(); + } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/03 20:28:16 1.2 @@ -24,7 +24,7 @@ * SERVICE_XML_MODE. */ -public class MobyDataSimpleInstance extends MobyPrimaryDataSimple implements MobyDataInstance{ +public class MobyDataSimpleInstance extends MobyPrimaryDataSimple implements MobyDataInstance, Cloneable{ public static final int CENTRAL_XML_MODE = 124; public static final int SERVICE_XML_MODE = 891; protected int xmlMode = SERVICE_XML_MODE; @@ -36,10 +36,10 @@ * If you're looking to pass in an XML string for the constructor, you can't. You can use * the one argument constructor or this one, then use setValue(String). */ - public MobyDataSimpleInstance(MobyDataType dataType, String name, String value){ + public MobyDataSimpleInstance(MobyDataType dataType, String name, String id){ super(name); setDataType(dataType); - setId(value); + setId(id); } /** @@ -51,11 +51,27 @@ } /** + * Creates a simple object from the input instance, as opposed to clone, which creates + * an exact copy. + */ + public MobyDataSimpleInstance(MobyDataSimpleInstance mdsi){ + super(mdsi.getName()); + } + + /** * Standard constructor, build the object value using a DOM element. * @throws MobyException if the XML passed in does not have a moby:Simple root node */ public MobyDataSimpleInstance(Central mobyCentral, Element simple) throws MobyException{ super(MobyPrefixResolver.getAttr(simple, "articleName")); + + if(!simple.getLocalName().equals("Simple") || !(simple.getNamespaceURI() == null || + simple.getNamespaceURI().length() == 0 || + simple.getNamespaceURI().equals(MobyPrefixResolver.MOBY_XML_NAMESPACE))){ + throw new MobyException("Element passed to MobyDataSimpleInstance was not a moby:Simple, but " + + simple.getNodeName()); + } + NodeList children = simple.getElementsByTagName("*"); if(children == null || children.getLength() == 0){ throw new MobyException("Simple element (" + simple + @@ -172,6 +188,26 @@ public String toString(){ return dataValue; } + + /** + * Simply calls new constructor with object's existing data type, name and value. + * Subclasses should override this method if more datafields need to be copied for + * an accurate clone of the Moby Data Instance (i.e. anything but a base object). The + * subclasses should ensure that they also return a MobyDataSimpleInstance + * + * @return an object of class MobyDataSimpleInstance + */ + public Object clone(){ + MobyDataSimpleInstance copy = null; + copy = new MobyDataSimpleInstance(getName()); + copy.setDataType(getDataType()); + copy.setNamespaces(getNamespaces()); + copy.setId(getId()); + if(!isObject){ // Complex object that has its own XML representation we'll just copy over + copy.setValue(getValue()); + } + return copy; + } /** * Produces a full-blown XML fragment that depending on the value of getXmlMode() is either From mwilkinson at pub.open-bio.org Fri Sep 10 19:34:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Fri, 10 Sep 2004 19:34:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409102334.i8ANYbGt014004@pub.open-bio.org> mwilkinson Fri Sep 10 19:34:37 EDT 2004 Update of /home/repository/moby/moby-live/Accessories In directory pub.open-bio.org:/tmp/cvs-serv13986/Accessories Log Message: Directory /home/repository/moby/moby-live/Accessories added to the repository moby-live/Accessories - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 12:58:56 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 12:58:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131658.i8DGwulk031796@pub.open-bio.org> kawas Mon Sep 13 12:58:55 EDT 2004 Update of /home/repository/moby/Accessories In directory pub.open-bio.org:/tmp/cvs-serv31772 Log Message: Create module Status: Vendor Tag: vendor-tag Release Tags: release-tag No conflicts created by this import Accessories - Imported sources rcsdiff: /home/repository/moby/Accessories/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/Accessories/RCS/Imported,v: No such file or directory rcsdiff: /home/repository/moby/Accessories/RCS/sources,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:11:43 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:11:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131811.i8DIBhls032217@pub.open-bio.org> kawas Mon Sep 13 14:11:43 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv32193/ObjectCreationTool Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool added to the repository moby-live/Accessories/ObjectCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrgX032309@pub.open-bio.org> kawas Mon Sep 13 14:13:52 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv32284/img Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img added to the repository moby-live/Accessories/ObjectCreationTool/img - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDr3F032345@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrhb032327@pub.open-bio.org> kawas Mon Sep 13 14:13:52 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrZm032404@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrwf032386@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDswG032453@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrtB032365@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsIE032517@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby/client Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby/client - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDslx032428@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsib032493@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsW0032475@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org In directory pub.open-bio.org:/tmp/cvs-serv32284/org Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org added to the repository moby-live/Accessories/ObjectCreationTool/org - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtnW032535@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby/shared Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtJG032635@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/util Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/util - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtTf032574@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDt5r032556@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtMo032617@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object/creation/applet Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtJD032597@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object/creation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEA1W032718@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/text Added Files: AlignCenter16.gif AlignLeft16.gif AlignJustify16.gif AlignRight16.gif Bold16.gif Bold24.gif Italic24.gif AlignCenter24.gif Normal24.gif AlignRight24.gif AlignJustify24.gif Italic16.gif Normal16.gif AlignLeft24.gif Underline16.gif Underline24.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text AlignCenter16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Bold16.gif,NONE,1.1 Bold24.gif,NONE,1.1 Italic24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Normal24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Italic16.gif,NONE,1.1 Normal16.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Underline16.gif,NONE,1.1 Underline24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEAut032687@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/general Added Files: SaveAs24.gif Redo16.gif About24.gif Bookmarks24.gif Paste16.gif AlignRight24.gif Cut24.gif Delete16.gif PageSetup16.gif AlignLeft24.gif Replace24.gif FindAgain16.gif Edit16.gif Save24.gif Export24.gif AlignBottom24.gif SaveAs16.gif Save16.gif AlignTop16.gif Export16.gif Paste24.gif History16.gif Print24.gif Help16.gif PageSetup24.gif AlignTop24.gif AlignBottom16.gif Bookmarks16.gif Import16.gif PrintPreview24.gif Information16.gif SendMail16.gif SendMail24.gif SaveAll24.gif Replace16.gif ZoomOut16.gif ZoomIn24.gif Add24.gif Copy24.gif ComposeMail16.gif Import24.gif Remove24.gif FindAgain24.gif ContextualHelp24.gif SaveAll16.gif History24.gif Stop24.gif Redo24.gif Print16.gif Edit24.gif ComposeMail24.gif Open16.gif AlignJustifyVertical24.gif Help24.gif Find24.gif New24.gif TipOfTheDay16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif About16.gif Add16.gif Copy16.gif PrintPreview16.gif ZoomOut24.gif New16.gif Open24.gif Remove16.gif AlignLeft16.gif ContextualHelp16.gif Preferences16.gif AlignJustifyHorizontal16.gif Cut16.gif Refresh24.gif AlignCenter24.gif Search24.gif Zoom24.gif Delete24.gif Properties24.gif ZoomIn16.gif TipOfTheDay24.gif Zoom16.gif Refresh16.gif Information24.gif Undo16.gif Search16.gif Preferences24.gif Properties16.gif Undo24.gif Stop16.gif AlignCenter16.gif Find16.gif AlignRight16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general SaveAs24.gif,NONE,1.1 Redo16.gif,NONE,1.1 About24.gif,NONE,1.1 Bookmarks24.gif,NONE,1.1 Paste16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Cut24.gif,NONE,1.1 Delete16.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Replace24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Edit16.gif,NONE,1.1 Save24.gif,NONE,1.1 Export24.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 Save16.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Export16.gif,NONE,1.1 Paste24.gif,NONE,1.1 History16.gif,NONE,1.1 Print24.gif,NONE,1.1 Help16.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignBottom16.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 Import16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Information16.gif,NONE,1.1 SendMail16.gif,NONE,1.1 SendMail24.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 Replace16.gif,NONE,1.1 ZoomOut16.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 Add24.gif,NONE,1.1 Copy24.gif,NONE,1.1 ComposeMail16.gif,NONE! ,1.1 Import24.gif,NONE,1.1 Remove24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 History24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Redo24.gif,NONE,1.1 Print16.gif,NONE,1.1 Edit24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 Open16.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Help24.gif,NONE,1.1 Find24.gif,NONE,1.1 New24.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 About16.gif,NONE,1.1 Add16.gif,NONE,1.1 Copy16.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 New16.gif,NONE,1.1 Open24.gif,NONE,1.1 Remove16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 ContextualHelp16.gif,NONE,1.1 Preferences16.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 Cut16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Search24.gif,NONE,1.1 Zoom24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Properties24.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 Zoom16.gif,NONE! ,1.1 Refresh16.gif,NONE,1.1 Information24.gif,NONE,1.1 Undo16! .gif,NONE,1.1 Search16.gif,NONE,1.1 Preferences24.gif,NONE,1.1 Properties16.gif,NONE,1.1 Undo24.gif,NONE,1.1 Stop16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Find16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEADs032702@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32666/org/biomoby/shared Added Files: PendingCurationException.java MobyObject.java MobyDataType.java MobyDataInstance.java MobyDataSetInstance.java MobyDataSimpleInstance.java MobyDataSecondaryInstance.java MobyPrimaryDataSet.java NoSuccessException.java MobyNamespace.java MobyException.java Central.java MobyServiceType.java MobySecondaryData.java MobyNativeService.java MobyData.java MobyPrefixResolver.java SOAPException.java MobyService.java MobyDataServiceAssocInstance.java MobyPrimaryDataSimple.java Utils.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/biomoby/shared PendingCurationException.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyDataType.java,NONE,1.1 MobyDataInstance.java,NONE,1.1 MobyDataSetInstance.java,NONE,1.1 MobyDataSimpleInstance.java,NONE,1.1 MobyDataSecondaryInstance.java,NONE,1.1 MobyPrimaryDataSet.java,NONE,1.1 NoSuccessException.java,NONE,1.1 MobyNamespace.java,NONE,1.1 MobyException.java,NONE,1.1 Central.java,NONE,1.1 MobyServiceType.java,NONE,1.1 MobySecondaryData.java,NONE,1.1 MobyNativeService.java,NONE,1.1 MobyData.java,NONE,1.1 MobyPrefixResolver.java,NONE,1.1 SOAPException.java,NONE,1.1 MobyService.java,NONE,1.1 MobyDataServiceAssocInstance.java,NONE,1.1 MobyPrimaryDataSimple.java,NONE,1.1 Utils.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBmj032734@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv32666/org/mobycentral/util Added Files: MobyXML.java TreeLoaderThread.java Registration.java MobyUtilities.java MobyPlainText.java Household.java Pair.java Construct.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/mobycentral/util MobyXML.java,NONE,1.1 TreeLoaderThread.java,NONE,1.1 Registration.java,NONE,1.1 MobyUtilities.java,NONE,1.1 MobyPlainText.java,NONE,1.1 Household.java,NONE,1.1 Pair.java,NONE,1.1 Construct.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDKl000389@pub.open-bio.org> kawas Mon Sep 13 14:14:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/media Added Files: Play24.gif Pause24.gif Pause16.gif Rewind24.gif Stop24.gif StepForward24.gif Volume24.gif Movie24.gif Volume16.gif FastForward16.gif StepBack24.gif Movie16.gif StepForward16.gif Play16.gif FastForward24.gif StepBack16.gif Rewind16.gif Stop16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media Play24.gif,NONE,1.1 Pause24.gif,NONE,1.1 Pause16.gif,NONE,1.1 Rewind24.gif,NONE,1.1 Stop24.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Volume24.gif,NONE,1.1 Movie24.gif,NONE,1.1 Volume16.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Movie16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Play16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 Rewind16.gif,NONE,1.1 Stop16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEB4Z032752@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/development Added Files: Application16.gif Bean16.gif Application24.gif J2EEApplicationClientAdd24.gif J2EEServer24.gif WebComponent24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBean16.gif Host24.gif EnterpriseJavaBean24.gif ApplicationDeploy16.gif BeanAdd16.gif Jar16.gif BeanAdd24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClient16.gif Bean24.gif War24.gif WebComponentAdd16.gif J2EEApplicationClient24.gif Host16.gif J2EEServer16.gif JarAdd24.gif WarAdd16.gif ApplicationDeploy24.gif WebComponentAdd24.gif J2EEApplication24.gif Jar24.gif JarAdd16.gif Applet16.gif WebComponent16.gif War16.gif Server24.gif EnterpriseJavaBeanJar24.gif WarAdd24.gif Server16.gif Applet24.gif J2EEApplication16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development Application16.gif,NONE,1.1 Bean16.gif,NONE,1.1 Application24.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Host24.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 Jar16.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 Bean24.gif,NONE,1.1 War24.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 Host16.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 JarAdd24.gif,NONE,1.1 WarAdd16.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 Jar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 Applet16.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 War16.gif,NONE,1.1 Server24.gif,NONE,1.1 EnterpriseJavaBean! Jar24.gif,NONE,1.1 WarAdd24.gif,NONE,1.1 Server16.gif,NONE,1.1 Applet24.gif,NONE,1.1 J2EEApplication16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDSe000371@pub.open-bio.org> kawas Mon Sep 13 14:14:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/table Added Files: ColumnDelete16.gif RowDelete16.gif RowInsertAfter16.gif ColumnInsertAfter24.gif RowInsertBefore24.gif ColumnInsertBefore24.gif ColumnInsertAfter16.gif RowInsertAfter24.gif ColumnDelete24.gif RowInsertBefore16.gif ColumnInsertBefore16.gif RowDelete24.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table ColumnDelete16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 ColumnInsertAfter16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBBa000338@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv32666/img Added Files: LICENSE bio.gif moby.gif MOBY-S.jpeg java.gif moby1.gif left.gif moby_small.gif middle.gif right.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img LICENSE,NONE,1.1 bio.gif,NONE,1.1 moby.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 java.gif,NONE,1.1 moby1.gif,NONE,1.1 left.gif,NONE,1.1 moby_small.gif,NONE,1.1 middle.gif,NONE,1.1 right.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBZk000304@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/navigation Added Files: Home16.gif Up24.gif Down16.gif Up16.gif Forward24.gif Home24.gif Forward16.gif Back24.gif Down24.gif Back16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation Home16.gif,NONE,1.1 Up24.gif,NONE,1.1 Down16.gif,NONE,1.1 Up16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Home24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Back24.gif,NONE,1.1 Down24.gif,NONE,1.1 Back16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBLc000322@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32666/org/biomoby/client Added Files: ServletFileCache.java MobyRequest.java SimpleCache.java FilterServices.java ServiceConnections.java GraphsServlet.java RDF.java Graphviz.java ServicesEdge.java FileCache.java CentralImpl.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/biomoby/client ServletFileCache.java,NONE,1.1 MobyRequest.java,NONE,1.1 SimpleCache.java,NONE,1.1 FilterServices.java,NONE,1.1 ServiceConnections.java,NONE,1.1 GraphsServlet.java,NONE,1.1 RDF.java,NONE,1.1 Graphviz.java,NONE,1.1 ServicesEdge.java,NONE,1.1 FileCache.java,NONE,1.1 CentralImpl.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIECTo000353@pub.open-bio.org> kawas Mon Sep 13 14:14:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv32666/org/mobycentral/object/creation/applet Added Files: ObjectCreationTool.java MobyTree.java ButtonActions.java FieldFocusListeners.java MobyUserPanel.java ButtonBeautifier.java FieldKeyListener.java TreeListener.java PanelFactory.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet ObjectCreationTool.java,NONE,1.1 MobyTree.java,NONE,1.1 ButtonActions.java,NONE,1.1 FieldFocusListeners.java,NONE,1.1 MobyUserPanel.java,NONE,1.1 ButtonBeautifier.java,NONE,1.1 FieldKeyListener.java,NONE,1.1 TreeListener.java,NONE,1.1 PanelFactory.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 14:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDcg000410@pub.open-bio.org> kawas Mon Sep 13 14:14:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv32666 Added Files: .project .classpath Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool .project,NONE,1.1 .classpath,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWQs001120@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWA8001084@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets added to the repository moby-live/Accessories/ObjectCreationTool/Applets - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWTb001102@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/Demo Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo added to the repository moby-live/Accessories/ObjectCreationTool/Applets/Demo - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXCP001159@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXUl001265@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXx9001182@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXP9001139@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXqa001202@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXKK001286@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/lib Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib added to the repository moby-live/Accessories/ObjectCreationTool/Applets/lib - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXZX001306@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/offline Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline added to the repository moby-live/Accessories/ObjectCreationTool/Applets/offline - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCX76001247@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCX3Q001226@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJV8W001373@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/general Added Files: ZoomOut16.gif Add16.gif Copy16.gif AlignRight16.gif PrintPreview16.gif AlignLeft16.gif Add24.gif Import16.gif Redo16.gif Import24.gif Edit16.gif Refresh24.gif Export24.gif Stop24.gif About16.gif Remove16.gif Undo16.gif AlignCenter16.gif Find16.gif Undo24.gif Remove24.gif ZoomIn24.gif Search16.gif History16.gif Copy24.gif ComposeMail16.gif Help16.gif History24.gif Cut16.gif Paste24.gif Refresh16.gif Replace16.gif Properties16.gif Replace24.gif About24.gif AlignTop24.gif AlignRight24.gif Print16.gif Paste16.gif ContextualHelp24.gif Information16.gif Save16.gif ContextualHelp16.gif AlignTop16.gif Information24.gif SaveAll16.gif Properties24.gif SaveAs16.gif Find24.gif AlignJustifyHorizontal24.gif Zoom24.gif Preferences16.gif Edit24.gif SendMail16.gif PageSetup24.gif AlignBottom24.gif PageSetup16.gif TipOfTheDay16.gif AlignJustifyVertical16.gif Search24.gif ZoomOut24.gif Print24.gif Delete16.gif Export16.gif SendMail24.gif SaveAll24.gif AlignLeft24.gif Help24.gif FindAgain24.gif Zoom16.gif Open24.gif SaveAs24.gif Preferences24.gif Save24.gif New24.gif AlignJustifyVertical24.gif Delete24.gif Redo24.gif Bookmarks24.gif FindAgain16.gif Stop16.gif AlignBottom16.gif AlignJustifyHorizontal16.gif AlignCenter24.gif ComposeMail24.gif ZoomIn16.gif PrintPreview24.gif Open16.gif Bookmarks16.gif New16.gif Cut24.gif TipOfTheDay24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general ZoomOut16.gif,NONE,1.1 Add16.gif,NONE,1.1 Copy16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Add24.gif,NONE,1.1 Import16.gif,NONE,1.1 Redo16.gif,NONE,1.1 Import24.gif,NONE,1.1 Edit16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 Export24.gif,NONE,1.1 Stop24.gif,NONE,1.1 About16.gif,NONE,1.1 Remove16.gif,NONE,1.1 Undo16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Find16.gif,NONE,1.1 Undo24.gif,NONE,1.1 Remove24.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 Search16.gif,NONE,1.1 History16.gif,NONE,1.1 Copy24.gif,NONE,1.1 ComposeMail16.gif,NONE,1.1 Help16.gif,NONE,1.1 History24.gif,NONE,1.1 Cut16.gif,NONE,1.1 Paste24.gif,NONE,1.1 Refresh16.gif,NONE,1.1 Replace16.gif,NONE,1.1 Properties16.gif,NONE,1.1 Replace24.gif,NONE,1.1 About24.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Print16.gif,NONE,1.1 Paste16.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 Informatio! n16.gif,NONE,1.1 Save16.gif,NONE,1.1 ContextualHelp16.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Information24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 Properties24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 Find24.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 Zoom24.gif,NONE,1.1 Preferences16.gif,NONE,1.1 Edit24.gif,NONE,1.1 SendMail16.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 Search24.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 Print24.gif,NONE,1.1 Delete16.gif,NONE,1.1 Export16.gif,NONE,1.1 SendMail24.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Help24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 Zoom16.gif,NONE,1.1 Open24.gif,NONE,1.1 SaveAs24.gif,NONE,1.1 Preferences24.gif,NONE,1.1 Save24.gif,NONE,1.1 New24.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Redo24.gif,NONE,1.1 Bookmarks24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Stop16.gif,NONE,1.1 AlignBot! tom16.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 Alig! nCenter24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Open16.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 New16.gif,NONE,1.1 Cut24.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJVOl001388@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/navigation Added Files: Down16.gif Forward24.gif Up24.gif Home16.gif Down24.gif Forward16.gif Up16.gif Back24.gif Home24.gif Back16.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Down16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Up24.gif,NONE,1.1 Home16.gif,NONE,1.1 Down24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Up16.gif,NONE,1.1 Back24.gif,NONE,1.1 Home24.gif,NONE,1.1 Back16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWNX001456@pub.open-bio.org> kawas Mon Sep 13 16:19:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/media Added Files: Pause24.gif Rewind24.gif StepForward24.gif Movie16.gif Stop16.gif FastForward24.gif Pause16.gif Volume16.gif Volume24.gif Play16.gif Movie24.gif FastForward16.gif StepBack24.gif Stop24.gif Play24.gif StepBack16.gif StepForward16.gif Rewind16.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media Pause24.gif,NONE,1.1 Rewind24.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Movie16.gif,NONE,1.1 Stop16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 Pause16.gif,NONE,1.1 Volume16.gif,NONE,1.1 Volume24.gif,NONE,1.1 Play16.gif,NONE,1.1 Movie24.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Play24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Rewind16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJVuk001404@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/table Added Files: ColumnDelete16.gif ColumnInsertBefore16.gif RowInsertAfter24.gif ColumnInsertAfter16.gif RowDelete16.gif RowInsertBefore16.gif ColumnDelete24.gif RowDelete24.gif RowInsertBefore24.gif RowInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 ColumnInsertAfter16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWvL001439@pub.open-bio.org> kawas Mon Sep 13 16:19:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/development Added Files: J2EEApplication16.gif WebComponent24.gif J2EEServer16.gif JarAdd24.gif J2EEApplicationClient16.gif J2EEApplicationClientAdd16.gif ApplicationDeploy16.gif J2EEApplicationClientAdd24.gif BeanAdd16.gif Application24.gif EnterpriseJavaBean16.gif Applet24.gif War24.gif BeanAdd24.gif Host24.gif Jar24.gif J2EEApplicationClient24.gif WebComponent16.gif Application16.gif WarAdd16.gif J2EEApplication24.gif Server16.gif Jar16.gif Bean16.gif WebComponentAdd24.gif EnterpriseJavaBeanJar24.gif JarAdd16.gif EnterpriseJavaBean24.gif Server24.gif ApplicationDeploy24.gif War16.gif Applet16.gif EnterpriseJavaBeanJar16.gif WarAdd24.gif Bean24.gif Host16.gif WebComponentAdd16.gif J2EEServer24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development J2EEApplication16.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 JarAdd24.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 Application24.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Applet24.gif,NONE,1.1 War24.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 Host24.gif,NONE,1.1 Jar24.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 Application16.gif,NONE,1.1 WarAdd16.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 Server16.gif,NONE,1.1 Jar16.gif,NONE,1.1 Bean16.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 EnterpriseJavaBeanJar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 Server24.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 War16.gif,NONE,1.1 Applet16.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE! ,1.1 WarAdd24.gif,NONE,1.1 Bean24.gif,NONE,1.1 Host16.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWWl001420@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/text Added Files: AlignLeft24.gif Underline16.gif Bold24.gif Bold16.gif AlignRight16.gif Underline24.gif AlignJustify16.gif AlignJustify24.gif Normal24.gif AlignCenter24.gif AlignCenter16.gif Italic24.gif AlignLeft16.gif Italic16.gif Normal16.gif AlignRight24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text AlignLeft24.gif,NONE,1.1 Underline16.gif,NONE,1.1 Bold24.gif,NONE,1.1 Bold16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Underline24.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Normal24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Italic24.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Italic16.gif,NONE,1.1 Normal16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJaa0001535@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/Demo Added Files: jena.jar icu4j.jar xercesImpl.jar index.htm Demo.jar commons-logging.jar demo2.htm Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/Demo jena.jar,NONE,1.1 icu4j.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 index.htm,NONE,1.1 Demo.jar,NONE,1.1 commons-logging.jar,NONE,1.1 demo2.htm,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:35 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJZbq001481@pub.open-bio.org> kawas Mon Sep 13 16:19:35 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/lib Added Files: antlr.jar xalan.jar log4j-1.2.7.jar jdom.jar jaxrpc.jar jaxen-core.jar commons-discovery.jar wsdl4j.jar saaj.jar axis.jar adenine.jar activation.jar concurrent.jar jena.jar junit.jar servlet.jar xercesImpl.jar jakarta-oro-2.0.5.jar saxpath.jar xml-apis.jar rdf-api-2001-01-19.jar icu4j.jar jaxen-jdom.jar commons-logging.jar alltools.jar axis-ant.jar Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/lib antlr.jar,NONE,1.1 xalan.jar,NONE,1.1 log4j-1.2.7.jar,NONE,1.1 jdom.jar,NONE,1.1 jaxrpc.jar,NONE,1.1 jaxen-core.jar,NONE,1.1 commons-discovery.jar,NONE,1.1 wsdl4j.jar,NONE,1.1 saaj.jar,NONE,1.1 axis.jar,NONE,1.1 adenine.jar,NONE,1.1 activation.jar,NONE,1.1 concurrent.jar,NONE,1.1 jena.jar,NONE,1.1 junit.jar,NONE,1.1 servlet.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 jakarta-oro-2.0.5.jar,NONE,1.1 saxpath.jar,NONE,1.1 xml-apis.jar,NONE,1.1 rdf-api-2001-01-19.jar,NONE,1.1 icu4j.jar,NONE,1.1 jaxen-jdom.jar,NONE,1.1 commons-logging.jar,NONE,1.1 alltools.jar,NONE,1.1 axis-ant.jar,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJaC1001513@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets Added Files: Untitled-2.htm tree-app.jar index-old.html service.jar service.html service-app.jar index.htm tree.jar Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets Untitled-2.htm,NONE,1.1 tree-app.jar,NONE,1.1 index-old.html,NONE,1.1 service.jar,NONE,1.1 service.html,NONE,1.1 service-app.jar,NONE,1.1 index.htm,NONE,1.1 tree.jar,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJa9U001496@pub.open-bio.org> kawas Mon Sep 13 16:19:35 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img Added Files: moby_small.gif left.gif LICENSE java.gif MOBY-S.jpeg middle.gif right.gif moby1.gif moby.gif bio.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img moby_small.gif,NONE,1.1 left.gif,NONE,1.1 LICENSE,NONE,1.1 java.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 middle.gif,NONE,1.1 right.gif,NONE,1.1 moby1.gif,NONE,1.1 moby.gif,NONE,1.1 bio.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJalF001550@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/offline Added Files: Namespaces Services Objects Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/offline Namespaces,NONE,1.1 Services,NONE,1.1 Objects,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:21:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:21:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132021.i8DKL3wf001599@pub.open-bio.org> kawas Mon Sep 13 16:21:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1578 Added Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 16:28:00 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132028.i8DKS0PM001776@pub.open-bio.org> kawas Mon Sep 13 16:28:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1751 Modified Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:21:03 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:28:00 1.2 @@ -34,7 +34,7 @@ There are also many various DEBUG flags that when enabled print out various pieces of information. - 3. There is a runnable version of the code located in the /moby-live/Accessories/ObjectToolApplet + 3. There is a runnable version of the code located in the /moby-live/Accessories/Applets To notify me of bugs or if you have comments please email me at the address below Eddie Kawas From kawas at pub.open-bio.org Mon Sep 13 16:30:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:30:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132030.i8DKUCRc001903@pub.open-bio.org> kawas Mon Sep 13 16:30:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1878 Modified Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:28:00 1.2 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:30:12 1.3 @@ -34,7 +34,7 @@ There are also many various DEBUG flags that when enabled print out various pieces of information. - 3. There is a runnable version of the code located in the /moby-live/Accessories/Applets + 3. There is a runnable version of the code located in the /moby-live/Accessories/ObjectCreationTool/Applets To notify me of bugs or if you have comments please email me at the address below Eddie Kawas From kawas at pub.open-bio.org Mon Sep 13 16:51:51 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:51:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132051.i8DKpp3m002023@pub.open-bio.org> kawas Mon Sep 13 16:51:51 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1990/Applets Modified Files: index.htm tree.jar tree-app.jar Log Message: Recreated the jar files and modified the applet page html moby-live/Accessories/ObjectCreationTool/Applets index.htm,1.1,1.2 tree.jar,1.1,1.2 tree-app.jar,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm 2004/09/13 20:19:36 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm 2004/09/13 20:51:50 1.2 @@ -10,7 +10,13 @@ Moby Object Creation Tool - +

=================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar 2004/09/13 20:19:36 1.1 and /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar 2004/09/13 20:51:50 1.2 differ rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar 2004/09/13 20:19:36 1.1 and /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar 2004/09/13 20:51:51 1.2 differ rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar: diff failed From mwilkinson at pub.open-bio.org Tue Sep 14 17:32:35 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 14 Sep 2004 17:32:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142132.i8ELWZGP006220@pub.open-bio.org> mwilkinson Tue Sep 14 17:32:35 EDT 2004 Update of /home/repository/moby/moby-live/Database In directory pub.open-bio.org:/tmp/cvs-serv6201 Modified Files: mobycentral.mysql Log Message: updating empty database schema moby-live/Database mobycentral.mysql,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Database/mobycentral.mysql,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Database/mobycentral.mysql 2003/05/24 20:22:15 1.3 +++ /home/repository/moby/moby-live/Database/mobycentral.mysql 2004/09/14 21:32:35 1.4 @@ -92,6 +92,7 @@ authoritative enum('1','0') NOT NULL default '0', description text NOT NULL, service_instance_id int(10) unsigned NOT NULL auto_increment, + signatureURL varchar(255), PRIMARY KEY (service_instance_id), UNIQUE KEY servicename (servicename,authority_id) ) TYPE=MyISAM; From mwilkinson at pub.open-bio.org Tue Sep 14 17:36:20 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 14 Sep 2004 17:36:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142136.i8ELaK7G006269@pub.open-bio.org> mwilkinson Tue Sep 14 17:36:20 EDT 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv6250 Modified Files: INSTALL Log Message: typos moby-live/Perl INSTALL,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/INSTALL 2004/07/28 23:00:09 1.2 +++ /home/repository/moby/moby-live/Perl/INSTALL 2004/09/14 21:36:20 1.3 @@ -8,7 +8,7 @@ For details on how to configure your own MOBY Central registry, should you want to set one up (you DO NOT -need to set up a registry to acess nor service MOBY-S +need to set up a registry to access nor serve MOBY-S Services) please visit the "Installing a Local Registy" link on the biomoby.org homepage. From mwilkinson at pub.open-bio.org Tue Sep 14 18:05:04 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 14 Sep 2004 18:05:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142205.i8EM54PZ006416@pub.open-bio.org> mwilkinson Tue Sep 14 18:05:04 EDT 2004 Update of /home/repository/moby/moby-live/Database In directory pub.open-bio.org:/tmp/cvs-serv6401 Added Files: mobycentral.config Log Message: adding a template mobycentral.config file moby-live/Database mobycentral.config,NONE,1.1 From kawas at pub.open-bio.org Thu Sep 16 10:22:56 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu, 16 Sep 2004 10:22:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409161422.i8GEMut9014234@pub.open-bio.org> kawas Thu Sep 16 10:22:56 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv14209/org/biomoby/client Modified Files: CentralImpl.java Log Message: fixed buf2->buf3 bug. moby-live/Accessories/ObjectCreationTool/org/biomoby/client CentralImpl.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java 2004/09/13 18:14:11 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java 2004/09/16 14:22:56 1.2 @@ -956,11 +956,11 @@ Hashtable childrenHAS = dataType.getHASChildren(); for (Enumeration en = childrenHAS.keys(); en.hasMoreElements();) { String name = (String) en.nextElement(); - buf2.append(""); - buf2.append(children.get(name)); - buf2.append(""); + buf3.append(""); + buf3.append(children.get(name)); + buf3.append(""); } // done addition From mwilkinson at pub.open-bio.org Thu Sep 16 18:21:02 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 16 Sep 2004 18:21:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409162221.i8GML2lO015538@pub.open-bio.org> mwilkinson Thu Sep 16 18:21:02 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv15519/MOBY Modified Files: Central.pm Log Message: as per Martin's observation, there is no need to pass the RDF as CDATA. This required changes in both the client and server libraries. Everyone needs to do a CVS update to use it moby-live/Perl/MOBY Central.pm,1.140,1.141 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.140 retrieving revision 1.141 diff -u -r1.140 -r1.141 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/26 20:52:28 1.140 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/09/16 22:21:01 1.141 @@ -165,11 +165,17 @@ $RDF = $details->{RDF}; +# return " +# $id +# $success +# +# +# "; return " $id $success - + $RDF "; } From mwilkinson at pub.open-bio.org Thu Sep 16 18:21:02 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 16 Sep 2004 18:21:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409162221.i8GML2oV015557@pub.open-bio.org> mwilkinson Thu Sep 16 18:21:02 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv15519/MOBY/Client Modified Files: Central.pm Log Message: as per Martin's observation, there is no need to pass the RDF as CDATA. This required changes in both the client and server libraries. Everyone needs to do a CVS update to use it moby-live/Perl/MOBY/Client Central.pm,1.79,1.80 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.79 retrieving revision 1.80 diff -u -r1.79 -r1.80 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/08/11 16:27:48 1.79 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/09/16 22:21:02 1.80 @@ -1656,7 +1656,7 @@ my $id = &_nodeTextContent($Object, 'id'); my $success = &_nodeTextContent($Object, 'success'); my $message = &_nodeTextContent($Object, 'message'); - my $RDF = &_nodeTextContent($Object, 'RDF'); + my $RDF = &_nodeRawContent($Object, 'RDF'); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, @@ -1691,6 +1691,22 @@ return $content; } +sub _nodeRawContent { + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ($DOM, $node) = @_; + my $x = $DOM->getElementsByTagName($node); + unless ($x->item(0)){return}; + my @child = $x->item(0)->getChildNodes; + my $content; + foreach (@child){ + #print $_->getNodeTypeName, "\t", $_->toString,"\n"; +# next unless $_->getNodeType == TEXT_NODE; + $content .= $_->toString; + } + return $content; +} + sub _nodeArrayContent { # will get array content of all child $node from given $DOM From gss at pub.open-bio.org Tue Sep 21 11:36:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 21 Sep 2004 11:36:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409211536.i8LFa62b009514@pub.open-bio.org> gss Tue Sep 21 11:36:06 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv9492/WebRoot/images Removed Files: rdf-logo.PNG Log Message: Changed size; stored as different name moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images rdf-logo.PNG,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/rdf-logo.PNG,v: No such file or directory From gss at pub.open-bio.org Tue Sep 21 11:36:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 21 Sep 2004 11:36:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409211536.i8LFaZ0c009550@pub.open-bio.org> gss Tue Sep 21 11:36:35 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv9529/WebRoot/images Added Files: rdf-logo.png Log Message: Added "RDF" to image moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images rdf-logo.png,NONE,1.1 From kawas at pub.open-bio.org Tue Sep 21 21:49:59 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:49:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220149.i8M1nxbi011675@pub.open-bio.org> kawas Tue Sep 21 21:49:58 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool Removed Files: .classpath .project README.TXT Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool .classpath,1.1,NONE .project,1.1,NONE README.TXT,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/.classpath,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/.project,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/README.TXT,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:00 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o0nX011705@pub.open-bio.org> kawas Tue Sep 21 21:50:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/Demo Removed Files: Demo.jar commons-logging.jar demo2.htm icu4j.jar index.htm jena.jar xercesImpl.jar Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/Demo Demo.jar,1.1,NONE commons-logging.jar,1.1,NONE demo2.htm,1.1,NONE icu4j.jar,1.1,NONE index.htm,1.1,NONE jena.jar,1.1,NONE xercesImpl.jar,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/Demo.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/demo2.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/icu4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/index.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/jena.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/xercesImpl.jar,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:01 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o1pf011789@pub.open-bio.org> kawas Tue Sep 21 21:50:01 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1! ,NONE WebComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE 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rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:01 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o1WM011731@pub.open-bio.org> kawas Tue Sep 21 21:50:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img Removed Files: LICENSE MOBY-S.jpeg bio.gif java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: 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directory From kawas at pub.open-bio.org Tue Sep 21 21:50:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o3al011899@pub.open-bio.org> kawas Tue Sep 21 21:50:01 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif ZoomOut16.gif ZoomOut24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE AlignJustifyHorizontal24.gif,1.1,NONE AlignJustifyVertical16.gif,1.1,NONE AlignJustifyVertical24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE AlignTop16.gif,1.1,NONE AlignTop24.gif,1.1,NONE Bookmarks16.gif,1.1,NONE Bookmarks24.gif,1.1,NONE ComposeMail16.gif,1.1,NONE ComposeMail24.gif,1.1,NONE ContextualHelp16.gif,1.1,NONE ContextualHelp24.gif,1.1,NONE Copy16.gif,1.1,NONE Copy24.gif,1.1,NONE Cut16.gif,1.1,NONE Cut24.gif,1.1,NONE Delete16.gif,1.1,NONE Delete24.gif,1.1,NONE Edit16.gif,1.1,NONE Edit24.gif,1.1,NONE Export16.gif,1.1,NONE Export24.gif,1.1,NONE Find16.gif,1.1,NONE Find24.gif,1.1,NONE FindAgain1! 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Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE TipOfTheDay16.! gif,1.1,NONE TipOfTheDay24.gif,1.1,NONE Undo16.gif,1.1,NONE Undo24.gif,1.1,NONE Zoom16.gif,1.1,NONE Zoom24.gif,1.1,NONE ZoomIn16.gif,1.1,NONE ZoomIn24.gif,1.1,NONE ZoomOut16.gif,1.1,NONE ZoomOut24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/About16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/About24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/Add16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/Add24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o4gF011988@pub.open-bio.org> kawas Tue Sep 21 21:50:04 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowInsertBefore24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE 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From kawas at pub.open-bio.org Tue Sep 21 21:50:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o3PN011933@pub.open-bio.org> kawas Tue Sep 21 21:50:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o46J011958@pub.open-bio.org> kawas Tue Sep 21 21:50:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o4BG012022@pub.open-bio.org> kawas Tue Sep 21 21:50:04 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o9KA012089@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/offline Removed Files: Namespaces Objects Services Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/offline Namespaces,1.1,NONE Objects,1.1,NONE Services,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Namespaces,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Objects,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Services,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oA15012115@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img Removed Files: LICENSE MOBY-S.jpeg bio.gif java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/bio.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/java.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/left.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/middle.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby1.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby_small.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/right.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oARW012176@pub.open-bio.org> kawas Tue Sep 21 21:50:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1,NONE We! bComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE WebComponentAdd24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Applet16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Applet24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Application16.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEApplicationClientAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEServer16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEServer24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Jar16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Jar24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/JarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBGQ012378@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowInsertBefore24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertBefore24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBqD012348@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBQ5012286@pub.open-bio.org> kawas Tue Sep 21 21:50:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif ZoomOut16.gif ZoomOut24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Search24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/SendMail16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/SendMail24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/TipOfTheDay16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/TipOfTheDay24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Undo16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Undo24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Zoom16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Zoom24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oDnV012478@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/biomoby/shared Removed Files: Central.java MobyData.java MobyDataInstance.java MobyDataSecondaryInstance.java MobyDataServiceAssocInstance.java MobyDataSetInstance.java MobyDataSimpleInstance.java MobyDataType.java MobyException.java MobyNamespace.java MobyNativeService.java MobyObject.java MobyPrefixResolver.java MobyPrimaryDataSet.java MobyPrimaryDataSimple.java MobySecondaryData.java MobyService.java MobyServiceType.java NoSuccessException.java PendingCurationException.java SOAPException.java Utils.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/biomoby/shared Central.java,1.1,NONE MobyData.java,1.1,NONE MobyDataInstance.java,1.1,NONE MobyDataSecondaryInstance.java,1.1,NONE MobyDataServiceAssocInstance.java,1.1,NONE MobyDataSetInstance.java,1.1,NONE MobyDataSimpleInstance.java,1.1,NONE MobyDataType.java,1.1,NONE MobyException.java,1.1,NONE MobyNamespace.java,1.1,NONE MobyNativeService.java,1.1,NONE MobyObject.java,1.1,NONE MobyPrefixResolver.java,1.1,NONE MobyPrimaryDataSet.java,1.1,NONE MobyPrimaryDataSimple.java,1.1,NONE MobySecondaryData.java,1.1,NONE MobyService.java,1.1,NONE MobyServiceType.java,1.1,NONE NoSuccessException.java,1.1,NONE PendingCurationException.java,1.1,NONE SOAPException.java,1.1,NONE Utils.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/Central.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSecondaryInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataServiceAssocInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSetInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSimpleInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyNamespace.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyNativeService.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrefixResolver.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrimaryDataSet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrimaryDataSimple.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobySecondaryData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyService.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyServiceType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/NoSuccessException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/PendingCurationException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/SOAPException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/Utils.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:14 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oEFE012532@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/mobycentral/util Removed Files: Construct.java Household.java MobyPlainText.java MobyUtilities.java MobyXML.java Pair.java Registration.java TreeLoaderThread.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/mobycentral/util Construct.java,1.1,NONE Household.java,1.1,NONE MobyPlainText.java,1.1,NONE MobyUtilities.java,1.1,NONE MobyXML.java,1.1,NONE Pair.java,1.1,NONE Registration.java,1.1,NONE TreeLoaderThread.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Construct.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Household.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyPlainText.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyUtilities.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyXML.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Pair.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Registration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/TreeLoaderThread.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oC8s012441@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/biomoby/client Removed Files: CentralImpl.java FileCache.java FilterServices.java GraphsServlet.java Graphviz.java MobyRequest.java RDF.java ServiceConnections.java ServicesEdge.java ServletFileCache.java SimpleCache.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/biomoby/client CentralImpl.java,1.2,NONE FileCache.java,1.1,NONE FilterServices.java,1.1,NONE GraphsServlet.java,1.1,NONE Graphviz.java,1.1,NONE MobyRequest.java,1.1,NONE RDF.java,1.1,NONE ServiceConnections.java,1.1,NONE ServicesEdge.java,1.1,NONE ServletFileCache.java,1.1,NONE SimpleCache.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/CentralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/FileCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/FilterServices.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/GraphsServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/Graphviz.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/MobyRequest.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/RDF.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServiceConnections.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServicesEdge.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServletFileCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/SimpleCache.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o9i4012071@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/lib Removed Files: activation.jar adenine.jar alltools.jar antlr.jar axis-ant.jar axis.jar commons-discovery.jar commons-logging.jar concurrent.jar icu4j.jar jakarta-oro-2.0.5.jar jaxen-core.jar jaxen-jdom.jar jaxrpc.jar jdom.jar jena.jar junit.jar log4j-1.2.7.jar rdf-api-2001-01-19.jar saaj.jar saxpath.jar servlet.jar wsdl4j.jar xalan.jar xercesImpl.jar xml-apis.jar Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/lib activation.jar,1.1,NONE adenine.jar,1.1,NONE alltools.jar,1.1,NONE antlr.jar,1.1,NONE axis-ant.jar,1.1,NONE axis.jar,1.1,NONE commons-discovery.jar,1.1,NONE commons-logging.jar,1.1,NONE concurrent.jar,1.1,NONE icu4j.jar,1.1,NONE jakarta-oro-2.0.5.jar,1.1,NONE jaxen-core.jar,1.1,NONE jaxen-jdom.jar,1.1,NONE jaxrpc.jar,1.1,NONE jdom.jar,1.1,NONE jena.jar,1.1,NONE junit.jar,1.1,NONE log4j-1.2.7.jar,1.1,NONE rdf-api-2001-01-19.jar,1.1,NONE saaj.jar,1.1,NONE saxpath.jar,1.1,NONE servlet.jar,1.1,NONE wsdl4j.jar,1.1,NONE xalan.jar,1.1,NONE xercesImpl.jar,1.1,NONE xml-apis.jar,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/activation.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/adenine.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/alltools.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/antlr.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/axis-ant.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/axis.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/commons-discovery.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/concurrent.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/icu4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jakarta-oro-2.0.5.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxen-core.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxen-jdom.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxrpc.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jdom.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jena.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/junit.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/log4j-1.2.7.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/rdf-api-2001-01-19.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/saaj.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/saxpath.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/servlet.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/wsdl4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xalan.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xercesImpl.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xml-apis.jar,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBSb012412@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignLeft24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignRight16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignRight24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Bold16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Bold24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oDVb012505@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/mobycentral/object/creation/applet Removed Files: ButtonActions.java ButtonBeautifier.java FieldFocusListeners.java FieldKeyListener.java MobyTree.java MobyUserPanel.java ObjectCreationTool.java PanelFactory.java TreeListener.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet ButtonActions.java,1.1,NONE ButtonBeautifier.java,1.1,NONE FieldFocusListeners.java,1.1,NONE FieldKeyListener.java,1.1,NONE MobyTree.java,1.1,NONE MobyUserPanel.java,1.1,NONE ObjectCreationTool.java,1.1,NONE PanelFactory.java,1.1,NONE TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ButtonActions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/FieldFocusListeners.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/FieldKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/MobyTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/MobyUserPanel.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ObjectCreationTool.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/PanelFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/TreeListener.java,v: No such file or directory From kawas at pub.open-bio.org Tue Sep 21 21:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oB40012320@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Pause16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Pause24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Play16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Play24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Rewind16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Rewind24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHiW015522@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv15476/src/Clients Modified Files: MobyCmdLineClient.java PopulateLocalCentralForTesting.java TestingCentral.java Log Message: new registration procedure, etc. moby-live/Java/src/Clients MobyCmdLineClient.java,1.4,1.5 PopulateLocalCentralForTesting.java,1.1,1.2 TestingCentral.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/05/18 10:13:16 1.4 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/22 21:11:17 1.5 @@ -221,11 +221,24 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i]); + data.addChild (null, hasas [i], MobyRelationship.HASA); } else if (pos == hasas[i].length() - 1) { - data.addChild (null, hasas [i].substring (0, pos)); + data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HASA); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1)); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HASA); + } + } + } + if ((param = cmd.getParam ("-rd-has")) != null ) { + String[] hasas = StringUtils.split (param, ","); + for (int i = 0; i < hasas.length; i++) { + int pos = hasas[i].indexOf (":"); + if (pos == -1) { + data.addChild (null, hasas [i], MobyRelationship.HAS); + } else if (pos == hasas[i].length() - 1) { + data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HAS); + } else { + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HAS); } } } @@ -273,7 +286,15 @@ service.setAuthoritative (param.equals ("1") ? true : false); } service.setURL (cmd.getParam ("-rs-url")); - if ((param = cmd.getParam ("-rs-in")) != null ) { + service.setSignatureURL (cmd.getParam ("-rs-rdf")); + if ( (param = cmd.getParam ("-rs-rdfpath")) != null ) { + service.setPathToRDF (param); + } else { + File tmpFile = File.createTempFile ("Moby-RDF." + service.getName() + ".", ".xml"); + service.setPathToRDF (tmpFile.getAbsolutePath()); + } + + if ( (param = cmd.getParam ("-rs-in")) != null ) { String[] inputs = StringUtils.split (param, ","); for (int i = 0; i < inputs.length; i++) { String[] parts = StringUtils.split (inputs[i], "="); @@ -346,7 +367,9 @@ if ((param = cmd.getParam ("-rs-out")) != null ) { String[] outs = StringUtils.split (param, ","); for (int i = 0; i < outs.length; i++) { - service.addOutput (new MobyPrimaryDataSimple (outs[i])); + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (outs[i])); + service.addOutput (data); } } if ((param = cmd.getParam ("-rs-ofile")) != null ) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2003/10/17 13:13:34 1.1 +++ /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/22 21:11:17 1.2 @@ -240,10 +240,10 @@ protected MobyDataType[] createAllDataTypes() { MobyDataType data1 = createDataType (dataType_1); data1.addParentName ("Object"); - data1.addChild ("address", "string"); - data1.addChild ("age", "integer"); - data1.addChild ("salary", "float"); - data1.addChild ("born", "datetime"); + data1.addChild ("address", "string", MobyRelationship.HASA); + data1.addChild ("age", "integer", MobyRelationship.HASA); + data1.addChild ("salary", "float", MobyRelationship.HASA); + data1.addChild ("born", "datetime", MobyRelationship.HASA); MobyDataType data2 = createDataType (dataType_2); data2.addParentName ("Object"); MobyDataType data3 = createDataType (dataType_3); @@ -253,8 +253,8 @@ MobyDataType data5 = createDataType (dataType_5); data5.addParentName (dataType_3); data5.addParentName (dataType_2); - data5.addChild ("range_min", "integer"); - data5.addChild ("range_max", "integer"); + data5.addChild ("range_min", "integer", MobyRelationship.HAS); + data5.addChild ("range_max", "integer", MobyRelationship.HAS); return new MobyDataType [] { data1, data2, data3, data4, data5 }; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2003/10/17 13:13:34 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/22 21:11:17 1.3 @@ -122,7 +122,7 @@ // command-line parameters int i = 0; while (i < args.length) { - if (args[i].equals ("-help") || args[i].equals ("-")) { + if (args[i].equals ("-help") || args[i].equals ("-h")) { System.out.println ("Usage: java TestingCentral [-e ] [-u ] [-debug]"); System.exit (0); @@ -160,6 +160,7 @@ // create service proxy... TestingCentral helper = new TestingCentral(); Central worker = new CentralImpl (endpoint, uri); + worker.setDebug (debug); // ...and call other methods: String result; @@ -246,9 +247,9 @@ try { start ("registerDataType - 2"); data2.addParentName (data1.getName()); - data2.addChild ("len", "Integer"); - data2.addChild ("sub", "String"); - data2.addChild ("real_type", data3.getName()); + data2.addChild ("len", "Integer", MobyRelationship.HASA); + data2.addChild ("sub", "String", MobyRelationship.HAS); + data2.addChild ("real_type", data3.getName(), MobyRelationship.HASA); worker.registerDataType (data2); ok(); } catch (MobyException e) { error (e); @@ -283,7 +284,8 @@ MobySecondaryData secData1 = helper.createSecondaryData ("Secondary_A", "Integer"); MobySecondaryData secData2 = helper.createSecondaryData ("Secondary_B", "String"); - MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", name3); +// MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", name3); + MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", "DateTime"); MobyService service = helper.createService ("MyTestingService_" + new Date().getTime()); service.setType (stype.getName()); From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHwP015495@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv15476/docs Modified Files: ChangeLog Log Message: new registration procedure, etc. moby-live/Java/docs ChangeLog,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/03 20:28:16 1.17 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/22 21:11:17 1.18 @@ -1,3 +1,27 @@ +2004-09-22 Martin Senger + + * Fixed option -rs-out in MobyCmdLineClient. + + * Added a -debug option to the TestingCentral client. + + * Fixed TestingCentral client - it used incorectly user-defined + data type in the output secondary article. + + * Added HAS relationship type for children of MobyDataType + objects. It uses a new class MobyRelationship (meaning that + methods returning children in MobyDataType got new signatures). + + * Changes reflecting new service registration procedure: + - MobyService has new members with corresponding set/get methods + for storing 'signatureURL' and a fully qualified path to the + place where the service signature (an RDF document) can be + stored). + - CentralImpl stores retrieved RDF in a local file (read API for + MobyService class, it explains what CentralImpl is doing). + - command-line program MobyCmdLineClient got few new options in + order to deal with 'signatureURL' (see its new help). + + 2004-09-03 Paul Gordon * First commit of data instance classes for base objects (Floats, Integers, Strings), From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHCA015542@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv15476/src/Clients/help Modified Files: MobyCmdLineClient_usage.txt Log Message: new registration procedure, etc. moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/05/18 10:13:16 1.4 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/09/22 21:11:17 1.5 @@ -88,12 +88,13 @@ -rd-email -rd-isa this should be a comma-delimited list of names of the - parent data types (but Moby accept now only one parent) + parent data types (but Moby accepts now only one parent) -rd-hasa - this should be a comma-delimited list of names of the + -rd-has + these should be comma-delimited lists of names of the data types referred from this data type; every element of this list may have two parts - separated by a colon: : + separated by a colon: : To register a service type: @@ -123,6 +124,19 @@ -rs-url -rs-main use: 1 or 0 + -rs-rdf + points to your HTTP space + to a place where an RDF describing this service will be + -rs-rdfpath + if the service registration is succesful, the returned + RDF is copied to a file given by + (which completes the registration process); + use it, however, with caution because this client + overwrites a possibly existing document (it does not + merge the new RDF with the possibly existing one); + Default: it creates a temporary file where the + returned RDF is stored + -rs-in are comma-delimited names of inputs; each of them is a pair of an input type and a namespace From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBH3G015567@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv15476/src/main/org/biomoby/client Modified Files: CentralImpl.java Graphviz.java Log Message: new registration procedure, etc. moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.13,1.14 Graphviz.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/05/18 10:13:17 1.13 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/22 21:11:17 1.14 @@ -178,30 +178,37 @@ * Parse the given XML sniplet to find tag 'success'. If it has value '1' * look further for tag 'id' and return it back (or return an empty string * if ID is not there). Otherwise raise an exception with the 'culprit' - * and with the message from the tag 'message'. + * and with the message from the tag 'message'.

+ * + * The return value is a two-element long array. The first element + * is the ID (given by BioMobe registry), and the second element + * is RDF corresponding with the registered object (BioMoby + * returns this only for service instances, so for other objects + * this will be null).

* * This is how the XML is supposed to look: * * * * + * * * * Success takes the value "1" to indicate success, "0" to * indicate failure, and "-1" to indicate "Pending Curation". - * - * I keep 'id' in but it does not seem to be used anymore by the current - * Moby Central. *************************************************************************/ - protected String checkRegistration (String xml, Object culprit) + protected String[] checkRegistration (String xml, Object culprit) throws MobyException, NoSuccessException, PendingCurationException { - String id = "", success = "0", message = ""; + String id = "", success = "0", message = "", rdf = ""; // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(xml));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document=docBuilder.parse(new StringBufferInputStream(xml)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } Element root = document.getDocumentElement(); NodeList children = root.getChildNodes(); @@ -212,12 +219,23 @@ if (elem.getNodeName().equals ("id")) { if (elem.getFirstChild() != null) id = elem.getFirstChild().getNodeValue(); - } else if (elem.getNodeName().equals ("success")) { + } else if (elem.getNodeName().equals("success")) { if (elem.getFirstChild() != null) success = elem.getFirstChild().getNodeValue(); } else if (elem.getNodeName().equals ("message")) { if (elem.getFirstChild() != null) message = elem.getFirstChild().getNodeValue(); + } else if (elem.getNodeName().equals ("RDF")) { + // well, this is a simple, but most time working, + // hack... I actually do not know how to extract the + // whole subtree from a Document (without using XPath, + // XSLT or similar) ... let me know please if you know + int fromPos = xml.indexOf (""); + int toPos = xml.indexOf (""); + if (fromPos > -1 && toPos > fromPos) + rdf = xml.substring (fromPos, toPos + 6); +// if (elem.getFirstChild() != null) +// rdf = elem.getFirstChild().getNodeValue(); } } @@ -225,7 +243,7 @@ throw new NoSuccessException (message, culprit); else if (success.equals ("-1")) throw new PendingCurationException(); - return id; + return new String[] { id, rdf }; } /************************************************************************** @@ -414,8 +432,11 @@ throws MobyException { Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(xml));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(xml)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("Service"); MobyService[] results = new MobyService [list.getLength()]; @@ -506,7 +527,7 @@ // First, check to se if we have the values cached from a previous call // in this instance - if(useCache && cache.containsKey("retrieveServiceNames")) + if (useCache && cache.containsKey("retrieveServiceNames")) return (Map) cache.get("retrieveServiceNames"); String result = (String)doCall ("retrieveServiceNames", @@ -515,8 +536,11 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("serviceName"); for (int i = 0; i < list.getLength(); i++) { @@ -526,7 +550,7 @@ } // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveServiceNames", results); return results; } @@ -543,16 +567,19 @@ throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveServiceProviders")) - return (String[]) cache.get("retrieveServiceProviders"); + if (useCache && cache.containsKey ("retrieveServiceProviders")) + return (String[]) cache.get ("retrieveServiceProviders"); String result = (String)doCall ("retrieveServiceProviders", new Object[] {}); // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("serviceProvider"); String[] results = new String [list.getLength()]; @@ -560,7 +587,7 @@ results[i] = ((Element)list.item (i)).getAttribute ("name"); // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveServiceProviders", results); return results; } @@ -579,7 +606,7 @@ public Map getServiceTypes() throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveServiceTypes")) + if (useCache && cache.containsKey ("retrieveServiceTypes")) return (Map) cache.get("retrieveServiceTypes"); String result = (String)doCall ("retrieveServiceTypes", @@ -588,7 +615,8 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} + try { + document = docBuilder.parse(new StringBufferInputStream(result));} catch(Exception e){throw new MobyException(e.toString());} NodeList list = document.getElementsByTagName ("serviceType"); @@ -634,31 +662,33 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace"); - if(list == null || list.getLength() == 0){ - throw new MobyException("Could not find Namespace children of response root node " + - document.getDocumentElement()); + if (list == null || list.getLength() == 0) { + throw new MobyException ("Could not find Namespace children of response root node " + + document.getDocumentElement()); } int length = list.getLength(); for (int i = 0; i < length; i++) { Element elem = (Element)list.item (i); NodeList children = elem.getElementsByTagName("Description"); - if(children.item(0).hasChildNodes()){ + if (children.item(0).hasChildNodes()) { children.item(0).normalize(); results.put (elem.getAttribute ("name"), children.item(0).getFirstChild().getNodeValue()); - } - else{ + } else { // No description provided results.put (elem.getAttribute ("name"), ""); } } - + // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveNamespaces", results); return results; } @@ -677,7 +707,7 @@ public Map getDataTypeNames() throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveObjectNames")) + if (useCache && cache.containsKey("retrieveObjectNames")) return (Map) cache.get("retrieveObjectNames"); String result = (String)doCall ("retrieveObjectNames", @@ -686,8 +716,11 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("Object"); for (int i = 0; i < list.getLength(); i++) { @@ -702,7 +735,7 @@ } } - if(useCache) + if (useCache) cache.put("retrieveObjectNames", results); return results; } @@ -723,6 +756,10 @@ * urn:lsid:biomoby.org:objectclass:string * urn:lsid:biomoby.org:objectclass:string * + * + * urn:lsid:biomoby.org:objectclass:string + * urn:lsid:biomoby.org:objectclass:string + * * * *************************************************************************/ @@ -730,9 +767,9 @@ throws MobyException, NoSuccessException { // See if we've already retrieved the DataType and cached it - if(cache.containsKey("retrieveObjectDefinition"+dataTypeName)) - return (MobyDataType) cache.get("retrieveObjectDefinition"+dataTypeName); - + if (cache.containsKey("retrieveObjectDefinition" + dataTypeName)) + return (MobyDataType) cache.get("retrieveObjectDefinition" + dataTypeName); + String result = (String)doCall ("retrieveObjectDefinition", new Object[] { @@ -743,18 +780,21 @@ // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("retrieveObjectDefinition"); if (list == null || list.getLength() == 0) - throw new NoSuccessException ("Data Type name was not founnd.", + throw new NoSuccessException ("Data Type name was not found.", dataTypeName); MobyDataType data = null; Element elem = (Element)list.item (0); NodeList children = elem.getChildNodes(); - // first find the "real" data type name + // first find the "real" (LSID-ized) data type name for (int j = 0; j < children.getLength(); j++) { String nodeName = children.item (j).getNodeName(); if (nodeName.equals ("objectType")) { @@ -792,7 +832,18 @@ for (int k = 0; k < belows.getLength(); k++) { if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), - belows.item (k).getFirstChild().getNodeValue() ); + belows.item (k).getFirstChild().getNodeValue(), + MobyRelationship.HASA ); + } + } + } else if (relationshipType.endsWith ("has")) { + + NodeList belows = children.item (j).getChildNodes(); + for (int k = 0; k < belows.getLength(); k++) { + if (belows.item (k).getNodeName().equals ("objectType")) { + data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), + belows.item (k).getFirstChild().getNodeValue(), + MobyRelationship.HAS ); } } } @@ -804,42 +855,6 @@ /************************************************************************** * B - * - * - * ]]> - * - * - * ... - * ... - * - * - *************************************************************************/ -// public String getDataType (String dataTypeName) -// throws MobyException, NoSuccessException { -// String result = -// (String)doCall ("retrieveObjectSchema", -// new Object[] { -// "" + -// "" + dataTypeName + "" + -// "" -// }); - -// // parse returned XML (hack: taking blindly everything in the Schema tag) -// String xsd = ""; -// int pos = result.indexOf (""); -// if (pos == 1) -// throw new NoSuccessException ("Data Type name was not founnd.", -// dataTypeName); -// int pos2 = result.indexOf (""); -// if (pos2 < pos) -// throw new NoSuccessException ("Something wrong with the returned XML.", -// result); -// return result.substring (pos + 8, pos2); -// } - - /************************************************************************** - * B *************************************************************************/ public String getServiceWSDL (String serviceName) throws MobyException, NoSuccessException { @@ -889,7 +904,7 @@ } /************************************************************************* - * B + * *************************************************************************/ public void registerDataType (MobyDataType dataType) throws MobyException, NoSuccessException, PendingCurationException { @@ -904,16 +919,24 @@ buf.append ("\n"); } - // build the HASA tag (expressing containment of data types) - Hashtable children = dataType.getChildren(); - StringBuffer buf2 = new StringBuffer(); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { - String name = (String)en.nextElement(); - buf2.append (""); - buf2.append (children.get (name)); - buf2.append (""); + // build the HASA/HAS tags (expressing containments of data types) + MobyRelationship[] children = dataType.getChildren(); + StringBuffer buf2 = new StringBuffer(); // for HASA + StringBuffer buf3 = new StringBuffer(); // for HAS + for (int i = 0; i < children.length; i++) { + if (children[i].getRelationshipType() == MobyRelationship.HASA) { + buf2.append (""); + buf2.append (children[i].getDataTypeName()); + buf2.append (""); + } else if (children[i].getRelationshipType() == MobyRelationship.HAS) { + buf3.append (""); + buf3.append (children[i].getDataTypeName()); + buf3.append (""); + } } String result = @@ -927,30 +950,15 @@ "" + "" + new String (buf2) + "" + + "" + new String (buf3) + + "" + "" + dataType.getAuthority() + "" + "" + dataType.getEmailContact() + "" + "" }); - dataType.setId (checkRegistration (result, dataType)); + dataType.setId (checkRegistration (result, dataType)[0]); } -// -// NewObjectType -// -// -// -// ExistingObjectType -// ... -// ... -// -// ... -// ... -// Your.URI.here -// You at your.address.com -// - /************************************************************************* * B *************************************************************************/ @@ -995,7 +1003,7 @@ "" + "" }); - serviceType.setId (checkRegistration (result, serviceType)); + serviceType.setId (checkRegistration (result, serviceType)[0]); } // @@ -1042,7 +1050,7 @@ "" + "" }); - namespace.setId (checkRegistration (result, namespace)); + namespace.setId (checkRegistration (result, namespace)[0]); } /************************************************************************* @@ -1074,6 +1082,7 @@ "" + service.getName() + "" + "" + service.getType() + "" + "" + service.getAuthority() + "" + + "" + service.getSignatureURL() + "" + "" + service.getURL() + "" + "" + service.getEmailContact() + "" + "" + (service.isAuthoritative() ? "1" : "0") + "" + @@ -1084,7 +1093,22 @@ buildOutputTag (service) + "" }); - service.setId (checkRegistration (result, service)); + String[] registered = checkRegistration (result, service); + service.setId (registered [0]); + service.setRDF (registered [1]); + String pathToRDF = service.getPathToRDF(); + if ( ! pathToRDF.equals ("") ) { + File fileRDF = new File (pathToRDF); + try { + PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF)); + fileout.println (registered [1]); + fileout.close(); + } catch (IOException e) { + throw new MobyException ("Failed to save RDF in '" + fileRDF.getAbsolutePath() + "'. " + + e.toString() + + "\nReturned RDF:\n" + registered [1]); + } + } } /************************************************************************* @@ -1390,11 +1414,13 @@ } /** - * By default, caching is enabled to reduce network traffic and XML parsing. Setting - * this to false will clear the cache, and not cache any further calls unless it is - * set to true again. - * - * @param shouldCache whether retrieveXXX call results should be cached in case they are called again (i.e. don't requery MobyCentral every time) + * By default, caching is enabled to reduce network traffic. + * Setting this to false will clear the cache, and not cache any + * further calls unless it is set to true again.

+ * + * @param shouldCache whether retrieveXXX call results should be + * cached in case they are called again (i.e. don't requery + * MobyCentral every time) */ public void setCacheMode(boolean shouldCache){ useCache = shouldCache; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2003/11/25 13:18:10 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/22 21:11:17 1.3 @@ -6,11 +6,14 @@ package org.biomoby.client; -import org.biomoby.shared.*; - -import java.net.*; -import java.util.*; -import java.io.*; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Properties; + +import org.biomoby.shared.MobyDataType; +import org.biomoby.shared.MobyRelationship; +import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.Utils; /** * A utility class that understands how to create @@ -134,15 +137,15 @@ buf.append (trName (name)); buf.append (";\n"); } - Hashtable children = type.getChildren(); - if (children.size() > 0) { + MobyRelationship[] children = type.getChildren(); + if (children.length > 0) { String dummyName = trName (name) + "_HASA"; buf.append ("\t" + trName (name) + " -> " + dummyName); buf.append (" [style=dotted,dir=forward,arrowhead=none,arrowtail=ediamond];\n"); StringBuffer hasaBuf = new StringBuffer(); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { - String childName = (String)en.nextElement(); - String childType = Utils.pureName ((String)children.get (childName)); + for (int i = 0; i < children.length; i++) { + String childName = Utils.pureName (children[i].getName()); + String childType = Utils.pureName (children[i].getDataTypeName()); if (childType == null) childType = "n/a"; // should not happen I guess hasaBuf.append (" | {" + childType + "|" + childName + "}"); From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBH8l015617@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv15476/src/support Modified Files: README _README.FIRST_ Log Message: new registration procedure, etc. moby-live/Java/src/support README,1.3,1.4 _README.FIRST_,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/support/README 2003/11/08 00:27:24 1.3 +++ /home/repository/moby/moby-live/Java/src/support/README 2004/09/22 21:11:17 1.4 @@ -1,5 +1,5 @@ This directory contains Moby clients in Java, ready to be used and to -communicate with a real Moby server. More documentation is available +communicate with a real Moby registry. More documentation is available in the 'docs' directory. A full distribution with sources is available from the BioMoby home page http://biomoby.org. @@ -8,9 +8,10 @@ Invoke available clients using provided (and very simple) scripts (use those ending with '.bat' for Windows OS): - sh ./run-cmdline-client -help - sh ./run-testing-central - sh ./run-graphs-client -help + sh ./run/run-cmdline-client -help + sh ./run/run-testing-central + sh ./run/run-graphs-client -help + etc. Or, on Unix platforms, use chmod to make the scripts above executable and call them without 'sh' (note that this small inconvenience is due =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/_README.FIRST_,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/support/_README.FIRST_ 2003/09/25 02:35:02 1.1 +++ /home/repository/moby/moby-live/Java/src/support/_README.FIRST_ 2004/09/22 21:11:17 1.2 @@ -1,6 +1,6 @@ Files in this directory are used as templates when creating a binary distribution. They are not intended to be used per se. For invoking -various clients, use scripts available in the main directory above. +various clients, use scripts available in the build/run directory. -------------------------------------------------------------------- Comments to the biomoby mailing lists, or directly to Martin Senger From senger at pub.open-bio.org Wed Sep 22 17:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHe1015594@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv15476/src/main/org/biomoby/shared Modified Files: MobyDataType.java MobyPrimaryDataSimple.java MobyService.java Added Files: MobyRelationship.java Log Message: new registration procedure, etc. moby-live/Java/src/main/org/biomoby/shared MobyRelationship.java,NONE,1.1 MobyDataType.java,1.2,1.3 MobyPrimaryDataSimple.java,1.1,1.2 MobyService.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/03/09 00:20:13 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/22 21:11:17 1.3 @@ -11,15 +11,14 @@ /** - * A container representing a data type used in the Moby registry. - * The Moby data types are used to specify what types of inputs and - * outputs are needed or produced by Moby services. - *

+ * A container representing a data type used in the Moby registry (in + * the BioMoby speak it is called "Object Class"). The Moby data + * types are used to specify what types of inputs and outputs are + * needed or produced by Moby services.

* - * This container is used mainly to register a new data type in a + * This container is used mainly to register a new data type into a * Moby registry, and to find services with this particular input or - * output data type. - *

+ * output data type.

* * @author Martin Senger * @version $Id$ @@ -32,12 +31,18 @@ protected String emailContact = ""; protected String description = ""; protected String[] parentNames = new String[] { }; - protected Hashtable children = new Hashtable(); + protected MobyRelationship[] children = new MobyRelationship[] { }; protected String id = null; /************************************************************************** - * Default constructor. Other characteristics are empty - which is usually - * wrong - therefore use 'set' method to fill them. + * Default constructor. Other characteristics are empty - which is + * usually wrong - you should use 'set' methods to fill them + * before using this instance.

+ * + * @param name of this data type (e.g. GenericSequence, or + * String). The name can be either a simple string (e.g. Object), + * or a full-blown LSID + * (e.g. urn:lsid:biomoby.org:objectclass:Object). *************************************************************************/ public MobyDataType (String name) { this.name = name; @@ -47,34 +52,76 @@ return name; } + /** + * Return an ID that is given to this data type during its + * registration. The ID seems to be used only for de-registration + * of this data type; you are not supposed to fill it when you + * create an instance of this object. + */ public String getId() { return id; } + + /** + * @see #getId + */ public void setId (String value) { id = value; } + /** + * Return an authority for this data type. The authority is an URI + * of this data type provider. Very often empty. + */ public String getAuthority() { return authority; } + /** + * @see #getAuthority + */ public void setAuthority (String value) { authority = (value == null ? "" : value); } + /** + * Return a contact email. The purpose of this field is still a + * bit obscure - but I think that the intention is to use it in + * the process of de-registration of this data type. + */ public String getEmailContact() { return emailContact; } + /** + * @see #getEmailContact + */ public void setEmailContact (String value) { emailContact = (value == null ? "" : value); } + /** + * Return a (usually) human readable description of this data + * type. + */ public String getDescription() { return description; } + /** + * @see #getDescription + */ public void setDescription (String value) { description = (value == null ? "" : value); } + /** + * Return names of all parental data types (as stored in the + * BioMoby class ontology). Note, however, that the current + * BioMoby API (0.8) does not expect (probably even does not + * allow) multiple-inheritance.

+ * + * @return (at the moment) none (for the root data type) or one + * name. The name is an LSID + * (e.g. urn:lsid:biomoby.org:objectclass:Object). + */ public String[] getParentNames() { synchronized (parentNames) { String[] names = new String [parentNames.length]; @@ -82,6 +129,12 @@ return names; } } + /** + * @see #getParentNames + * @param value is a set of parent names (usually just one name, + * however). If it is null all parents set previously are + * forgotten. + */ public void setParentNames (String[] value) { synchronized (parentNames) { if (value == null) @@ -92,6 +145,13 @@ } } } + /** + * Add one parent of this data type.

+ * + * @see #getParentNames + * @param value is a name of a parental data type. A null value is + * ignored. + */ public void addParentName (String value) { if (value != null) { synchronized (parentNames) { @@ -105,53 +165,90 @@ } /** - * Describes what children this data type has (expressing ontology - * term HAS-A). The returned value is a hashtable with: - *

    - *
  • key is a (unique) name of this child a data type - *
  • value is a name of a data type representing this child - *
+ * Return children of this data type, and the way how they are + * ontologically related to this data type. The returned elements + * are containers, each of them defining the child data type, + * under what name it is used here (the BioMoby API calls this + * name an "article name"), and what relationship it has to this + * data type (HAS, HASA).

+ * + * Note that it does not return children that belong to the parent + * types - in other words it does not go up through the whole + * ontology tree to find all children.

+ * + * @see MobyRelationship.HAS + * @see MobyRelationship.HASA */ - public Hashtable getChildren() { + public MobyRelationship[] getChildren() { return children; } - public void setChildren (Hashtable value) { - children = (value == null ? new Hashtable() : value); + /** + * @see #getChildren + * @param value is an array of children. If it is null all + * children set previously are forgotten. + */ + public void setChildren (MobyRelationship[] value) { + children = (value == null ? new MobyRelationship[] {} : value); } /** - * 'name' is a name given to this child (attribute) - * 'typeName' is a name of a type represented by this child + * @see #getChildren + * @param child a new child to be added. If null it is ignored. */ - public void addChild (String name, String typeName) { + public void addChild (MobyRelationship child) { + if (child != null) { + synchronized (children) { + int len = children.length + 1; + MobyRelationship[] newChildren = new MobyRelationship [len]; + System.arraycopy (children, 0, newChildren, 0, len-1); + newChildren [len - 1] = child; + setChildren (newChildren); + } + } + } + /** + * Create a {@link MobyRelationship MobyRelationship} object from + * given parameters and add it as a new child.

+ * + * @see #getChildren + * @param name is a name how the new child is known to this data + * type (an "article name" in the BioMoby speak), + * e.g. 'length'. Because of the backward compatibility it accepts + * also a null or empty string here - but according to the BioMoby + * API (0.8) this name should be always given. + * @param typeName is a name of the child data type, + * e.g. 'Integer'. If null it is ignored. + * @param relationshipType is either {@link MobyRelationship.HASA + * HASA} or {@link MobyRelationship.HAS HAS}. If it is something + * else it is silenty changed to {@link MobyRelationship.HASA + * HASA}. + */ + public void addChild (String name, String typeName, int relationshipType) { if (typeName != null) { - if (name == null || name.equals ("")) - name = typeName; -// children.put (typeName, name); - children.put (name, typeName); + if (name == null) name = ""; + if (relationshipType != MobyRelationship.HASA && + relationshipType != MobyRelationship.HAS) + relationshipType = MobyRelationship.HASA; + addChild (new MobyRelationship (name, typeName, relationshipType)); } } - public String toString() { StringBuffer buf = new StringBuffer(); buf.append ("Name: " + name + "\n"); buf.append ("Auth: " + authority + "\n"); buf.append ("Desc: " + description + "\n"); buf.append ("Contact: " + emailContact + "\n"); - buf.append ("ID: " + id + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); buf.append ("Parents:\n"); for (int i = 0 ; i < parentNames.length; i++) { buf.append (Utils.format (null, 1)); buf.append (parentNames [i]); buf.append ("\n"); } - buf.append ("Children:\n"); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { + buf.append ("Children (only those registered here):\n"); + for (int i = 0 ; i < children.length; i++) { buf.append (Utils.format (null, 1)); - String key = (String)en.nextElement(); - buf.append (key); - buf.append (" => "); - buf.append (children.get (key)); + buf.append (children[i].toString()); buf.append ("\n"); } return new String (buf); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2003/09/24 14:33:37 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2004/09/22 21:11:17 1.2 @@ -104,7 +104,7 @@ buf.append (name); buf.append ("\">\n"); buf.append (""); - buf.append (dataType.getName()); + if (dataType != null) buf.append (dataType.getName()); buf.append ("\n"); if (namespaces.size() > 0) { for (Enumeration en = namespaces.elements(); en.hasMoreElements(); ) { @@ -121,7 +121,7 @@ public String toString() { StringBuffer buf = new StringBuffer(); buf.append ("Name: " + name + "\n"); - buf.append ("ID: " + id + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); if (dataType != null) buf.append ("Data Type:\n" + dataType.format (1)); buf.append ("Namespaces:\n"); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2004/04/01 23:24:27 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2004/09/22 21:11:17 1.3 @@ -10,12 +10,12 @@ import java.util.*; /** - * A container representing a service. - *

+ * A container representing a service. But do not be too excited - + * this is not a real service but only its definition as it appears in + * the BioMoby regustry.

* * This container is used mainly to register a new service in a - * Moby registry, and to find registered services later. - *

+ * Moby registry, and to find registered services later.

* * @author Martin Senger * @version $Id$ @@ -30,6 +30,9 @@ protected String type = ""; protected String description = ""; protected String url = ""; + protected String signatureURL = ""; + protected String rdf = ""; + protected String pathToRDF = ""; protected boolean authoritativeService = true; protected String id = null; @@ -39,8 +42,9 @@ protected Vector primaryOutputs = new Vector(); /************************************************************************** - * Default constructor. Other characteristics are empty - which is usually - * wrong - therefore use 'set' method to fill them. + * Default constructor. Other characteristics are empty - which is + * usually wrong - therefore use 'set' methods to fill them before + * using this instance. *************************************************************************/ public MobyService (String name) { this.name = name; @@ -50,9 +54,21 @@ return name; } + /** + * Return an ID that is given to this service instance during its + * registration. The ID is used only for de-registration of this + * service instance (you are not supposed to fill it when you + * create an instance of this object). But it soon becomes + * obsolete anyway because of the new way of registering services + * (see {@link #getSignatureURL}).

+ */ public String getId() { return id; } + /** + * Don't use it. + * @see #getId + */ public void setId (String value) { id = value; } @@ -99,13 +115,89 @@ type = (value == null ? "" : value); } + /** + * Return a URL where this service is being served from. It is a + * URL where the clients of this service are going when they want + * to use it.

+ * + * Note that there is nothing in the BioMoby registry remembering + * (registering) a namespace of your service. Therefore, your + * service is supposed to use always the namespace + * http://biomoby.org.

+ */ public String getURL() { return url; } + /** + * @see #getURL + */ public void setURL (String value) { url = (value == null ? "" : value); } + /** + * Return a URL pointing to an RDF document that contains this + * service description (signature). Note that this RDF document + * can include also other things, such as other service + * signatures.

+ * + * This is how it works: + *

    + * + *
  1. When you register a service (using an instance of this + * class) you put here (by calling {@link #setSignatureURL}) a + * URL pointing to your HTTP space, to an RDF + * document. But this document does not need to exist yet. + * + *
  2. After a successful registration this instance will have + * an RDF document with this service signature. You can obtain + * it by calling {@link #getRDF}. + * + *
  3. You are expected to copy this RDF document to the place + * that you had suggested in step 1. Failing to do it will + * result in de-registrating your service automatically + * sometimes later. Therefore, if your service is only a testing + * one, do not copy RDF anywhere and the service will disappear. + * + *
  4. Some implementations of the {@link Central} interface + * (such as its default implementation {@link + * org.biomoby.client.CentralImpl CentralImpl} can copy the RDF + * document for you if you put here a fully qualified path to + * the file where the RDF document should be put (by calling + * {@link #setPathToRDF}). + * + *
+ */ + public String getSignatureURL() { + return signatureURL; + } + /** + * @see #getSignatureURL + */ + public void setSignatureURL (String value) { + signatureURL = (value == null ? "" : value); + } + + /** + * @see #getSignatureURL + */ + public String getPathToRDF() { + return pathToRDF; + } + public void setPathToRDF (String value) { + pathToRDF = (value == null ? "" : value); + } + + /** + * @see #getSignatureURL + */ + public String getRDF() { + return rdf; + } + public void setRDF (String value) { + rdf = (value == null ? "" : value); + } + public void setInputs (MobyData[] value) { if (value == null) { primaryInputs.clear(); @@ -176,14 +268,16 @@ public String toString() { StringBuffer buf = new StringBuffer(); - buf.append ("Name: " + name + "\n"); - buf.append ("Type: " + type + "\n"); - buf.append ("Category: " + category + "\n"); - buf.append ("Auth: " + authority + "\n"); - buf.append ("Desc: " + description + "\n"); - buf.append ("URL: " + url + "\n"); - buf.append ("Contact: " + emailContact + "\n"); - buf.append ("ID: " + id + "\n"); + buf.append ("Name: " + name + "\n"); + buf.append ("Type: " + type + "\n"); + buf.append ("Category: " + category + "\n"); + buf.append ("Auth: " + authority + "\n"); + buf.append ("Desc: " + description + "\n"); + buf.append ("URL: " + url + "\n"); + buf.append ("Contact: " + emailContact + "\n"); + buf.append ("Signature URL: " + signatureURL + "\n"); + buf.append ("Path to RDF: " + pathToRDF + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); buf.append ("\nPrimary inputs:\n"); for (Enumeration en = primaryInputs.elements(); en.hasMoreElements(); ) From senger at pub.open-bio.org Wed Sep 22 19:20:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 19:20:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222320.i8MNKHtJ015938@pub.open-bio.org> senger Wed Sep 22 19:20:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv15920/src/config Log Message: Directory /home/repository/moby/moby-live/Java/src/config added to the repository moby-live/Java/src/config - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/directory,v: No such file or directory From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1B1016161@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs/API In directory pub.open-bio.org:/tmp/cvs-serv16113/docs/API Modified Files: .cvsignore.template Log Message: enhanced build.xml to support other subprojects moby-live/Java/docs/API .cvsignore.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2003/09/25 12:27:47 1.2 +++ /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2004/09/23 00:18:01 1.3 @@ -4,4 +4,4 @@ *-list class-use org - +resources From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1dB016176@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv16113/src/config Added Files: run-any-client run-any-client.bat run-cmdline-client run-cmdline-client.bat run-graphs-client run-graphs-client.bat run-testing-central run-testing-central.bat source.me.csh source.me.sh Log Message: enhanced build.xml to support other subprojects moby-live/Java/src/config run-any-client,NONE,1.1 run-any-client.bat,NONE,1.1 run-cmdline-client,NONE,1.1 run-cmdline-client.bat,NONE,1.1 run-graphs-client,NONE,1.1 run-graphs-client.bat,NONE,1.1 run-testing-central,NONE,1.1 run-testing-central.bat,NONE,1.1 source.me.csh,NONE,1.1 source.me.sh,NONE,1.1 From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1gA016142@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java In directory pub.open-bio.org:/tmp/cvs-serv16113 Modified Files: build.xml Removed Files: run-any-client run-any-client.bat run-cmdline-client run-cmdline-client.bat run-graphs-client run-graphs-client.bat run-testing-central run-testing-central.bat Log Message: enhanced build.xml to support other subprojects moby-live/Java build.xml,1.6,1.7 run-any-client,1.1,NONE run-any-client.bat,1.1,NONE run-cmdline-client,1.2,NONE run-cmdline-client.bat,1.2,NONE run-graphs-client,1.1,NONE run-graphs-client.bat,1.1,NONE run-testing-central,1.2,NONE run-testing-central.bat,1.2,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/build.xml 2003/11/09 01:05:02 1.6 +++ /home/repository/moby/moby-live/Java/build.xml 2004/09/23 00:18:00 1.7 @@ -22,6 +22,7 @@ + @@ -43,6 +44,7 @@ + @@ -79,6 +81,18 @@ + + + + + + + + + + + + @@ -115,6 +129,20 @@ + + + + + + + + + + + + + + @@ -135,6 +163,7 @@ + @@ -156,6 +185,19 @@ + + + + + + + + + + + + + @@ -209,12 +251,24 @@ + + + + + + + + + + + + - Missing one or more third-party libraries. @@ -240,6 +294,18 @@ + + + + + + + + + + + @@ -407,6 +473,20 @@ + + + + + + + + + + + + + + rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-any-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-any-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-cmdline-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-cmdline-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-graphs-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-graphs-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-testing-central,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-testing-central.bat,v: No such file or directory From senger at pub.open-bio.org Wed Sep 22 20:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I15k016197@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv16113/src/support Modified Files: README Log Message: enhanced build.xml to support other subprojects moby-live/Java/src/support README,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/README,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/support/README 2004/09/22 21:11:17 1.4 +++ /home/repository/moby/moby-live/Java/src/support/README 2004/09/23 00:18:01 1.5 @@ -8,9 +8,9 @@ Invoke available clients using provided (and very simple) scripts (use those ending with '.bat' for Windows OS): - sh ./run/run-cmdline-client -help - sh ./run/run-testing-central - sh ./run/run-graphs-client -help + sh ./run-cmdline-client -help + sh ./run-testing-central + sh ./run-graphs-client -help etc. Or, on Unix platforms, use chmod to make the scripts above executable From senger at pub.open-bio.org Thu Sep 23 06:20:29 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKTMn017972@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv17926/src/Clients Modified Files: MobyCmdLineClient.java PopulateLocalCentralForTesting.java TestingCentral.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/Clients MobyCmdLineClient.java,1.5,1.6 PopulateLocalCentralForTesting.java,1.2,1.3 TestingCentral.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/22 21:11:17 1.5 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/23 10:20:29 1.6 @@ -221,11 +221,11 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i], MobyRelationship.HASA); + data.addChild (null, hasas [i], Central.iHASA); } else if (pos == hasas[i].length() - 1) { - data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HASA); + data.addChild (hasas [i].substring (0, pos), null, Central.iHASA); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HASA); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), Central.iHASA); } } } @@ -234,11 +234,11 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i], MobyRelationship.HAS); + data.addChild (null, hasas [i], Central.iHAS); } else if (pos == hasas[i].length() - 1) { - data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HAS); + data.addChild (hasas [i].substring (0, pos), null, Central.iHAS); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HAS); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), Central.iHAS); } } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/22 21:11:17 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/23 10:20:29 1.3 @@ -240,10 +240,10 @@ protected MobyDataType[] createAllDataTypes() { MobyDataType data1 = createDataType (dataType_1); data1.addParentName ("Object"); - data1.addChild ("address", "string", MobyRelationship.HASA); - data1.addChild ("age", "integer", MobyRelationship.HASA); - data1.addChild ("salary", "float", MobyRelationship.HASA); - data1.addChild ("born", "datetime", MobyRelationship.HASA); + data1.addChild ("address", "string", Central.iHASA); + data1.addChild ("age", "integer", Central.iHASA); + data1.addChild ("salary", "float", Central.iHASA); + data1.addChild ("born", "datetime", Central.iHASA); MobyDataType data2 = createDataType (dataType_2); data2.addParentName ("Object"); MobyDataType data3 = createDataType (dataType_3); @@ -253,8 +253,8 @@ MobyDataType data5 = createDataType (dataType_5); data5.addParentName (dataType_3); data5.addParentName (dataType_2); - data5.addChild ("range_min", "integer", MobyRelationship.HAS); - data5.addChild ("range_max", "integer", MobyRelationship.HAS); + data5.addChild ("range_min", "integer", Central.iHAS); + data5.addChild ("range_max", "integer", Central.iHAS); return new MobyDataType [] { data1, data2, data3, data4, data5 }; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/23 10:20:29 1.4 @@ -247,9 +247,9 @@ try { start ("registerDataType - 2"); data2.addParentName (data1.getName()); - data2.addChild ("len", "Integer", MobyRelationship.HASA); - data2.addChild ("sub", "String", MobyRelationship.HAS); - data2.addChild ("real_type", data3.getName(), MobyRelationship.HASA); + data2.addChild ("len", "Integer", Central.iHASA); + data2.addChild ("sub", "String", Central.iHAS); + data2.addChild ("real_type", data3.getName(), Central.iHASA); worker.registerDataType (data2); ok(); } catch (MobyException e) { error (e); From senger at pub.open-bio.org Thu Sep 23 06:20:29 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKT07017945@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv17926/docs Modified Files: ChangeLog Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/docs ChangeLog,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/22 21:11:17 1.18 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/23 10:20:29 1.19 @@ -1,3 +1,8 @@ +2004-09-23 Martin Senger + + * Moved constants ISA, HAS, HASA from MobyRelationship to Central + (as iHAS, iHASA and iISA). + 2004-09-22 Martin Senger * Fixed option -rs-out in MobyCmdLineClient. From senger at pub.open-bio.org Thu Sep 23 06:20:30 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKUR8017992@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv17926/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/22 21:11:17 1.14 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/23 10:20:29 1.15 @@ -833,7 +833,7 @@ if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), belows.item (k).getFirstChild().getNodeValue(), - MobyRelationship.HASA ); + Central.iHASA ); } } } else if (relationshipType.endsWith ("has")) { @@ -843,7 +843,7 @@ if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), belows.item (k).getFirstChild().getNodeValue(), - MobyRelationship.HAS ); + Central.iHAS ); } } } @@ -924,13 +924,13 @@ StringBuffer buf2 = new StringBuffer(); // for HASA StringBuffer buf3 = new StringBuffer(); // for HAS for (int i = 0; i < children.length; i++) { - if (children[i].getRelationshipType() == MobyRelationship.HASA) { + if (children[i].getRelationshipType() == Central.iHASA) { buf2.append (""); buf2.append (children[i].getDataTypeName()); buf2.append (""); - } else if (children[i].getRelationshipType() == MobyRelationship.HAS) { + } else if (children[i].getRelationshipType() == Central.iHAS) { buf3.append (""); From senger at pub.open-bio.org Thu Sep 23 06:20:30 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKUIn018025@pub.open-bio.org> senger Thu Sep 23 06:20:30 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv17926/src/main/org/biomoby/shared Modified Files: Central.java MobyDataSimpleInstance.java MobyDataType.java MobyRelationship.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/main/org/biomoby/shared Central.java,1.5,1.6 MobyDataSimpleInstance.java,1.2,1.3 MobyDataType.java,1.3,1.4 MobyRelationship.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/05/18 10:13:17 1.5 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/23 10:20:29 1.6 @@ -48,15 +48,38 @@ public interface Central { - /** A name for the relationship type "is a". */ + /** A relationship type expressing a straight inheritance (as + * string). If Object_A ISA Object_B then all attributes of + * Object_B are guaranteed to be present in Object_A. + */ static final String ISA = "ISA"; - /** A name for the relationship type "has a". */ + /** A relationship type expressing a contaiment (as string). If + * Object_A HASA Object_B then Object_B is an object inside of + * Object_A in one copy only. */ static final String HASA = "HASA"; - /** A name for the relationship type "has". */ + /** A relationship type expressing a contaiment (as string). If + * Object_A HAS Object_B then Object_B is an object inside of + * Object_A in one or more copies. */ static final String HAS = "HAS"; + /** A relationship type expressing a straight inheritance (as + * integer). If Object_A ISA Object_B then all attributes of + * Object_B are guaranteed to be present in Object_A. + */ + static final int iISA = 1; + + /** A relationship type expressing a contaiment (as integer). If + * Object_A HASA Object_B then Object_B is an object inside of + * Object_A in one copy only. */ + static final int iHASA = 2; + + /** A relationship type expressing a contaiment (as integer). If + * Object_A HAS Object_B then Object_B is an object inside of + * Object_A in one or more copies. */ + static final int iHAS = 3; + /************************************************************************** * Get a (redundant) list of all registered service names. *

@@ -309,7 +332,7 @@ /************************************************************************** * Find service matching both all non-empty fields in the 'pattern' and - * the 'keywords', and take into account also the whole ontology tree: + * the 'keywords', and take into account also the whole ontology tree. *

* @param includeChildrenServiceTypes - if true (which is default) * then it discovers also services that are child types (more @@ -351,4 +374,12 @@ * Reports whether server responses are being cached or not. *************************************************************************/ boolean getCacheMode(); + + + // Work in progress: +// http://biomoby.org/RESOURCES/MOBY-S/Objects +// http://biomoby.org/RESOURCES/MOBY-S/Services +// http://biomoby.org/RESOURCES/MOBY-S/Namespaces +// http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances + } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/03 20:28:16 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/23 10:20:29 1.3 @@ -140,7 +140,7 @@ } /** - * Used to set the data instance value based on a ID string (i.e. just an Object) + * Used to set the data instance value based on an ID string. E.i. just an Object. */ public void setId(String value){ super.setId(value); @@ -214,7 +214,7 @@ * a template for use in MOBY Central services, or a Simple element for use in calling a service * instance. * - * @returns the MOBY XML representation of the data instance + * @return the MOBY XML representation of the data instance */ public String toXML(){ if(xmlMode == SERVICE_XML_MODE) =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/23 10:20:29 1.4 @@ -176,8 +176,8 @@ * types - in other words it does not go up through the whole * ontology tree to find all children.

* - * @see MobyRelationship.HAS - * @see MobyRelationship.HASA + * @see Central#iHAS + * @see Central#iHASA */ public MobyRelationship[] getChildren() { return children; @@ -216,18 +216,18 @@ * also a null or empty string here - but according to the BioMoby * API (0.8) this name should be always given. * @param typeName is a name of the child data type, - * e.g. 'Integer'. If null it is ignored. - * @param relationshipType is either {@link MobyRelationship.HASA - * HASA} or {@link MobyRelationship.HAS HAS}. If it is something - * else it is silenty changed to {@link MobyRelationship.HASA + * e.g. 'Integer'. If it is null it is ignored. + * @param relationshipType is either {@link Central#iHASA + * HASA} or {@link Central#iHAS HAS}. If it is something + * else it is silenty changed to {@link Central#iHASA * HASA}. */ public void addChild (String name, String typeName, int relationshipType) { if (typeName != null) { if (name == null) name = ""; - if (relationshipType != MobyRelationship.HASA && - relationshipType != MobyRelationship.HAS) - relationshipType = MobyRelationship.HASA; + if (relationshipType != Central.iHASA && + relationshipType != Central.iHAS) + relationshipType = Central.iHASA; addChild (new MobyRelationship (name, typeName, relationshipType)); } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java 2004/09/22 21:11:17 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java 2004/09/23 10:20:29 1.2 @@ -20,25 +20,9 @@ public class MobyRelationship { - /** A relationship type expressing a straight inheritance. If - * Object_A ISA Object_B then all attributes of Object_B are - * guaranteed to be present in Object_A. - */ - public static final int ISA = 1; - - /** A relationship type expressing a contaiment. If Object_A HASA - * Object_B then Object_B is an object inside of Object_A in one - * copy only. */ - public static final int HASA = 2; - - /** A relationship type expressing a contaiment. If Object_A HAS - * Object_B then Object_B is an object inside of Object_A in one - * or more copies. */ - public static final int HAS = 3; - protected String name; // articleName protected String dataTypeName; - protected int relationshipType = HASA; + protected int relationshipType = Central.iHASA; /************************************************************************** * Default (and only) constructor.

@@ -50,15 +34,15 @@ * should be always given. * @param dataTypeName is a name of a data type that is defined by * this relationship, e.g. 'Integer'. - * @param relationshipType is either {@link #HASA} or {@link - * #HAS}. If it is something else it is silently changed to {@link - * #HASA}. + * @param relationshipType is either {@link Central#iHASA HASA} or {@link + * Central#iHAS HAS}. If it is something else it is silently changed to {@link + * Central#iHASA HASA}. *************************************************************************/ public MobyRelationship (String name, String dataTypeName, int relationshipType) { this.name = name; this.dataTypeName = dataTypeName; - if (relationshipType != HASA && relationshipType != HAS) - relationshipType = HASA; + if (relationshipType != Central.iHASA && relationshipType != Central.iHAS) + relationshipType = Central.iHASA; this.relationshipType = relationshipType; } @@ -78,8 +62,8 @@ } /** - * Return type of this relationship. It is either {@link #HASA} or - * {@link #HAS}. + * Return type of this relationship. It is either {@link Central#iHASA HASA} or + * {@link Central#iHAS HAS}. */ public int getRelationshipType() { return relationshipType; @@ -93,9 +77,9 @@ */ public static String type2str (int relationshipType) { switch (relationshipType) { - case HASA: return "HASA"; - case HAS: return "HAS"; - case ISA: return "ISA"; + case Central.iHASA: return Central.HASA; + case Central.iHAS: return Central.HAS; + case Central.iISA: return Central.ISA; default: return "unknown"; } } From kawas at pub.open-bio.org Thu Sep 23 10:27:08 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu, 23 Sep 2004 10:27:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231427.i8NER8aO019251@pub.open-bio.org> kawas Thu Sep 23 10:27:08 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv19222 Removed Files: Untitled-2.htm index-old.html index.htm service-app.jar service.html service.jar tree-app.jar tree.jar Log Message: removed the files and will commit them to their proper packages. part 3 (i missed a few) moby-live/Accessories/ObjectCreationTool/Applets Untitled-2.htm,1.1,NONE index-old.html,1.1,NONE index.htm,1.2,NONE service-app.jar,1.1,NONE service.html,1.1,NONE service.jar,1.1,NONE tree-app.jar,1.2,NONE tree.jar,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/Untitled-2.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/index-old.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/index.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service-app.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/tree-app.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/tree.jar,v: No such file or directory From senger at pub.open-bio.org Fri Sep 24 15:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquZ7032093@pub.open-bio.org> senger Fri Sep 24 15:52:55 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv32055/src/Clients/help Modified Files: MobyGraphs_usage.txt Log Message: signatureURL was missing in service response object moby-live/Java/src/Clients/help MobyGraphs_usage.txt,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2003/11/25 13:18:10 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2004/09/24 19:52:55 1.4 @@ -1,12 +1,23 @@ Usage: java MobyGraphs -h[elp] - java MobyGraphs + java MobyGraphs [] - -q ... quiet mode +where specify what Moby registry to connect to: - -d ... graph showing data types - -s ... graph showing service instances - -t ... graph showing service types + -e + ia an endpoint of a Moby registry + (default: http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY-Central.pl) + -uri + is a URI defining Moby registry's namespace + (default: http://mobycentral.cbr.nrc.ca/MOBY/Central) + +where are: + + -q ... quiet mode + + -d ... make graph showing data types + -s ... make graph showing service instances + -t ... make graph showing service types output format: -dot ... (this is default) From senger at pub.open-bio.org Fri Sep 24 15:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquwd032118@pub.open-bio.org> senger Fri Sep 24 15:52:56 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32055/src/main/org/biomoby/client Modified Files: CentralImpl.java Graphviz.java Log Message: signatureURL was missing in service response object moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.15,1.16 Graphviz.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/23 10:20:29 1.15 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/24 19:52:55 1.16 @@ -407,8 +407,9 @@ * * Service_Ontology_Term * moby - * http://service.endpoint.here/scriptname * your at email.addy.here + * http://service.RDF.here + * http://service.endpoint.here/scriptname * 1 * * @@ -453,6 +454,8 @@ service.setCategory (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("URL")) { service.setURL (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("signatureURL")) { + service.setSignatureURL (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("contactEmail")) { service.setEmailContact (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("serviceType")) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/24 19:52:56 1.4 @@ -93,8 +93,8 @@ edgeAttrs.append ("]"); } buf.append ("\t" + - edge.sourceService.getName() + " -> " + - edge.targetService.getName() + + quoteIt (edge.sourceService.getName()) + " -> " + + quoteIt (edge.targetService.getName()) + new String (edgeAttrs) + "\n"); } } @@ -132,15 +132,15 @@ String[] parents = type.getParentNames(); for (int i = 0; i < parents.length; i++) { buf.append ("\t"); - buf.append (trName (Utils.pureName (parents[i]))); + buf.append (quoteIt (trName (Utils.pureName (parents[i])))); buf.append (" -> "); - buf.append (trName (name)); + buf.append (quoteIt (trName (name))); buf.append (";\n"); } MobyRelationship[] children = type.getChildren(); if (children.length > 0) { String dummyName = trName (name) + "_HASA"; - buf.append ("\t" + trName (name) + " -> " + dummyName); + buf.append ("\t" + quoteIt (trName (name)) + " -> " + quoteIt (dummyName)); buf.append (" [style=dotted,dir=forward,arrowhead=none,arrowtail=ediamond];\n"); StringBuffer hasaBuf = new StringBuffer(); for (int i = 0; i < children.length; i++) { @@ -150,7 +150,7 @@ childType = "n/a"; // should not happen I guess hasaBuf.append (" | {" + childType + "|" + childName + "}"); } - buf.append ("\t" + dummyName + " [shape=record, label=\"HAS[A]"); + buf.append ("\t" + quoteIt (dummyName) + " [shape=record, label=\"HAS[A]"); buf.append (hasaBuf); buf.append ("\"];\n"); } @@ -187,9 +187,9 @@ String[] parents = type.getParentNames(); for (int i = 0; i < parents.length; i++) { buf.append ("\t"); - buf.append (trName (Utils.pureName (parents[i])).toLowerCase()); + buf.append (quoteIt (trName (Utils.pureName (parents[i])).toLowerCase())); buf.append (" -> "); - buf.append (trName (name).toLowerCase()); + buf.append (quoteIt (trName (name).toLowerCase())); buf.append (";\n"); } } @@ -219,4 +219,16 @@ return name.replace ('-', '_'); } + /************************************************************************* + * Surround given text by quotes. This will prevent errors + * encoutered by 'dot' when names have whitespaces or when they + * are identical to the 'dot's keywords (such as 'edge'). + * + * @param name to be quoted + * @return changed 'name' + *************************************************************************/ + public static String quoteIt (String name) { + return "\"" + name + "\""; + } + } From senger at pub.open-bio.org Fri Sep 24 15:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquf9032137@pub.open-bio.org> senger Fri Sep 24 15:52:56 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32055/src/main/org/biomoby/shared Modified Files: Central.java Log Message: signatureURL was missing in service response object moby-live/Java/src/main/org/biomoby/shared Central.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/23 10:20:29 1.6 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/24 19:52:56 1.7 @@ -381,5 +381,6 @@ // http://biomoby.org/RESOURCES/MOBY-S/Services // http://biomoby.org/RESOURCES/MOBY-S/Namespaces // http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances +// http://biomoby.org/RESOURCES/MOBY-S/FULL } From senger at pub.open-bio.org Fri Sep 24 15:52:55 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJqt8S032074@pub.open-bio.org> senger Fri Sep 24 15:52:55 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv32055/docs Modified Files: ChangeLog Log Message: signatureURL was missing in service response object moby-live/Java/docs ChangeLog,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/23 10:20:29 1.19 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/24 19:52:55 1.20 @@ -1,3 +1,7 @@ +2004-09-24 Martin Senger + + * Fixed signatureURL in service response object. + 2004-09-23 Martin Senger * Moved constants ISA, HAS, HASA from MobyRelationship to Central From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPQa019481@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIP3o019502@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIP4h019445@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui added to the repository moby-live/Java/src/main/org/biomoby/client/gui - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPR2019463@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPCb019520@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPO0019539@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQo0019584@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQsK019606@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQqn019624@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/serviceTypeCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQhh019647@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/util Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util added to the repository moby-live/Java/src/main/org/biomoby/client/util - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQ9d019557@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 16:18:37 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIbV7019697@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/general Added Files: Remove24.gif Save16.gif SaveAs24.gif AlignTop16.gif Refresh24.gif TipOfTheDay24.gif Paste24.gif PageSetup24.gif Export24.gif Import24.gif AlignBottom16.gif Stop24.gif FindAgain16.gif Stop16.gif ZoomIn16.gif AlignRight16.gif SaveAll24.gif Delete16.gif Zoom24.gif SaveAll16.gif Properties24.gif SendMail24.gif Paste16.gif Refresh16.gif Open16.gif Cut24.gif PrintPreview16.gif ComposeMail16.gif History16.gif About24.gif Edit24.gif SaveAs16.gif AlignCenter24.gif Search16.gif AlignTop24.gif AlignJustifyHorizontal24.gif Information24.gif Copy16.gif Help16.gif ZoomOut16.gif PageSetup16.gif AlignJustifyVertical24.gif Import16.gif AlignRight24.gif Redo16.gif Save24.gif Add16.gif AlignJustifyVertical16.gif Cut16.gif Find24.gif Remove16.gif Properties16.gif Undo16.gif TipOfTheDay16.gif History24.gif ZoomIn24.gif AlignJustifyHorizontal16.gif About16.gif Undo24.gif ContextualHelp24.gif Export16.gif Print24.gif Redo24.gif SendMail16.gif Add24.gif ComposeMail24.gif ZoomOut24.gif Replace16.gif Help24.gif Delete24.gif Edit16.gif New24.gif Preferences16.gif Zoom16.gif Find16.gif AlignCenter16.gif New16.gif AlignBottom24.gif Copy24.gif AlignLeft16.gif Information16.gif Bookmarks24.gif Preferences24.gif ContextualHelp16.gif Open24.gif FindAgain24.gif Bookmarks16.gif PrintPreview24.gif Replace24.gif AlignLeft24.gif Print16.gif Search24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general Remove24.gif,NONE,1.1 Save16.gif,NONE,1.1 SaveAs24.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 Paste24.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 Export24.gif,NONE,1.1 Import24.gif,NONE,1.1 AlignBottom16.gif,NONE,1.1 Stop24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Stop16.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 Delete16.gif,NONE,1.1 Zoom24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 Properties24.gif,NONE,1.1 SendMail24.gif,NONE,1.1 Paste16.gif,NONE,1.1 Refresh16.gif,NONE,1.1 Open16.gif,NONE,1.1 Cut24.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 ComposeMail16.gif,NONE,1.1 History16.gif,NONE,1.1 About24.gif,NONE,1.1 Edit24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Search16.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 Information24.gif,NONE,1.1 Copy16.gif,NONE,1.1 Help16.gif,NONE,1.1 ! ZoomOut16.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Import16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Redo16.gif,NONE,1.1 Save24.gif,NONE,1.1 Add16.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 Cut16.gif,NONE,1.1 Find24.gif,NONE,1.1 Remove16.gif,NONE,1.1 Properties16.gif,NONE,1.1 Undo16.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 History24.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 About16.gif,NONE,1.1 Undo24.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 Export16.gif,NONE,1.1 Print24.gif,NONE,1.1 Redo24.gif,NONE,1.1 SendMail16.gif,NONE,1.1 Add24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 Replace16.gif,NONE,1.1 Help24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Edit16.gif,NONE,1.1 New24.gif,NONE,1.1 Preferences16.gif,NONE,1.1 Zoom16.gif,NONE,1.1 Find16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 New16.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 Copy24.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Information16.gif,NONE,1.1 Bo! okmarks24.gif,NONE,1.1 Preferences24.gif,NONE,1.1 ContextualH! elp16.gif,NONE,1.1 Open24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Replace24.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Print16.gif,NONE,1.1 Search24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcvj019800@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Added Files: Back24.gif Back16.gif Down16.gif Home24.gif Up24.gif Forward16.gif Up16.gif Home16.gif Forward24.gif Down24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Back24.gif,NONE,1.1 Back16.gif,NONE,1.1 Down16.gif,NONE,1.1 Home24.gif,NONE,1.1 Up24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Up16.gif,NONE,1.1 Home16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Down24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIc6e019818@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img Added Files: LICENSE moby_small.gif middle.gif java.gif MOBY-S.jpeg left.gif bio.gif moby1.gif moby.gif right.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img LICENSE,NONE,1.1 moby_small.gif,NONE,1.1 middle.gif,NONE,1.1 java.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 left.gif,NONE,1.1 bio.gif,NONE,1.1 moby1.gif,NONE,1.1 moby.gif,NONE,1.1 right.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcS2019782@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/table Added Files: ColumnInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif ColumnInsertAfter24.gif ColumnDelete16.gif ColumnInsertBefore16.gif RowInsertBefore24.gif ColumnInsertBefore24.gif ColumnDelete24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table ColumnInsertAfter16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 ColumnDelete16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcsS019834@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/text Added Files: AlignLeft24.gif AlignCenter16.gif Underline16.gif AlignLeft16.gif Normal16.gif Bold24.gif AlignRight24.gif Normal24.gif Italic24.gif Underline24.gif AlignRight16.gif Italic16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif Bold16.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text AlignLeft24.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Underline16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Normal16.gif,NONE,1.1 Bold24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Normal24.gif,NONE,1.1 Italic24.gif,NONE,1.1 Underline24.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Italic16.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Bold16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcru019764@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/serviceTypeCreationTool Added Files: ServiceTypeApplet.java README Household.java Construct.java MobyTree.java Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,NONE,1.1 README,NONE,1.1 Household.java,NONE,1.1 Construct.java,NONE,1.1 MobyTree.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIct2019729@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/development Added Files: JarAdd24.gif War16.gif EnterpriseJavaBeanJar16.gif WebComponentAdd16.gif WebComponent24.gif Host24.gif J2EEApplicationClient16.gif EnterpriseJavaBean24.gif J2EEServer16.gif Server16.gif J2EEApplicationClientAdd16.gif J2EEApplication24.gif War24.gif ApplicationDeploy16.gif Host16.gif Application16.gif J2EEApplication16.gif J2EEServer24.gif ApplicationDeploy24.gif Server24.gif BeanAdd24.gif Bean24.gif Jar24.gif Applet24.gif Jar16.gif BeanAdd16.gif WebComponent16.gif EnterpriseJavaBean16.gif Bean16.gif Applet16.gif Application24.gif J2EEApplicationClientAdd24.gif J2EEApplicationClient24.gif WarAdd24.gif WarAdd16.gif EnterpriseJavaBeanJar24.gif JarAdd16.gif WebComponentAdd24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development JarAdd24.gif,NONE,1.1 War16.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 Host24.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 Server16.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 War24.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 Host16.gif,NONE,1.1 Application16.gif,NONE,1.1 J2EEApplication16.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 Server24.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 Bean24.gif,NONE,1.1 Jar24.gif,NONE,1.1 Applet24.gif,NONE,1.1 Jar16.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Bean16.gif,NONE,1.1 Applet16.gif,NONE,1.1 Application24.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 WarAdd24.gif! ,NONE,1.1 WarAdd16.gif,NONE,1.1 EnterpriseJavaBeanJar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcg6019746@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/util Added Files: TreeLoaderThread.java REGEXP.java Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/util TreeLoaderThread.java,NONE,1.1 REGEXP.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 16:18:37 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIbgL019712@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/media Added Files: Play16.gif StepForward16.gif Movie16.gif StepBack24.gif Rewind16.gif Volume24.gif Stop16.gif Pause16.gif Play24.gif Volume16.gif FastForward24.gif FastForward16.gif StepForward24.gif Pause24.gif StepBack16.gif Rewind24.gif Stop24.gif Movie24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media Play16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Movie16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Rewind16.gif,NONE,1.1 Volume24.gif,NONE,1.1 Stop16.gif,NONE,1.1 Pause16.gif,NONE,1.1 Play24.gif,NONE,1.1 Volume16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Pause24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 Rewind24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Movie24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 17:02:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:02:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272102.i8RL26T2020147@pub.open-bio.org> kawas Mon Sep 27 17:02:06 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20123/org/biomoby/client/gui/util Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util added to the repository moby-live/Java/src/main/org/biomoby/client/gui/util - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 17:02:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:02:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272102.i8RL29Ak020181@pub.open-bio.org> kawas Mon Sep 27 17:02:09 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20160/org/biomoby/client/gui/util Added Files: REGEXP.java TreeLoaderThread.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,NONE,1.1 TreeLoaderThread.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 17:06:17 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:06:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272106.i8RL6HA6020232@pub.open-bio.org> kawas Mon Sep 27 17:06:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20203/org/biomoby/client/gui/util Modified Files: REGEXP.java TreeLoaderThread.java Log Message: fixed some imports and ensured that code is in the gui package moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.1,1.2 TreeLoaderThread.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:02:09 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:06:17 1.2 @@ -1,4 +1,4 @@ -package org.biomoby.client.util; +package org.biomoby.client.gui.util; import java.util.regex.Matcher; import java.util.regex.Pattern; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:02:09 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:06:17 1.2 @@ -1,4 +1,4 @@ -package org.biomoby.client.util; +package org.biomoby.client.gui.util; import javax.swing.SwingUtilities; /** From kawas at pub.open-bio.org Mon Sep 27 17:06:17 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:06:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272106.i8RL6HGO020251@pub.open-bio.org> kawas Mon Sep 27 17:06:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20203/org/biomoby/client/gui/serviceTypeCreationTool Modified Files: ServiceTypeApplet.java Log Message: fixed some imports and ensured that code is in the gui package moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 20:18:38 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 21:06:17 1.2 @@ -26,8 +26,8 @@ import javax.swing.tree.TreePath; import org.biomoby.client.CentralImpl; -import org.biomoby.client.util.REGEXP; -import org.biomoby.client.util.TreeLoaderThread; +import org.biomoby.client.gui.util.REGEXP; +import org.biomoby.client.gui.util.TreeLoaderThread; import org.biomoby.shared.Central; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyServiceType; From kawas at pub.open-bio.org Mon Sep 27 17:26:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:26:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272126.i8RLQsHn020435@pub.open-bio.org> kawas Mon Sep 27 17:26:54 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20410/org/biomoby/client/gui/util Modified Files: REGEXP.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:26:54 1.3 @@ -5,62 +5,56 @@ /** * - * @author Edward Kawas - *

- * This class provides the methods necessary to validate email - * addresses, - *

- * URLs, and URIs. + * @author Eddie Kawas + *

Created for the Biomoby Project + *

This class was created to provide the necessary methods to validate email addresses + *

URLs, and URIs. + *

For questions, comments, or bugs + *

email me at edward.kawas at gmail.com */ - public class REGEXP { - /* - * regular expressions used for validation. - */ - private final static String EMAIL = "(^[\\w]+\\+?\\w*(\\.[\\w]+)*@[\\w]{2,}\\.[\\w]{2,}(\\.[\\w]{2,})*$)"; - - private final static String URI = - //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; - //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per - // rfc 2396 appendix a. - "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; - - private final static String URL = "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; - - /** - * - * @param address - - * the string to validate. - * @return true is address is a valid email address, false otherwise. - */ - public static boolean isValidEmailAddress(String address) { - Pattern p = Pattern.compile(EMAIL); - Matcher m = p.matcher(address); - return m.matches(); - } - - /** - * - * @param uri - - * the string to validate. - * @return true if the uri is a valid uri, false otherwise. - */ - public static boolean isValidURI(String uri) { - Pattern p = Pattern.compile(URI); - Matcher m = p.matcher(uri); - return m.matches(); - } - - /** - * - * @param url - - * the string to validate. - * @return true if url is a valid URL, false otherwise. - */ - public static boolean isValidURL(String url) { - Pattern p = Pattern.compile(URL); - Matcher m = p.matcher(url); - return m.matches(); - } + /* + * regular expressions used for validation. + */ + private final static String EMAIL = "(^[\\w]+\\+?\\w*(\\.[\\w]+)*@[\\w]{2,}\\.[\\w]{2,}(\\.[\\w]{2,})*$)"; + private final static String URI = + //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; + //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per rfc 2396 appendix a. + "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; + private final static String URL = + "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; + + /** + * + * @param address - the string to validate. + * @return true is address is a valid email address, false otherwise. + */ + public static boolean isValidEmailAddress(String address) { + Pattern p = Pattern.compile(EMAIL); + Matcher m = p.matcher(address); + return m.matches(); + } + + /** + * + * @param uri - the string to validate. + * @return true if the uri is a valid uri, false otherwise. + */ + public static boolean isValidURI(String uri) { + Pattern p = Pattern.compile(URI); + Matcher m = p.matcher(uri); + return m.matches(); + } + + /** + * + * @param url - the string to validate. + * @return true if url is a valid URL, false otherwise. + */ + public static boolean isValidURL(String url) { + Pattern p = Pattern.compile(URL); + Matcher m = p.matcher(url); + return m.matches(); + } } \ No newline at end of file From kawas at pub.open-bio.org Mon Sep 27 17:27:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:27:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272127.i8RLR4J3020465@pub.open-bio.org> kawas Mon Sep 27 17:27:04 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20440/org/biomoby/client/gui/util Modified Files: TreeLoaderThread.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util TreeLoaderThread.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:27:04 1.3 @@ -2,17 +2,14 @@ import javax.swing.SwingUtilities; /** - * This is the 3rd version of SwingWorker (also known as - * SwingWorker 3), an abstract class that you subclass to - * perform GUI-related work in a dedicated thread. For - * instructions on and examples of using this class, see: - * - * http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html - * - * Note that the API changed slightly in the 3rd version: - * You must now invoke start() on the SwingWorker after - * creating it. + * @author Sun Micro Systems + *

This class was created to provide an abstract class that you subclass to + *

perform GUI-related work in a dedicated thread. + * @see http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html + *

For questions, comments, or bugs + *

email me at edward.kawas at gmail.com */ + public abstract class TreeLoaderThread { private Object value; // see getValue(), setValue() From kawas at pub.open-bio.org Mon Sep 27 17:29:08 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:29:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLT8YU020499@pub.open-bio.org> kawas Mon Sep 27 17:29:08 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20475/org/biomoby/client/gui/serviceInstanceCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 17:29:15 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:29:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLTFxU020541@pub.open-bio.org> kawas Mon Sep 27 17:29:15 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20520/org/biomoby/client/gui/serviceInstanceCreationTool Added Files: MobyCollection.java MobyUtilities.java NamespaceListener.java Construct.java NamespaceTree.java Pair.java MobyTree.java README Household.java TreeListener.java HelpActionListener.java ServiceCreationTool.java InputOutputActionListener.java ServiceInstancePanelFactory.java Service.java ButtonBeautifier.java ServiceActionListener.java InputOutputFocusListener.java MobyInputOutputData.java ServiceFocusListener.java ServiceTypeTree.java Log Message: ServiceInstanceBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyCollection.java,NONE,1.1 MobyUtilities.java,NONE,1.1 NamespaceListener.java,NONE,1.1 Construct.java,NONE,1.1 NamespaceTree.java,NONE,1.1 Pair.java,NONE,1.1 MobyTree.java,NONE,1.1 README,NONE,1.1 Household.java,NONE,1.1 TreeListener.java,NONE,1.1 HelpActionListener.java,NONE,1.1 ServiceCreationTool.java,NONE,1.1 InputOutputActionListener.java,NONE,1.1 ServiceInstancePanelFactory.java,NONE,1.1 Service.java,NONE,1.1 ButtonBeautifier.java,NONE,1.1 ServiceActionListener.java,NONE,1.1 InputOutputFocusListener.java,NONE,1.1 MobyInputOutputData.java,NONE,1.1 ServiceFocusListener.java,NONE,1.1 ServiceTypeTree.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 17:29:15 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:29:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLTFwG020556@pub.open-bio.org> kawas Mon Sep 27 17:29:15 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv20520 Added Files: .cvsignore Log Message: ServiceInstanceBuilder initial commit moby-live/Java/src/main .cvsignore,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 18:07:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 18:07:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272207.i8RM7Ctp021120@pub.open-bio.org> kawas Mon Sep 27 18:07:12 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv21097 Removed Files: REGEXP.java TreeLoaderThread.java Log Message: no message moby-live/Java/src/main/org/biomoby/client/util REGEXP.java,1.1,NONE TreeLoaderThread.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/REGEXP.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/TreeLoaderThread.java,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 18:10:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 18:10:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272210.i8RMA6nZ021205@pub.open-bio.org> kawas Mon Sep 27 18:10:06 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv21181/org/biomoby/client/gui/objectCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 18:15:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 18:15:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272215.i8RMFDkX021327@pub.open-bio.org> kawas Mon Sep 27 18:15:13 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv21306/org/biomoby/client/gui/objectCreationTool Added Files: ButtonBeautifier.java MobyUtilities.java TreeListener.java MobyUserPanel.java Construct.java FieldFocusListeners.java FieldKeyListener.java Pair.java MobyXML.java ButtonActions.java PanelFactory.java MobyTree.java Household.java Registration.java ObjectCreationTool.java MobyPlainText.java Log Message: ObjectCreationTool initial commit moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool ButtonBeautifier.java,NONE,1.1 MobyUtilities.java,NONE,1.1 TreeListener.java,NONE,1.1 MobyUserPanel.java,NONE,1.1 Construct.java,NONE,1.1 FieldFocusListeners.java,NONE,1.1 FieldKeyListener.java,NONE,1.1 Pair.java,NONE,1.1 MobyXML.java,NONE,1.1 ButtonActions.java,NONE,1.1 PanelFactory.java,NONE,1.1 MobyTree.java,NONE,1.1 Household.java,NONE,1.1 Registration.java,NONE,1.1 ObjectCreationTool.java,NONE,1.1 MobyPlainText.java,NONE,1.1 From gordonp at pub.open-bio.org Fri Sep 3 20:28:16 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Fri, 3 Sep 2004 16:28:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409032028.i83KSGf5010451@pub.open-bio.org> gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv10407/src/main/org/biomoby/client Modified Files: MobyRequest.java Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/src/main/org/biomoby/client MobyRequest.java,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/07/07 16:02:47 1.4 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/MobyRequest.java 2004/09/03 20:28:16 1.5 @@ -506,6 +506,24 @@ throw new MobyException("The MOBY payload has no text contents at all"); } + // Check if the payload is an XML document. If not, try a last ditch effort + // by base64 decoding the contents. This is technically not allowable in the + // MOBY spec, but we are being lenient. + if(!responseString.startsWith(" gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv10407/docs Modified Files: ChangeLog Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/docs ChangeLog,1.16,1.17 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/07/07 16:07:46 1.16 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/03 20:28:16 1.17 @@ -1,3 +1,11 @@ +2004-09-03 Paul Gordon + + * First commit of data instance classes for base objects (Floats, Integers, Strings), + and updates to Simple and Service Associated Instance objects to deal with the new + object types. You can now create these objects (no XML knowledge required) for + use in services, and you can create complex Moby objects using DOM fragments. + Aggregation of base objects to create complex objects still needs to be implemented. + 2004-07-07 Paul Gordon * Modifications to MobyRequest to handle Axis 1.1beta, and a variety of From gordonp at pub.open-bio.org Fri Sep 3 20:28:16 2004 From: gordonp at pub.open-bio.org (Paul Gordon) Date: Fri, 3 Sep 2004 16:28:16 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409032028.i83KSGmd010476@pub.open-bio.org> gordonp Fri Sep 3 16:28:16 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv10407/src/main/org/biomoby/shared Modified Files: MobyDataServiceAssocInstance.java MobyDataSimpleInstance.java Added Files: MobyDataFloat.java MobyDataInt.java MobyDataString.java Log Message: Changes to introduction base data object instance classes (i.e. creating MOBY query data from Java objects, not handcrafted XML) moby-live/Java/src/main/org/biomoby/shared MobyDataFloat.java,NONE,1.1 MobyDataInt.java,NONE,1.1 MobyDataString.java,NONE,1.1 MobyDataServiceAssocInstance.java,1.1,1.2 MobyDataSimpleInstance.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataServiceAssocInstance.java 2004/09/03 20:28:16 1.2 @@ -3,30 +3,92 @@ import org.w3c.dom.Element; /** - * A convenience class that just associates a set of possible services to run with a data instance + * A convenience class that just associates a set of possible services to run with a data instance. */ public class MobyDataServiceAssocInstance extends MobyDataSimpleInstance{ + protected MobyDataSimpleInstance dataInstance; protected MobyService[] mobyServices; - public MobyDataServiceAssocInstance(MobyDataType type, String name, String value, MobyService[] services){ - super(type, name, value); + public MobyDataServiceAssocInstance(MobyDataType type, String name, String id, MobyService[] services){ + super(type, name, id); mobyServices = services; + dataInstance = this; } public MobyDataServiceAssocInstance(Central central, Element simple, MobyService[] services) throws MobyException{ super(central, simple); mobyServices = services; + dataInstance = this; } public MobyDataServiceAssocInstance(MobyDataSimpleInstance mdsi, MobyService[] services){ - super(mdsi.getDataType(), mdsi.getName(), mdsi.getId()); - setValue(mdsi.getValue()); + super(mdsi.getName()); + dataInstance = (MobyDataSimpleInstance) mdsi.clone(); mobyServices = services; } + public Object clone(){ + if(dataInstance == this){ + // Avoid recursion, we're using the simple instance base behaviours + return super.clone(); + } + else{ + // Clone according to the base instance's subclass specific methods + return new MobyDataServiceAssocInstance(dataInstance, mobyServices); + } + } + public MobyService[] getServices(){ return mobyServices; } + + public MobyDataType getDataType(){ + return dataInstance.getDataType(); + } + + public void setServices(MobyService[] services){ + mobyServices = services; + } + + public void setXmlMode(int mode) throws IllegalArgumentException{ + dataInstance.setXmlMode(mode); + } + + public String getValue(){ + return dataInstance.getValue(); + } + + public void setId(String value){ + dataInstance.setId(value); + } + + public String getId(){ + return dataInstance.getId(); + } + + public void addNamespace(MobyNamespace ns){ + dataInstance.addNamespace(ns); + } + + public MobyNamespace[] getNamespaces(){ + return dataInstance.getNamespaces(); + } + + public void setValue(Element simple) throws javax.xml.transform.TransformerException{ + dataInstance.setValue(simple); + } + + public void setValue(String value){ + dataInstance.setValue(value); + } + + public String toString(){ + return dataInstance.toString(); + } + + public String toXML(){ + return dataInstance.toXML(); + } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/04/21 17:26:46 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/03 20:28:16 1.2 @@ -24,7 +24,7 @@ * SERVICE_XML_MODE. */ -public class MobyDataSimpleInstance extends MobyPrimaryDataSimple implements MobyDataInstance{ +public class MobyDataSimpleInstance extends MobyPrimaryDataSimple implements MobyDataInstance, Cloneable{ public static final int CENTRAL_XML_MODE = 124; public static final int SERVICE_XML_MODE = 891; protected int xmlMode = SERVICE_XML_MODE; @@ -36,10 +36,10 @@ * If you're looking to pass in an XML string for the constructor, you can't. You can use * the one argument constructor or this one, then use setValue(String). */ - public MobyDataSimpleInstance(MobyDataType dataType, String name, String value){ + public MobyDataSimpleInstance(MobyDataType dataType, String name, String id){ super(name); setDataType(dataType); - setId(value); + setId(id); } /** @@ -51,11 +51,27 @@ } /** + * Creates a simple object from the input instance, as opposed to clone, which creates + * an exact copy. + */ + public MobyDataSimpleInstance(MobyDataSimpleInstance mdsi){ + super(mdsi.getName()); + } + + /** * Standard constructor, build the object value using a DOM element. * @throws MobyException if the XML passed in does not have a moby:Simple root node */ public MobyDataSimpleInstance(Central mobyCentral, Element simple) throws MobyException{ super(MobyPrefixResolver.getAttr(simple, "articleName")); + + if(!simple.getLocalName().equals("Simple") || !(simple.getNamespaceURI() == null || + simple.getNamespaceURI().length() == 0 || + simple.getNamespaceURI().equals(MobyPrefixResolver.MOBY_XML_NAMESPACE))){ + throw new MobyException("Element passed to MobyDataSimpleInstance was not a moby:Simple, but " + + simple.getNodeName()); + } + NodeList children = simple.getElementsByTagName("*"); if(children == null || children.getLength() == 0){ throw new MobyException("Simple element (" + simple + @@ -172,6 +188,26 @@ public String toString(){ return dataValue; } + + /** + * Simply calls new constructor with object's existing data type, name and value. + * Subclasses should override this method if more datafields need to be copied for + * an accurate clone of the Moby Data Instance (i.e. anything but a base object). The + * subclasses should ensure that they also return a MobyDataSimpleInstance + * + * @return an object of class MobyDataSimpleInstance + */ + public Object clone(){ + MobyDataSimpleInstance copy = null; + copy = new MobyDataSimpleInstance(getName()); + copy.setDataType(getDataType()); + copy.setNamespaces(getNamespaces()); + copy.setId(getId()); + if(!isObject){ // Complex object that has its own XML representation we'll just copy over + copy.setValue(getValue()); + } + return copy; + } /** * Produces a full-blown XML fragment that depending on the value of getXmlMode() is either From mwilkinson at pub.open-bio.org Fri Sep 10 23:34:37 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Fri, 10 Sep 2004 19:34:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409102334.i8ANYbGt014004@pub.open-bio.org> mwilkinson Fri Sep 10 19:34:37 EDT 2004 Update of /home/repository/moby/moby-live/Accessories In directory pub.open-bio.org:/tmp/cvs-serv13986/Accessories Log Message: Directory /home/repository/moby/moby-live/Accessories added to the repository moby-live/Accessories - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 16:58:56 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 12:58:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131658.i8DGwulk031796@pub.open-bio.org> kawas Mon Sep 13 12:58:55 EDT 2004 Update of /home/repository/moby/Accessories In directory pub.open-bio.org:/tmp/cvs-serv31772 Log Message: Create module Status: Vendor Tag: vendor-tag Release Tags: release-tag No conflicts created by this import Accessories - Imported sources rcsdiff: /home/repository/moby/Accessories/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/Accessories/RCS/Imported,v: No such file or directory rcsdiff: /home/repository/moby/Accessories/RCS/sources,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:11:43 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:11:43 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131811.i8DIBhls032217@pub.open-bio.org> kawas Mon Sep 13 14:11:43 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv32193/ObjectCreationTool Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool added to the repository moby-live/Accessories/ObjectCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrgX032309@pub.open-bio.org> kawas Mon Sep 13 14:13:52 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv32284/img Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img added to the repository moby-live/Accessories/ObjectCreationTool/img - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDr3F032345@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrhb032327@pub.open-bio.org> kawas Mon Sep 13 14:13:52 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrZm032404@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrwf032386@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDswG032453@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:53 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:53 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDrtB032365@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsIE032517@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby/client Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby/client - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDslx032428@pub.open-bio.org> kawas Mon Sep 13 14:13:53 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv32284/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table added to the repository moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsib032493@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDsW0032475@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org In directory pub.open-bio.org:/tmp/cvs-serv32284/org Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org added to the repository moby-live/Accessories/ObjectCreationTool/org - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtnW032535@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32284/org/biomoby/shared Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared added to the repository moby-live/Accessories/ObjectCreationTool/org/biomoby/shared - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtJG032635@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/util Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/util - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtTf032574@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDt5r032556@pub.open-bio.org> kawas Mon Sep 13 14:13:54 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtMo032617@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object/creation/applet Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:13:55 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:13:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131813.i8DIDtJD032597@pub.open-bio.org> kawas Mon Sep 13 14:13:55 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation In directory pub.open-bio.org:/tmp/cvs-serv32284/org/mobycentral/object/creation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation added to the repository moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 18:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEA1W032718@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/text Added Files: AlignCenter16.gif AlignLeft16.gif AlignJustify16.gif AlignRight16.gif Bold16.gif Bold24.gif Italic24.gif AlignCenter24.gif Normal24.gif AlignRight24.gif AlignJustify24.gif Italic16.gif Normal16.gif AlignLeft24.gif Underline16.gif Underline24.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text AlignCenter16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Bold16.gif,NONE,1.1 Bold24.gif,NONE,1.1 Italic24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Normal24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Italic16.gif,NONE,1.1 Normal16.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Underline16.gif,NONE,1.1 Underline24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEAut032687@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/general Added Files: SaveAs24.gif Redo16.gif About24.gif Bookmarks24.gif Paste16.gif AlignRight24.gif Cut24.gif Delete16.gif PageSetup16.gif AlignLeft24.gif Replace24.gif FindAgain16.gif Edit16.gif Save24.gif Export24.gif AlignBottom24.gif SaveAs16.gif Save16.gif AlignTop16.gif Export16.gif Paste24.gif History16.gif Print24.gif Help16.gif PageSetup24.gif AlignTop24.gif AlignBottom16.gif Bookmarks16.gif Import16.gif PrintPreview24.gif Information16.gif SendMail16.gif SendMail24.gif SaveAll24.gif Replace16.gif ZoomOut16.gif ZoomIn24.gif Add24.gif Copy24.gif ComposeMail16.gif Import24.gif Remove24.gif FindAgain24.gif ContextualHelp24.gif SaveAll16.gif History24.gif Stop24.gif Redo24.gif Print16.gif Edit24.gif ComposeMail24.gif Open16.gif AlignJustifyVertical24.gif Help24.gif Find24.gif New24.gif TipOfTheDay16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif About16.gif Add16.gif Copy16.gif PrintPreview16.gif ZoomOut24.gif New16.gif Open24.gif Remove16.gif AlignLeft16.gif ContextualHelp16.gif Preferences16.gif AlignJustifyHorizontal16.gif Cut16.gif Refresh24.gif AlignCenter24.gif Search24.gif Zoom24.gif Delete24.gif Properties24.gif ZoomIn16.gif TipOfTheDay24.gif Zoom16.gif Refresh16.gif Information24.gif Undo16.gif Search16.gif Preferences24.gif Properties16.gif Undo24.gif Stop16.gif AlignCenter16.gif Find16.gif AlignRight16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general SaveAs24.gif,NONE,1.1 Redo16.gif,NONE,1.1 About24.gif,NONE,1.1 Bookmarks24.gif,NONE,1.1 Paste16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Cut24.gif,NONE,1.1 Delete16.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Replace24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Edit16.gif,NONE,1.1 Save24.gif,NONE,1.1 Export24.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 Save16.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Export16.gif,NONE,1.1 Paste24.gif,NONE,1.1 History16.gif,NONE,1.1 Print24.gif,NONE,1.1 Help16.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignBottom16.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 Import16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Information16.gif,NONE,1.1 SendMail16.gif,NONE,1.1 SendMail24.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 Replace16.gif,NONE,1.1 ZoomOut16.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 Add24.gif,NONE,1.1 Copy24.gif,NONE,1.1 ComposeMail16.gif,NONE! ,1.1 Import24.gif,NONE,1.1 Remove24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 History24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Redo24.gif,NONE,1.1 Print16.gif,NONE,1.1 Edit24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 Open16.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Help24.gif,NONE,1.1 Find24.gif,NONE,1.1 New24.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 About16.gif,NONE,1.1 Add16.gif,NONE,1.1 Copy16.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 New16.gif,NONE,1.1 Open24.gif,NONE,1.1 Remove16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 ContextualHelp16.gif,NONE,1.1 Preferences16.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 Cut16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Search24.gif,NONE,1.1 Zoom24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Properties24.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 Zoom16.gif,NONE! ,1.1 Refresh16.gif,NONE,1.1 Information24.gif,NONE,1.1 Undo16! .gif,NONE,1.1 Search16.gif,NONE,1.1 Preferences24.gif,NONE,1.1 Properties16.gif,NONE,1.1 Undo24.gif,NONE,1.1 Stop16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Find16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEADs032702@pub.open-bio.org> kawas Mon Sep 13 14:14:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32666/org/biomoby/shared Added Files: PendingCurationException.java MobyObject.java MobyDataType.java MobyDataInstance.java MobyDataSetInstance.java MobyDataSimpleInstance.java MobyDataSecondaryInstance.java MobyPrimaryDataSet.java NoSuccessException.java MobyNamespace.java MobyException.java Central.java MobyServiceType.java MobySecondaryData.java MobyNativeService.java MobyData.java MobyPrefixResolver.java SOAPException.java MobyService.java MobyDataServiceAssocInstance.java MobyPrimaryDataSimple.java Utils.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/biomoby/shared PendingCurationException.java,NONE,1.1 MobyObject.java,NONE,1.1 MobyDataType.java,NONE,1.1 MobyDataInstance.java,NONE,1.1 MobyDataSetInstance.java,NONE,1.1 MobyDataSimpleInstance.java,NONE,1.1 MobyDataSecondaryInstance.java,NONE,1.1 MobyPrimaryDataSet.java,NONE,1.1 NoSuccessException.java,NONE,1.1 MobyNamespace.java,NONE,1.1 MobyException.java,NONE,1.1 Central.java,NONE,1.1 MobyServiceType.java,NONE,1.1 MobySecondaryData.java,NONE,1.1 MobyNativeService.java,NONE,1.1 MobyData.java,NONE,1.1 MobyPrefixResolver.java,NONE,1.1 SOAPException.java,NONE,1.1 MobyService.java,NONE,1.1 MobyDataServiceAssocInstance.java,NONE,1.1 MobyPrimaryDataSimple.java,NONE,1.1 Utils.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBmj032734@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv32666/org/mobycentral/util Added Files: MobyXML.java TreeLoaderThread.java Registration.java MobyUtilities.java MobyPlainText.java Household.java Pair.java Construct.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/mobycentral/util MobyXML.java,NONE,1.1 TreeLoaderThread.java,NONE,1.1 Registration.java,NONE,1.1 MobyUtilities.java,NONE,1.1 MobyPlainText.java,NONE,1.1 Household.java,NONE,1.1 Pair.java,NONE,1.1 Construct.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDKl000389@pub.open-bio.org> kawas Mon Sep 13 14:14:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/media Added Files: Play24.gif Pause24.gif Pause16.gif Rewind24.gif Stop24.gif StepForward24.gif Volume24.gif Movie24.gif Volume16.gif FastForward16.gif StepBack24.gif Movie16.gif StepForward16.gif Play16.gif FastForward24.gif StepBack16.gif Rewind16.gif Stop16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media Play24.gif,NONE,1.1 Pause24.gif,NONE,1.1 Pause16.gif,NONE,1.1 Rewind24.gif,NONE,1.1 Stop24.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Volume24.gif,NONE,1.1 Movie24.gif,NONE,1.1 Volume16.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Movie16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Play16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 Rewind16.gif,NONE,1.1 Stop16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEB4Z032752@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/development Added Files: Application16.gif Bean16.gif Application24.gif J2EEApplicationClientAdd24.gif J2EEServer24.gif WebComponent24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBean16.gif Host24.gif EnterpriseJavaBean24.gif ApplicationDeploy16.gif BeanAdd16.gif Jar16.gif BeanAdd24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClient16.gif Bean24.gif War24.gif WebComponentAdd16.gif J2EEApplicationClient24.gif Host16.gif J2EEServer16.gif JarAdd24.gif WarAdd16.gif ApplicationDeploy24.gif WebComponentAdd24.gif J2EEApplication24.gif Jar24.gif JarAdd16.gif Applet16.gif WebComponent16.gif War16.gif Server24.gif EnterpriseJavaBeanJar24.gif WarAdd24.gif Server16.gif Applet24.gif J2EEApplication16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development Application16.gif,NONE,1.1 Bean16.gif,NONE,1.1 Application24.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Host24.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 Jar16.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 Bean24.gif,NONE,1.1 War24.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 Host16.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 JarAdd24.gif,NONE,1.1 WarAdd16.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 Jar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 Applet16.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 War16.gif,NONE,1.1 Server24.gif,NONE,1.1 EnterpriseJavaBean! Jar24.gif,NONE,1.1 WarAdd24.gif,NONE,1.1 Server16.gif,NONE,1.1 Applet24.gif,NONE,1.1 J2EEApplication16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDSe000371@pub.open-bio.org> kawas Mon Sep 13 14:14:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/table Added Files: ColumnDelete16.gif RowDelete16.gif RowInsertAfter16.gif ColumnInsertAfter24.gif RowInsertBefore24.gif ColumnInsertBefore24.gif ColumnInsertAfter16.gif RowInsertAfter24.gif ColumnDelete24.gif RowInsertBefore16.gif ColumnInsertBefore16.gif RowDelete24.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table ColumnDelete16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 ColumnInsertAfter16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBBa000338@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv32666/img Added Files: LICENSE bio.gif moby.gif MOBY-S.jpeg java.gif moby1.gif left.gif moby_small.gif middle.gif right.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img LICENSE,NONE,1.1 bio.gif,NONE,1.1 moby.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 java.gif,NONE,1.1 moby1.gif,NONE,1.1 left.gif,NONE,1.1 moby_small.gif,NONE,1.1 middle.gif,NONE,1.1 right.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBZk000304@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv32666/img/toolbarButtonGraphics/navigation Added Files: Home16.gif Up24.gif Down16.gif Up16.gif Forward24.gif Home24.gif Forward16.gif Back24.gif Down24.gif Back16.gif Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation Home16.gif,NONE,1.1 Up24.gif,NONE,1.1 Down16.gif,NONE,1.1 Up16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Home24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Back24.gif,NONE,1.1 Down24.gif,NONE,1.1 Back16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEBLc000322@pub.open-bio.org> kawas Mon Sep 13 14:14:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32666/org/biomoby/client Added Files: ServletFileCache.java MobyRequest.java SimpleCache.java FilterServices.java ServiceConnections.java GraphsServlet.java RDF.java Graphviz.java ServicesEdge.java FileCache.java CentralImpl.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/biomoby/client ServletFileCache.java,NONE,1.1 MobyRequest.java,NONE,1.1 SimpleCache.java,NONE,1.1 FilterServices.java,NONE,1.1 ServiceConnections.java,NONE,1.1 GraphsServlet.java,NONE,1.1 RDF.java,NONE,1.1 Graphviz.java,NONE,1.1 ServicesEdge.java,NONE,1.1 FileCache.java,NONE,1.1 CentralImpl.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIECTo000353@pub.open-bio.org> kawas Mon Sep 13 14:14:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv32666/org/mobycentral/object/creation/applet Added Files: ObjectCreationTool.java MobyTree.java ButtonActions.java FieldFocusListeners.java MobyUserPanel.java ButtonBeautifier.java FieldKeyListener.java TreeListener.java PanelFactory.java Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet ObjectCreationTool.java,NONE,1.1 MobyTree.java,NONE,1.1 ButtonActions.java,NONE,1.1 FieldFocusListeners.java,NONE,1.1 MobyUserPanel.java,NONE,1.1 ButtonBeautifier.java,NONE,1.1 FieldKeyListener.java,NONE,1.1 TreeListener.java,NONE,1.1 PanelFactory.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 18:14:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 14:14:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409131814.i8DIEDcg000410@pub.open-bio.org> kawas Mon Sep 13 14:14:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv32666 Added Files: .project .classpath Log Message: Adding Object Creation Tool Source to CVS moby-live/Accessories/ObjectCreationTool .project,NONE,1.1 .classpath,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWQs001120@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWA8001084@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets added to the repository moby-live/Accessories/ObjectCreationTool/Applets - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCWTb001102@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/Demo Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo added to the repository moby-live/Accessories/ObjectCreationTool/Applets/Demo - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXCP001159@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXUl001265@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXx9001182@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXP9001139@pub.open-bio.org> kawas Mon Sep 13 16:12:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXqa001202@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXKK001286@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/lib Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib added to the repository moby-live/Accessories/ObjectCreationTool/Applets/lib - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCXZX001306@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/offline Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline added to the repository moby-live/Accessories/ObjectCreationTool/Applets/offline - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCX76001247@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:12:33 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:12:33 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132012.i8DKCX3Q001226@pub.open-bio.org> kawas Mon Sep 13 16:12:33 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv1060/Applets/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation added to the repository moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 13 20:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJV8W001373@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/general Added Files: ZoomOut16.gif Add16.gif Copy16.gif AlignRight16.gif PrintPreview16.gif AlignLeft16.gif Add24.gif Import16.gif Redo16.gif Import24.gif Edit16.gif Refresh24.gif Export24.gif Stop24.gif About16.gif Remove16.gif Undo16.gif AlignCenter16.gif Find16.gif Undo24.gif Remove24.gif ZoomIn24.gif Search16.gif History16.gif Copy24.gif ComposeMail16.gif Help16.gif History24.gif Cut16.gif Paste24.gif Refresh16.gif Replace16.gif Properties16.gif Replace24.gif About24.gif AlignTop24.gif AlignRight24.gif Print16.gif Paste16.gif ContextualHelp24.gif Information16.gif Save16.gif ContextualHelp16.gif AlignTop16.gif Information24.gif SaveAll16.gif Properties24.gif SaveAs16.gif Find24.gif AlignJustifyHorizontal24.gif Zoom24.gif Preferences16.gif Edit24.gif SendMail16.gif PageSetup24.gif AlignBottom24.gif PageSetup16.gif TipOfTheDay16.gif AlignJustifyVertical16.gif Search24.gif ZoomOut24.gif Print24.gif Delete16.gif Export16.gif SendMail24.gif SaveAll24.gif AlignLeft24.gif Help24.gif FindAgain24.gif Zoom16.gif Open24.gif SaveAs24.gif Preferences24.gif Save24.gif New24.gif AlignJustifyVertical24.gif Delete24.gif Redo24.gif Bookmarks24.gif FindAgain16.gif Stop16.gif AlignBottom16.gif AlignJustifyHorizontal16.gif AlignCenter24.gif ComposeMail24.gif ZoomIn16.gif PrintPreview24.gif Open16.gif Bookmarks16.gif New16.gif Cut24.gif TipOfTheDay24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general ZoomOut16.gif,NONE,1.1 Add16.gif,NONE,1.1 Copy16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Add24.gif,NONE,1.1 Import16.gif,NONE,1.1 Redo16.gif,NONE,1.1 Import24.gif,NONE,1.1 Edit16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 Export24.gif,NONE,1.1 Stop24.gif,NONE,1.1 About16.gif,NONE,1.1 Remove16.gif,NONE,1.1 Undo16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Find16.gif,NONE,1.1 Undo24.gif,NONE,1.1 Remove24.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 Search16.gif,NONE,1.1 History16.gif,NONE,1.1 Copy24.gif,NONE,1.1 ComposeMail16.gif,NONE,1.1 Help16.gif,NONE,1.1 History24.gif,NONE,1.1 Cut16.gif,NONE,1.1 Paste24.gif,NONE,1.1 Refresh16.gif,NONE,1.1 Replace16.gif,NONE,1.1 Properties16.gif,NONE,1.1 Replace24.gif,NONE,1.1 About24.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Print16.gif,NONE,1.1 Paste16.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 Informatio! n16.gif,NONE,1.1 Save16.gif,NONE,1.1 ContextualHelp16.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Information24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 Properties24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 Find24.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 Zoom24.gif,NONE,1.1 Preferences16.gif,NONE,1.1 Edit24.gif,NONE,1.1 SendMail16.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 Search24.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 Print24.gif,NONE,1.1 Delete16.gif,NONE,1.1 Export16.gif,NONE,1.1 SendMail24.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Help24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 Zoom16.gif,NONE,1.1 Open24.gif,NONE,1.1 SaveAs24.gif,NONE,1.1 Preferences24.gif,NONE,1.1 Save24.gif,NONE,1.1 New24.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Redo24.gif,NONE,1.1 Bookmarks24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Stop16.gif,NONE,1.1 AlignBot! tom16.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 Alig! nCenter24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Open16.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 New16.gif,NONE,1.1 Cut24.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJVOl001388@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/navigation Added Files: Down16.gif Forward24.gif Up24.gif Home16.gif Down24.gif Forward16.gif Up16.gif Back24.gif Home24.gif Back16.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Down16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Up24.gif,NONE,1.1 Home16.gif,NONE,1.1 Down24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Up16.gif,NONE,1.1 Back24.gif,NONE,1.1 Home24.gif,NONE,1.1 Back16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWNX001456@pub.open-bio.org> kawas Mon Sep 13 16:19:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/media Added Files: Pause24.gif Rewind24.gif StepForward24.gif Movie16.gif Stop16.gif FastForward24.gif Pause16.gif Volume16.gif Volume24.gif Play16.gif Movie24.gif FastForward16.gif StepBack24.gif Stop24.gif Play24.gif StepBack16.gif StepForward16.gif Rewind16.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media Pause24.gif,NONE,1.1 Rewind24.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Movie16.gif,NONE,1.1 Stop16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 Pause16.gif,NONE,1.1 Volume16.gif,NONE,1.1 Volume24.gif,NONE,1.1 Play16.gif,NONE,1.1 Movie24.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Play24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Rewind16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:31 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:31 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJVuk001404@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/table Added Files: ColumnDelete16.gif ColumnInsertBefore16.gif RowInsertAfter24.gif ColumnInsertAfter16.gif RowDelete16.gif RowInsertBefore16.gif ColumnDelete24.gif RowDelete24.gif RowInsertBefore24.gif RowInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 ColumnInsertAfter16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWvL001439@pub.open-bio.org> kawas Mon Sep 13 16:19:32 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/development Added Files: J2EEApplication16.gif WebComponent24.gif J2EEServer16.gif JarAdd24.gif J2EEApplicationClient16.gif J2EEApplicationClientAdd16.gif ApplicationDeploy16.gif J2EEApplicationClientAdd24.gif BeanAdd16.gif Application24.gif EnterpriseJavaBean16.gif Applet24.gif War24.gif BeanAdd24.gif Host24.gif Jar24.gif J2EEApplicationClient24.gif WebComponent16.gif Application16.gif WarAdd16.gif J2EEApplication24.gif Server16.gif Jar16.gif Bean16.gif WebComponentAdd24.gif EnterpriseJavaBeanJar24.gif JarAdd16.gif EnterpriseJavaBean24.gif Server24.gif ApplicationDeploy24.gif War16.gif Applet16.gif EnterpriseJavaBeanJar16.gif WarAdd24.gif Bean24.gif Host16.gif WebComponentAdd16.gif J2EEServer24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development J2EEApplication16.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 JarAdd24.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 Application24.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Applet24.gif,NONE,1.1 War24.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 Host24.gif,NONE,1.1 Jar24.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 Application16.gif,NONE,1.1 WarAdd16.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 Server16.gif,NONE,1.1 Jar16.gif,NONE,1.1 Bean16.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 EnterpriseJavaBeanJar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 Server24.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 War16.gif,NONE,1.1 Applet16.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE! ,1.1 WarAdd24.gif,NONE,1.1 Bean24.gif,NONE,1.1 Host16.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:32 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:32 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJWWl001420@pub.open-bio.org> kawas Mon Sep 13 16:19:31 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img/toolbarButtonGraphics/text Added Files: AlignLeft24.gif Underline16.gif Bold24.gif Bold16.gif AlignRight16.gif Underline24.gif AlignJustify16.gif AlignJustify24.gif Normal24.gif AlignCenter24.gif AlignCenter16.gif Italic24.gif AlignLeft16.gif Italic16.gif Normal16.gif AlignRight24.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text AlignLeft24.gif,NONE,1.1 Underline16.gif,NONE,1.1 Bold24.gif,NONE,1.1 Bold16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Underline24.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Normal24.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Italic24.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Italic16.gif,NONE,1.1 Normal16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJaa0001535@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/Demo Added Files: jena.jar icu4j.jar xercesImpl.jar index.htm Demo.jar commons-logging.jar demo2.htm Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/Demo jena.jar,NONE,1.1 icu4j.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 index.htm,NONE,1.1 Demo.jar,NONE,1.1 commons-logging.jar,NONE,1.1 demo2.htm,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:35 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJZbq001481@pub.open-bio.org> kawas Mon Sep 13 16:19:35 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/lib Added Files: antlr.jar xalan.jar log4j-1.2.7.jar jdom.jar jaxrpc.jar jaxen-core.jar commons-discovery.jar wsdl4j.jar saaj.jar axis.jar adenine.jar activation.jar concurrent.jar jena.jar junit.jar servlet.jar xercesImpl.jar jakarta-oro-2.0.5.jar saxpath.jar xml-apis.jar rdf-api-2001-01-19.jar icu4j.jar jaxen-jdom.jar commons-logging.jar alltools.jar axis-ant.jar Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/lib antlr.jar,NONE,1.1 xalan.jar,NONE,1.1 log4j-1.2.7.jar,NONE,1.1 jdom.jar,NONE,1.1 jaxrpc.jar,NONE,1.1 jaxen-core.jar,NONE,1.1 commons-discovery.jar,NONE,1.1 wsdl4j.jar,NONE,1.1 saaj.jar,NONE,1.1 axis.jar,NONE,1.1 adenine.jar,NONE,1.1 activation.jar,NONE,1.1 concurrent.jar,NONE,1.1 jena.jar,NONE,1.1 junit.jar,NONE,1.1 servlet.jar,NONE,1.1 xercesImpl.jar,NONE,1.1 jakarta-oro-2.0.5.jar,NONE,1.1 saxpath.jar,NONE,1.1 xml-apis.jar,NONE,1.1 rdf-api-2001-01-19.jar,NONE,1.1 icu4j.jar,NONE,1.1 jaxen-jdom.jar,NONE,1.1 commons-logging.jar,NONE,1.1 alltools.jar,NONE,1.1 axis-ant.jar,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJaC1001513@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets Added Files: Untitled-2.htm tree-app.jar index-old.html service.jar service.html service-app.jar index.htm tree.jar Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets Untitled-2.htm,NONE,1.1 tree-app.jar,NONE,1.1 index-old.html,NONE,1.1 service.jar,NONE,1.1 service.html,NONE,1.1 service-app.jar,NONE,1.1 index.htm,NONE,1.1 tree.jar,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJa9U001496@pub.open-bio.org> kawas Mon Sep 13 16:19:35 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/img Added Files: moby_small.gif left.gif LICENSE java.gif MOBY-S.jpeg middle.gif right.gif moby1.gif moby.gif bio.gif Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/img moby_small.gif,NONE,1.1 left.gif,NONE,1.1 LICENSE,NONE,1.1 java.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 middle.gif,NONE,1.1 right.gif,NONE,1.1 moby1.gif,NONE,1.1 moby.gif,NONE,1.1 bio.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:19:36 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:19:36 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132019.i8DKJalF001550@pub.open-bio.org> kawas Mon Sep 13 16:19:36 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv1336/Applets/offline Added Files: Namespaces Services Objects Log Message: Added the Applet files that users can utilize. moby-live/Accessories/ObjectCreationTool/Applets/offline Namespaces,NONE,1.1 Services,NONE,1.1 Objects,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:21:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:21:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132021.i8DKL3wf001599@pub.open-bio.org> kawas Mon Sep 13 16:21:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1578 Added Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 13 20:28:00 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:28:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132028.i8DKS0PM001776@pub.open-bio.org> kawas Mon Sep 13 16:28:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1751 Modified Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:21:03 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:28:00 1.2 @@ -34,7 +34,7 @@ There are also many various DEBUG flags that when enabled print out various pieces of information. - 3. There is a runnable version of the code located in the /moby-live/Accessories/ObjectToolApplet + 3. There is a runnable version of the code located in the /moby-live/Accessories/Applets To notify me of bugs or if you have comments please email me at the address below Eddie Kawas From kawas at pub.open-bio.org Mon Sep 13 20:30:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:30:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132030.i8DKUCRc001903@pub.open-bio.org> kawas Mon Sep 13 16:30:12 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv1878 Modified Files: README.TXT Log Message: moby-live/Accessories/ObjectCreationTool README.TXT,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:28:00 1.2 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/README.TXT 2004/09/13 20:30:12 1.3 @@ -34,7 +34,7 @@ There are also many various DEBUG flags that when enabled print out various pieces of information. - 3. There is a runnable version of the code located in the /moby-live/Accessories/Applets + 3. There is a runnable version of the code located in the /moby-live/Accessories/ObjectCreationTool/Applets To notify me of bugs or if you have comments please email me at the address below Eddie Kawas From kawas at pub.open-bio.org Mon Sep 13 20:51:51 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 13 Sep 2004 16:51:51 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409132051.i8DKpp3m002023@pub.open-bio.org> kawas Mon Sep 13 16:51:51 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv1990/Applets Modified Files: index.htm tree.jar tree-app.jar Log Message: Recreated the jar files and modified the applet page html moby-live/Accessories/ObjectCreationTool/Applets index.htm,1.1,1.2 tree.jar,1.1,1.2 tree-app.jar,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm 2004/09/13 20:19:36 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/index.htm 2004/09/13 20:51:50 1.2 @@ -10,7 +10,13 @@ Moby Object Creation Tool - +

=================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar 2004/09/13 20:19:36 1.1 and /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar 2004/09/13 20:51:50 1.2 differ rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree.jar: diff failed =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 Binary files /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar 2004/09/13 20:19:36 1.1 and /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar 2004/09/13 20:51:51 1.2 differ rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/tree-app.jar: diff failed From mwilkinson at pub.open-bio.org Tue Sep 14 21:32:35 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 14 Sep 2004 17:32:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142132.i8ELWZGP006220@pub.open-bio.org> mwilkinson Tue Sep 14 17:32:35 EDT 2004 Update of /home/repository/moby/moby-live/Database In directory pub.open-bio.org:/tmp/cvs-serv6201 Modified Files: mobycentral.mysql Log Message: updating empty database schema moby-live/Database mobycentral.mysql,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Database/mobycentral.mysql,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Database/mobycentral.mysql 2003/05/24 20:22:15 1.3 +++ /home/repository/moby/moby-live/Database/mobycentral.mysql 2004/09/14 21:32:35 1.4 @@ -92,6 +92,7 @@ authoritative enum('1','0') NOT NULL default '0', description text NOT NULL, service_instance_id int(10) unsigned NOT NULL auto_increment, + signatureURL varchar(255), PRIMARY KEY (service_instance_id), UNIQUE KEY servicename (servicename,authority_id) ) TYPE=MyISAM; From mwilkinson at pub.open-bio.org Tue Sep 14 21:36:20 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 14 Sep 2004 17:36:20 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142136.i8ELaK7G006269@pub.open-bio.org> mwilkinson Tue Sep 14 17:36:20 EDT 2004 Update of /home/repository/moby/moby-live/Perl In directory pub.open-bio.org:/tmp/cvs-serv6250 Modified Files: INSTALL Log Message: typos moby-live/Perl INSTALL,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Perl/INSTALL 2004/07/28 23:00:09 1.2 +++ /home/repository/moby/moby-live/Perl/INSTALL 2004/09/14 21:36:20 1.3 @@ -8,7 +8,7 @@ For details on how to configure your own MOBY Central registry, should you want to set one up (you DO NOT -need to set up a registry to acess nor service MOBY-S +need to set up a registry to access nor serve MOBY-S Services) please visit the "Installing a Local Registy" link on the biomoby.org homepage. From mwilkinson at pub.open-bio.org Tue Sep 14 22:05:04 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Tue, 14 Sep 2004 18:05:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409142205.i8EM54PZ006416@pub.open-bio.org> mwilkinson Tue Sep 14 18:05:04 EDT 2004 Update of /home/repository/moby/moby-live/Database In directory pub.open-bio.org:/tmp/cvs-serv6401 Added Files: mobycentral.config Log Message: adding a template mobycentral.config file moby-live/Database mobycentral.config,NONE,1.1 From kawas at pub.open-bio.org Thu Sep 16 14:22:56 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu, 16 Sep 2004 10:22:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409161422.i8GEMut9014234@pub.open-bio.org> kawas Thu Sep 16 10:22:56 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv14209/org/biomoby/client Modified Files: CentralImpl.java Log Message: fixed buf2->buf3 bug. moby-live/Accessories/ObjectCreationTool/org/biomoby/client CentralImpl.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java 2004/09/13 18:14:11 1.1 +++ /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/CentralImpl.java 2004/09/16 14:22:56 1.2 @@ -956,11 +956,11 @@ Hashtable childrenHAS = dataType.getHASChildren(); for (Enumeration en = childrenHAS.keys(); en.hasMoreElements();) { String name = (String) en.nextElement(); - buf2.append(""); - buf2.append(children.get(name)); - buf2.append(""); + buf3.append(""); + buf3.append(children.get(name)); + buf3.append(""); } // done addition From mwilkinson at pub.open-bio.org Thu Sep 16 22:21:02 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 16 Sep 2004 18:21:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409162221.i8GML2lO015538@pub.open-bio.org> mwilkinson Thu Sep 16 18:21:02 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY In directory pub.open-bio.org:/tmp/cvs-serv15519/MOBY Modified Files: Central.pm Log Message: as per Martin's observation, there is no need to pass the RDF as CDATA. This required changes in both the client and server libraries. Everyone needs to do a CVS update to use it moby-live/Perl/MOBY Central.pm,1.140,1.141 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v retrieving revision 1.140 retrieving revision 1.141 diff -u -r1.140 -r1.141 --- /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/08/26 20:52:28 1.140 +++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm 2004/09/16 22:21:01 1.141 @@ -165,11 +165,17 @@ $RDF = $details->{RDF}; +# return " +# $id +# $success +# +# +# "; return " $id $success - + $RDF "; } From mwilkinson at pub.open-bio.org Thu Sep 16 22:21:02 2004 From: mwilkinson at pub.open-bio.org (Mark Wilkinson) Date: Thu, 16 Sep 2004 18:21:02 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409162221.i8GML2oV015557@pub.open-bio.org> mwilkinson Thu Sep 16 18:21:02 EDT 2004 Update of /home/repository/moby/moby-live/Perl/MOBY/Client In directory pub.open-bio.org:/tmp/cvs-serv15519/MOBY/Client Modified Files: Central.pm Log Message: as per Martin's observation, there is no need to pass the RDF as CDATA. This required changes in both the client and server libraries. Everyone needs to do a CVS update to use it moby-live/Perl/MOBY/Client Central.pm,1.79,1.80 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v retrieving revision 1.79 retrieving revision 1.80 diff -u -r1.79 -r1.80 --- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/08/11 16:27:48 1.79 +++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm 2004/09/16 22:21:02 1.80 @@ -1656,7 +1656,7 @@ my $id = &_nodeTextContent($Object, 'id'); my $success = &_nodeTextContent($Object, 'success'); my $message = &_nodeTextContent($Object, 'message'); - my $RDF = &_nodeTextContent($Object, 'RDF'); + my $RDF = &_nodeRawContent($Object, 'RDF'); my $reg = MOBY::Client::Registration->new( success => $success, message => $message, @@ -1691,6 +1691,22 @@ return $content; } +sub _nodeRawContent { + # will get text of **all** child $node from the given $DOM + # regardless of their depth!! + my ($DOM, $node) = @_; + my $x = $DOM->getElementsByTagName($node); + unless ($x->item(0)){return}; + my @child = $x->item(0)->getChildNodes; + my $content; + foreach (@child){ + #print $_->getNodeTypeName, "\t", $_->toString,"\n"; +# next unless $_->getNodeType == TEXT_NODE; + $content .= $_->toString; + } + return $content; +} + sub _nodeArrayContent { # will get array content of all child $node from given $DOM From gss at pub.open-bio.org Tue Sep 21 15:36:06 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 21 Sep 2004 11:36:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409211536.i8LFa62b009514@pub.open-bio.org> gss Tue Sep 21 11:36:06 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv9492/WebRoot/images Removed Files: rdf-logo.PNG Log Message: Changed size; stored as different name moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images rdf-logo.PNG,1.1,NONE rcsdiff: /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images/RCS/rdf-logo.PNG,v: No such file or directory From gss at pub.open-bio.org Tue Sep 21 15:36:35 2004 From: gss at pub.open-bio.org (Gary Schlitz) Date: Tue, 21 Sep 2004 11:36:35 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409211536.i8LFaZ0c009550@pub.open-bio.org> gss Tue Sep 21 11:36:35 EDT 2004 Update of /home/repository/moby/moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images In directory pub.open-bio.org:/tmp/cvs-serv9529/WebRoot/images Added Files: rdf-logo.png Log Message: Added "RDF" to image moby-live/S-MOBY/ref-impl/semanticmoby.org/WebRoot/images rdf-logo.png,NONE,1.1 From kawas at pub.open-bio.org Wed Sep 22 01:49:59 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:49:59 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220149.i8M1nxbi011675@pub.open-bio.org> kawas Tue Sep 21 21:49:58 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool Removed Files: .classpath .project README.TXT Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool .classpath,1.1,NONE .project,1.1,NONE README.TXT,1.3,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/.classpath,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/.project,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/RCS/README.TXT,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:00 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:00 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o0nX011705@pub.open-bio.org> kawas Tue Sep 21 21:50:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/Demo Removed Files: Demo.jar commons-logging.jar demo2.htm icu4j.jar index.htm jena.jar xercesImpl.jar Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/Demo Demo.jar,1.1,NONE commons-logging.jar,1.1,NONE demo2.htm,1.1,NONE icu4j.jar,1.1,NONE index.htm,1.1,NONE jena.jar,1.1,NONE xercesImpl.jar,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/Demo.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/demo2.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/icu4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/index.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/jena.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/Demo/RCS/xercesImpl.jar,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:01 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o1pf011789@pub.open-bio.org> kawas Tue Sep 21 21:50:01 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1! ,NONE WebComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE 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rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:01 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o1WM011731@pub.open-bio.org> kawas Tue Sep 21 21:50:00 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img Removed Files: LICENSE MOBY-S.jpeg bio.gif java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: 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directory From kawas at pub.open-bio.org Wed Sep 22 01:50:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o3al011899@pub.open-bio.org> kawas Tue Sep 21 21:50:01 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif ZoomOut16.gif ZoomOut24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE AlignJustifyHorizontal24.gif,1.1,NONE AlignJustifyVertical16.gif,1.1,NONE AlignJustifyVertical24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE AlignTop16.gif,1.1,NONE AlignTop24.gif,1.1,NONE Bookmarks16.gif,1.1,NONE Bookmarks24.gif,1.1,NONE ComposeMail16.gif,1.1,NONE ComposeMail24.gif,1.1,NONE ContextualHelp16.gif,1.1,NONE ContextualHelp24.gif,1.1,NONE Copy16.gif,1.1,NONE Copy24.gif,1.1,NONE Cut16.gif,1.1,NONE Cut24.gif,1.1,NONE Delete16.gif,1.1,NONE Delete24.gif,1.1,NONE Edit16.gif,1.1,NONE Edit24.gif,1.1,NONE Export16.gif,1.1,NONE Export24.gif,1.1,NONE Find16.gif,1.1,NONE Find24.gif,1.1,NONE FindAgain1! 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Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE TipOfTheDay16.! gif,1.1,NONE TipOfTheDay24.gif,1.1,NONE Undo16.gif,1.1,NONE Undo24.gif,1.1,NONE Zoom16.gif,1.1,NONE Zoom24.gif,1.1,NONE ZoomIn16.gif,1.1,NONE ZoomIn24.gif,1.1,NONE ZoomOut16.gif,1.1,NONE ZoomOut24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/About16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/About24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/Add16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/Add24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o4gF011988@pub.open-bio.org> kawas Tue Sep 21 21:50:04 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowInsertBefore24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE 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From kawas at pub.open-bio.org Wed Sep 22 01:50:03 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:03 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o3PN011933@pub.open-bio.org> kawas Tue Sep 21 21:50:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o46J011958@pub.open-bio.org> kawas Tue Sep 21 21:50:03 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o4BG012022@pub.open-bio.org> kawas Tue Sep 21 21:50:04 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o9KA012089@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/offline Removed Files: Namespaces Objects Services Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/offline Namespaces,1.1,NONE Objects,1.1,NONE Services,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Namespaces,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Objects,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/offline/RCS/Services,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oA15012115@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img Removed Files: LICENSE MOBY-S.jpeg bio.gif java.gif left.gif middle.gif moby.gif moby1.gif moby_small.gif right.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img LICENSE,1.1,NONE MOBY-S.jpeg,1.1,NONE bio.gif,1.1,NONE java.gif,1.1,NONE left.gif,1.1,NONE middle.gif,1.1,NONE moby.gif,1.1,NONE moby1.gif,1.1,NONE moby_small.gif,1.1,NONE right.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/LICENSE,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/MOBY-S.jpeg,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/bio.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/java.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/left.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/middle.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby1.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/moby_small.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/RCS/right.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:10 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:10 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oARW012176@pub.open-bio.org> kawas Tue Sep 21 21:50:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/development Removed Files: Applet16.gif Applet24.gif Application16.gif Application24.gif ApplicationDeploy16.gif ApplicationDeploy24.gif Bean16.gif Bean24.gif BeanAdd16.gif BeanAdd24.gif EnterpriseJavaBean16.gif EnterpriseJavaBean24.gif EnterpriseJavaBeanJar16.gif EnterpriseJavaBeanJar24.gif Host16.gif Host24.gif J2EEApplication16.gif J2EEApplication24.gif J2EEApplicationClient16.gif J2EEApplicationClient24.gif J2EEApplicationClientAdd16.gif J2EEApplicationClientAdd24.gif J2EEServer16.gif J2EEServer24.gif Jar16.gif Jar24.gif JarAdd16.gif JarAdd24.gif Server16.gif Server24.gif War16.gif War24.gif WarAdd16.gif WarAdd24.gif WebComponent16.gif WebComponent24.gif WebComponentAdd16.gif WebComponentAdd24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development Applet16.gif,1.1,NONE Applet24.gif,1.1,NONE Application16.gif,1.1,NONE Application24.gif,1.1,NONE ApplicationDeploy16.gif,1.1,NONE ApplicationDeploy24.gif,1.1,NONE Bean16.gif,1.1,NONE Bean24.gif,1.1,NONE BeanAdd16.gif,1.1,NONE BeanAdd24.gif,1.1,NONE EnterpriseJavaBean16.gif,1.1,NONE EnterpriseJavaBean24.gif,1.1,NONE EnterpriseJavaBeanJar16.gif,1.1,NONE EnterpriseJavaBeanJar24.gif,1.1,NONE Host16.gif,1.1,NONE Host24.gif,1.1,NONE J2EEApplication16.gif,1.1,NONE J2EEApplication24.gif,1.1,NONE J2EEApplicationClient16.gif,1.1,NONE J2EEApplicationClient24.gif,1.1,NONE J2EEApplicationClientAdd16.gif,1.1,NONE J2EEApplicationClientAdd24.gif,1.1,NONE J2EEServer16.gif,1.1,NONE J2EEServer24.gif,1.1,NONE Jar16.gif,1.1,NONE Jar24.gif,1.1,NONE JarAdd16.gif,1.1,NONE JarAdd24.gif,1.1,NONE Server16.gif,1.1,NONE Server24.gif,1.1,NONE War16.gif,1.1,NONE War24.gif,1.1,NONE WarAdd16.gif,1.1,NONE WarAdd24.gif,1.1,NONE We! bComponent16.gif,1.1,NONE WebComponent24.gif,1.1,NONE WebComponentAdd16.gif,1.1,NONE WebComponentAdd24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Applet16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Applet24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Application16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Application24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/ApplicationDeploy16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/ApplicationDeploy24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Bean16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Bean24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/BeanAdd16.gif,v: No such file or directory rcsdiff: 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEApplicationClientAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEServer16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/J2EEServer24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Jar16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Jar24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/JarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/JarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Server16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/Server24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/War16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/War24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WarAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WarAdd24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponent16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponent24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponentAdd16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/development/RCS/WebComponentAdd24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBGQ012378@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/table Removed Files: ColumnDelete16.gif ColumnDelete24.gif ColumnInsertAfter16.gif ColumnInsertAfter24.gif ColumnInsertBefore16.gif ColumnInsertBefore24.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowInsertBefore24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table ColumnDelete16.gif,1.1,NONE ColumnDelete24.gif,1.1,NONE ColumnInsertAfter16.gif,1.1,NONE ColumnInsertAfter24.gif,1.1,NONE ColumnInsertBefore16.gif,1.1,NONE ColumnInsertBefore24.gif,1.1,NONE RowDelete16.gif,1.1,NONE RowDelete24.gif,1.1,NONE RowInsertAfter16.gif,1.1,NONE RowInsertAfter24.gif,1.1,NONE RowInsertBefore16.gif,1.1,NONE RowInsertBefore24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/ColumnInsertBefore24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowDelete16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowDelete24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertAfter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertAfter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertBefore16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/table/RCS/RowInsertBefore24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBqD012348@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/navigation Removed Files: Back16.gif Back24.gif Down16.gif Down24.gif Forward16.gif Forward24.gif Home16.gif Home24.gif Up16.gif Up24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation Back16.gif,1.1,NONE Back24.gif,1.1,NONE Down16.gif,1.1,NONE Down24.gif,1.1,NONE Forward16.gif,1.1,NONE Forward24.gif,1.1,NONE Home16.gif,1.1,NONE Home24.gif,1.1,NONE Up16.gif,1.1,NONE Up24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Back16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Back24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Down16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Down24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Forward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Forward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Home16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Home24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Up16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/navigation/RCS/Up24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBQ5012286@pub.open-bio.org> kawas Tue Sep 21 21:50:10 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/general Removed Files: About16.gif About24.gif Add16.gif Add24.gif AlignBottom16.gif AlignBottom24.gif AlignCenter16.gif AlignCenter24.gif AlignJustifyHorizontal16.gif AlignJustifyHorizontal24.gif AlignJustifyVertical16.gif AlignJustifyVertical24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif AlignTop16.gif AlignTop24.gif Bookmarks16.gif Bookmarks24.gif ComposeMail16.gif ComposeMail24.gif ContextualHelp16.gif ContextualHelp24.gif Copy16.gif Copy24.gif Cut16.gif Cut24.gif Delete16.gif Delete24.gif Edit16.gif Edit24.gif Export16.gif Export24.gif Find16.gif Find24.gif FindAgain16.gif FindAgain24.gif Help16.gif Help24.gif History16.gif History24.gif Import16.gif Import24.gif Information16.gif Information24.gif New16.gif New24.gif Open16.gif Open24.gif PageSetup16.gif PageSetup24.gif Paste16.gif Paste24.gif Preferences16.gif Preferences24.gif Print16.gif Print24.gif PrintPreview16.gif PrintPreview24.gif Properties16.gif Properties24.gif Redo16.gif Redo24.gif Refresh16.gif Refresh24.gif Remove16.gif Remove24.gif Replace16.gif Replace24.gif Save16.gif Save24.gif SaveAll16.gif SaveAll24.gif SaveAs16.gif SaveAs24.gif Search16.gif Search24.gif SendMail16.gif SendMail24.gif Stop16.gif Stop24.gif TipOfTheDay16.gif TipOfTheDay24.gif Undo16.gif Undo24.gif Zoom16.gif Zoom24.gif ZoomIn16.gif ZoomIn24.gif ZoomOut16.gif ZoomOut24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general About16.gif,1.1,NONE About24.gif,1.1,NONE Add16.gif,1.1,NONE Add24.gif,1.1,NONE AlignBottom16.gif,1.1,NONE AlignBottom24.gif,1.1,NONE AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustifyHorizontal16.gif,1.1,NONE 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/home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Search24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/SendMail16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/SendMail24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/TipOfTheDay16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/TipOfTheDay24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Undo16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Undo24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Zoom16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/Zoom24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomIn16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomIn24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomOut16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/general/RCS/ZoomOut24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oDnV012478@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/biomoby/shared Removed Files: Central.java MobyData.java MobyDataInstance.java MobyDataSecondaryInstance.java MobyDataServiceAssocInstance.java MobyDataSetInstance.java MobyDataSimpleInstance.java MobyDataType.java MobyException.java MobyNamespace.java MobyNativeService.java MobyObject.java MobyPrefixResolver.java MobyPrimaryDataSet.java MobyPrimaryDataSimple.java MobySecondaryData.java MobyService.java MobyServiceType.java NoSuccessException.java PendingCurationException.java SOAPException.java Utils.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/biomoby/shared Central.java,1.1,NONE MobyData.java,1.1,NONE MobyDataInstance.java,1.1,NONE MobyDataSecondaryInstance.java,1.1,NONE MobyDataServiceAssocInstance.java,1.1,NONE MobyDataSetInstance.java,1.1,NONE MobyDataSimpleInstance.java,1.1,NONE MobyDataType.java,1.1,NONE MobyException.java,1.1,NONE MobyNamespace.java,1.1,NONE MobyNativeService.java,1.1,NONE MobyObject.java,1.1,NONE MobyPrefixResolver.java,1.1,NONE MobyPrimaryDataSet.java,1.1,NONE MobyPrimaryDataSimple.java,1.1,NONE MobySecondaryData.java,1.1,NONE MobyService.java,1.1,NONE MobyServiceType.java,1.1,NONE NoSuccessException.java,1.1,NONE PendingCurationException.java,1.1,NONE SOAPException.java,1.1,NONE Utils.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/Central.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSecondaryInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataServiceAssocInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSetInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataSimpleInstance.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyDataType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyNamespace.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyNativeService.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyObject.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrefixResolver.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrimaryDataSet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyPrimaryDataSimple.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobySecondaryData.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyService.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/MobyServiceType.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/NoSuccessException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/PendingCurationException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/SOAPException.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/shared/RCS/Utils.java,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:14 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:14 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oEFE012532@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/mobycentral/util Removed Files: Construct.java Household.java MobyPlainText.java MobyUtilities.java MobyXML.java Pair.java Registration.java TreeLoaderThread.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/mobycentral/util Construct.java,1.1,NONE Household.java,1.1,NONE MobyPlainText.java,1.1,NONE MobyUtilities.java,1.1,NONE MobyXML.java,1.1,NONE Pair.java,1.1,NONE Registration.java,1.1,NONE TreeLoaderThread.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Construct.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Household.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyPlainText.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyUtilities.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/MobyXML.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Pair.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/Registration.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/util/RCS/TreeLoaderThread.java,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oC8s012441@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/biomoby/client Removed Files: CentralImpl.java FileCache.java FilterServices.java GraphsServlet.java Graphviz.java MobyRequest.java RDF.java ServiceConnections.java ServicesEdge.java ServletFileCache.java SimpleCache.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/biomoby/client CentralImpl.java,1.2,NONE FileCache.java,1.1,NONE FilterServices.java,1.1,NONE GraphsServlet.java,1.1,NONE Graphviz.java,1.1,NONE MobyRequest.java,1.1,NONE RDF.java,1.1,NONE ServiceConnections.java,1.1,NONE ServicesEdge.java,1.1,NONE ServletFileCache.java,1.1,NONE SimpleCache.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/CentralImpl.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/FileCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/FilterServices.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/GraphsServlet.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/Graphviz.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/MobyRequest.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/RDF.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServiceConnections.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServicesEdge.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/ServletFileCache.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/biomoby/client/RCS/SimpleCache.java,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1o9i4012071@pub.open-bio.org> kawas Tue Sep 21 21:50:09 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/Applets/lib Removed Files: activation.jar adenine.jar alltools.jar antlr.jar axis-ant.jar axis.jar commons-discovery.jar commons-logging.jar concurrent.jar icu4j.jar jakarta-oro-2.0.5.jar jaxen-core.jar jaxen-jdom.jar jaxrpc.jar jdom.jar jena.jar junit.jar log4j-1.2.7.jar rdf-api-2001-01-19.jar saaj.jar saxpath.jar servlet.jar wsdl4j.jar xalan.jar xercesImpl.jar xml-apis.jar Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/Applets/lib activation.jar,1.1,NONE adenine.jar,1.1,NONE alltools.jar,1.1,NONE antlr.jar,1.1,NONE axis-ant.jar,1.1,NONE axis.jar,1.1,NONE commons-discovery.jar,1.1,NONE commons-logging.jar,1.1,NONE concurrent.jar,1.1,NONE icu4j.jar,1.1,NONE jakarta-oro-2.0.5.jar,1.1,NONE jaxen-core.jar,1.1,NONE jaxen-jdom.jar,1.1,NONE jaxrpc.jar,1.1,NONE jdom.jar,1.1,NONE jena.jar,1.1,NONE junit.jar,1.1,NONE log4j-1.2.7.jar,1.1,NONE rdf-api-2001-01-19.jar,1.1,NONE saaj.jar,1.1,NONE saxpath.jar,1.1,NONE servlet.jar,1.1,NONE wsdl4j.jar,1.1,NONE xalan.jar,1.1,NONE xercesImpl.jar,1.1,NONE xml-apis.jar,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/activation.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/adenine.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/alltools.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/antlr.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/axis-ant.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/axis.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/commons-discovery.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/commons-logging.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/concurrent.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/icu4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jakarta-oro-2.0.5.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxen-core.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxen-jdom.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jaxrpc.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jdom.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/jena.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/junit.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/log4j-1.2.7.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/rdf-api-2001-01-19.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/saaj.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/saxpath.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/servlet.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/wsdl4j.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xalan.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xercesImpl.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/lib/RCS/xml-apis.jar,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oBSb012412@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/text Removed Files: AlignCenter16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif AlignLeft16.gif AlignLeft24.gif AlignRight16.gif AlignRight24.gif Bold16.gif Bold24.gif Italic16.gif Italic24.gif Normal16.gif Normal24.gif Underline16.gif Underline24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text AlignCenter16.gif,1.1,NONE AlignCenter24.gif,1.1,NONE AlignJustify16.gif,1.1,NONE AlignJustify24.gif,1.1,NONE AlignLeft16.gif,1.1,NONE AlignLeft24.gif,1.1,NONE AlignRight16.gif,1.1,NONE AlignRight24.gif,1.1,NONE Bold16.gif,1.1,NONE Bold24.gif,1.1,NONE Italic16.gif,1.1,NONE Italic24.gif,1.1,NONE Normal16.gif,1.1,NONE Normal24.gif,1.1,NONE Underline16.gif,1.1,NONE Underline24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignCenter16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignCenter24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignJustify16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignJustify24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignLeft16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignLeft24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignRight16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/AlignRight24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Bold16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Bold24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Italic16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Italic24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Normal16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Normal24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Underline16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/text/RCS/Underline24.gif,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oDVb012505@pub.open-bio.org> kawas Tue Sep 21 21:50:13 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/org/mobycentral/object/creation/applet Removed Files: ButtonActions.java ButtonBeautifier.java FieldFocusListeners.java FieldKeyListener.java MobyTree.java MobyUserPanel.java ObjectCreationTool.java PanelFactory.java TreeListener.java Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet ButtonActions.java,1.1,NONE ButtonBeautifier.java,1.1,NONE FieldFocusListeners.java,1.1,NONE FieldKeyListener.java,1.1,NONE MobyTree.java,1.1,NONE MobyUserPanel.java,1.1,NONE ObjectCreationTool.java,1.1,NONE PanelFactory.java,1.1,NONE TreeListener.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ButtonActions.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ButtonBeautifier.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/FieldFocusListeners.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/FieldKeyListener.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/MobyTree.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/MobyUserPanel.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/ObjectCreationTool.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/PanelFactory.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/org/mobycentral/object/creation/applet/RCS/TreeListener.java,v: No such file or directory From kawas at pub.open-bio.org Wed Sep 22 01:50:11 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Tue, 21 Sep 2004 21:50:11 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409220150.i8M1oB40012320@pub.open-bio.org> kawas Tue Sep 21 21:50:11 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv11651/ObjectCreationTool/img/toolbarButtonGraphics/media Removed Files: FastForward16.gif FastForward24.gif Movie16.gif Movie24.gif Pause16.gif Pause24.gif Play16.gif Play24.gif Rewind16.gif Rewind24.gif StepBack16.gif StepBack24.gif StepForward16.gif StepForward24.gif Stop16.gif Stop24.gif Volume16.gif Volume24.gif Log Message: removed the files and will commit them to their proper packages moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media FastForward16.gif,1.1,NONE FastForward24.gif,1.1,NONE Movie16.gif,1.1,NONE Movie24.gif,1.1,NONE Pause16.gif,1.1,NONE Pause24.gif,1.1,NONE Play16.gif,1.1,NONE Play24.gif,1.1,NONE Rewind16.gif,1.1,NONE Rewind24.gif,1.1,NONE StepBack16.gif,1.1,NONE StepBack24.gif,1.1,NONE StepForward16.gif,1.1,NONE StepForward24.gif,1.1,NONE Stop16.gif,1.1,NONE Stop24.gif,1.1,NONE Volume16.gif,1.1,NONE Volume24.gif,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/FastForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/FastForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Movie16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Movie24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Pause16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Pause24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Play16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Play24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Rewind16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Rewind24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepBack16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepBack24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepForward16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/StepForward24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Stop16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Stop24.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Volume16.gif,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/img/toolbarButtonGraphics/media/RCS/Volume24.gif,v: No such file or directory From senger at pub.open-bio.org Wed Sep 22 21:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHiW015522@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv15476/src/Clients Modified Files: MobyCmdLineClient.java PopulateLocalCentralForTesting.java TestingCentral.java Log Message: new registration procedure, etc. moby-live/Java/src/Clients MobyCmdLineClient.java,1.4,1.5 PopulateLocalCentralForTesting.java,1.1,1.2 TestingCentral.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/05/18 10:13:16 1.4 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/22 21:11:17 1.5 @@ -221,11 +221,24 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i]); + data.addChild (null, hasas [i], MobyRelationship.HASA); } else if (pos == hasas[i].length() - 1) { - data.addChild (null, hasas [i].substring (0, pos)); + data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HASA); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1)); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HASA); + } + } + } + if ((param = cmd.getParam ("-rd-has")) != null ) { + String[] hasas = StringUtils.split (param, ","); + for (int i = 0; i < hasas.length; i++) { + int pos = hasas[i].indexOf (":"); + if (pos == -1) { + data.addChild (null, hasas [i], MobyRelationship.HAS); + } else if (pos == hasas[i].length() - 1) { + data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HAS); + } else { + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HAS); } } } @@ -273,7 +286,15 @@ service.setAuthoritative (param.equals ("1") ? true : false); } service.setURL (cmd.getParam ("-rs-url")); - if ((param = cmd.getParam ("-rs-in")) != null ) { + service.setSignatureURL (cmd.getParam ("-rs-rdf")); + if ( (param = cmd.getParam ("-rs-rdfpath")) != null ) { + service.setPathToRDF (param); + } else { + File tmpFile = File.createTempFile ("Moby-RDF." + service.getName() + ".", ".xml"); + service.setPathToRDF (tmpFile.getAbsolutePath()); + } + + if ( (param = cmd.getParam ("-rs-in")) != null ) { String[] inputs = StringUtils.split (param, ","); for (int i = 0; i < inputs.length; i++) { String[] parts = StringUtils.split (inputs[i], "="); @@ -346,7 +367,9 @@ if ((param = cmd.getParam ("-rs-out")) != null ) { String[] outs = StringUtils.split (param, ","); for (int i = 0; i < outs.length; i++) { - service.addOutput (new MobyPrimaryDataSimple (outs[i])); + MobyPrimaryDataSimple data = new MobyPrimaryDataSimple ("dummy"); + data.setDataType (new MobyDataType (outs[i])); + service.addOutput (data); } } if ((param = cmd.getParam ("-rs-ofile")) != null ) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2003/10/17 13:13:34 1.1 +++ /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/22 21:11:17 1.2 @@ -240,10 +240,10 @@ protected MobyDataType[] createAllDataTypes() { MobyDataType data1 = createDataType (dataType_1); data1.addParentName ("Object"); - data1.addChild ("address", "string"); - data1.addChild ("age", "integer"); - data1.addChild ("salary", "float"); - data1.addChild ("born", "datetime"); + data1.addChild ("address", "string", MobyRelationship.HASA); + data1.addChild ("age", "integer", MobyRelationship.HASA); + data1.addChild ("salary", "float", MobyRelationship.HASA); + data1.addChild ("born", "datetime", MobyRelationship.HASA); MobyDataType data2 = createDataType (dataType_2); data2.addParentName ("Object"); MobyDataType data3 = createDataType (dataType_3); @@ -253,8 +253,8 @@ MobyDataType data5 = createDataType (dataType_5); data5.addParentName (dataType_3); data5.addParentName (dataType_2); - data5.addChild ("range_min", "integer"); - data5.addChild ("range_max", "integer"); + data5.addChild ("range_min", "integer", MobyRelationship.HAS); + data5.addChild ("range_max", "integer", MobyRelationship.HAS); return new MobyDataType [] { data1, data2, data3, data4, data5 }; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2003/10/17 13:13:34 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/22 21:11:17 1.3 @@ -122,7 +122,7 @@ // command-line parameters int i = 0; while (i < args.length) { - if (args[i].equals ("-help") || args[i].equals ("-")) { + if (args[i].equals ("-help") || args[i].equals ("-h")) { System.out.println ("Usage: java TestingCentral [-e ] [-u ] [-debug]"); System.exit (0); @@ -160,6 +160,7 @@ // create service proxy... TestingCentral helper = new TestingCentral(); Central worker = new CentralImpl (endpoint, uri); + worker.setDebug (debug); // ...and call other methods: String result; @@ -246,9 +247,9 @@ try { start ("registerDataType - 2"); data2.addParentName (data1.getName()); - data2.addChild ("len", "Integer"); - data2.addChild ("sub", "String"); - data2.addChild ("real_type", data3.getName()); + data2.addChild ("len", "Integer", MobyRelationship.HASA); + data2.addChild ("sub", "String", MobyRelationship.HAS); + data2.addChild ("real_type", data3.getName(), MobyRelationship.HASA); worker.registerDataType (data2); ok(); } catch (MobyException e) { error (e); @@ -283,7 +284,8 @@ MobySecondaryData secData1 = helper.createSecondaryData ("Secondary_A", "Integer"); MobySecondaryData secData2 = helper.createSecondaryData ("Secondary_B", "String"); - MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", name3); +// MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", name3); + MobySecondaryData secData3 = helper.createSecondaryData ("Secondary_C", "DateTime"); MobyService service = helper.createService ("MyTestingService_" + new Date().getTime()); service.setType (stype.getName()); From senger at pub.open-bio.org Wed Sep 22 21:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHwP015495@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv15476/docs Modified Files: ChangeLog Log Message: new registration procedure, etc. moby-live/Java/docs ChangeLog,1.17,1.18 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/03 20:28:16 1.17 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/22 21:11:17 1.18 @@ -1,3 +1,27 @@ +2004-09-22 Martin Senger + + * Fixed option -rs-out in MobyCmdLineClient. + + * Added a -debug option to the TestingCentral client. + + * Fixed TestingCentral client - it used incorectly user-defined + data type in the output secondary article. + + * Added HAS relationship type for children of MobyDataType + objects. It uses a new class MobyRelationship (meaning that + methods returning children in MobyDataType got new signatures). + + * Changes reflecting new service registration procedure: + - MobyService has new members with corresponding set/get methods + for storing 'signatureURL' and a fully qualified path to the + place where the service signature (an RDF document) can be + stored). + - CentralImpl stores retrieved RDF in a local file (read API for + MobyService class, it explains what CentralImpl is doing). + - command-line program MobyCmdLineClient got few new options in + order to deal with 'signatureURL' (see its new help). + + 2004-09-03 Paul Gordon * First commit of data instance classes for base objects (Floats, Integers, Strings), From senger at pub.open-bio.org Wed Sep 22 21:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHCA015542@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv15476/src/Clients/help Modified Files: MobyCmdLineClient_usage.txt Log Message: new registration procedure, etc. moby-live/Java/src/Clients/help MobyCmdLineClient_usage.txt,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/05/18 10:13:16 1.4 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyCmdLineClient_usage.txt 2004/09/22 21:11:17 1.5 @@ -88,12 +88,13 @@ -rd-email -rd-isa this should be a comma-delimited list of names of the - parent data types (but Moby accept now only one parent) + parent data types (but Moby accepts now only one parent) -rd-hasa - this should be a comma-delimited list of names of the + -rd-has + these should be comma-delimited lists of names of the data types referred from this data type; every element of this list may have two parts - separated by a colon: : + separated by a colon: : To register a service type: @@ -123,6 +124,19 @@ -rs-url -rs-main use: 1 or 0 + -rs-rdf + points to your HTTP space + to a place where an RDF describing this service will be + -rs-rdfpath + if the service registration is succesful, the returned + RDF is copied to a file given by + (which completes the registration process); + use it, however, with caution because this client + overwrites a possibly existing document (it does not + merge the new RDF with the possibly existing one); + Default: it creates a temporary file where the + returned RDF is stored + -rs-in are comma-delimited names of inputs; each of them is a pair of an input type and a namespace From senger at pub.open-bio.org Wed Sep 22 21:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBH3G015567@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv15476/src/main/org/biomoby/client Modified Files: CentralImpl.java Graphviz.java Log Message: new registration procedure, etc. moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.13,1.14 Graphviz.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/05/18 10:13:17 1.13 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/22 21:11:17 1.14 @@ -178,30 +178,37 @@ * Parse the given XML sniplet to find tag 'success'. If it has value '1' * look further for tag 'id' and return it back (or return an empty string * if ID is not there). Otherwise raise an exception with the 'culprit' - * and with the message from the tag 'message'. + * and with the message from the tag 'message'.

+ * + * The return value is a two-element long array. The first element + * is the ID (given by BioMobe registry), and the second element + * is RDF corresponding with the registered object (BioMoby + * returns this only for service instances, so for other objects + * this will be null).

* * This is how the XML is supposed to look: * * * * + * * * * Success takes the value "1" to indicate success, "0" to * indicate failure, and "-1" to indicate "Pending Curation". - * - * I keep 'id' in but it does not seem to be used anymore by the current - * Moby Central. *************************************************************************/ - protected String checkRegistration (String xml, Object culprit) + protected String[] checkRegistration (String xml, Object culprit) throws MobyException, NoSuccessException, PendingCurationException { - String id = "", success = "0", message = ""; + String id = "", success = "0", message = "", rdf = ""; // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(xml));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document=docBuilder.parse(new StringBufferInputStream(xml)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } Element root = document.getDocumentElement(); NodeList children = root.getChildNodes(); @@ -212,12 +219,23 @@ if (elem.getNodeName().equals ("id")) { if (elem.getFirstChild() != null) id = elem.getFirstChild().getNodeValue(); - } else if (elem.getNodeName().equals ("success")) { + } else if (elem.getNodeName().equals("success")) { if (elem.getFirstChild() != null) success = elem.getFirstChild().getNodeValue(); } else if (elem.getNodeName().equals ("message")) { if (elem.getFirstChild() != null) message = elem.getFirstChild().getNodeValue(); + } else if (elem.getNodeName().equals ("RDF")) { + // well, this is a simple, but most time working, + // hack... I actually do not know how to extract the + // whole subtree from a Document (without using XPath, + // XSLT or similar) ... let me know please if you know + int fromPos = xml.indexOf (""); + int toPos = xml.indexOf (""); + if (fromPos > -1 && toPos > fromPos) + rdf = xml.substring (fromPos, toPos + 6); +// if (elem.getFirstChild() != null) +// rdf = elem.getFirstChild().getNodeValue(); } } @@ -225,7 +243,7 @@ throw new NoSuccessException (message, culprit); else if (success.equals ("-1")) throw new PendingCurationException(); - return id; + return new String[] { id, rdf }; } /************************************************************************** @@ -414,8 +432,11 @@ throws MobyException { Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(xml));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(xml)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("Service"); MobyService[] results = new MobyService [list.getLength()]; @@ -506,7 +527,7 @@ // First, check to se if we have the values cached from a previous call // in this instance - if(useCache && cache.containsKey("retrieveServiceNames")) + if (useCache && cache.containsKey("retrieveServiceNames")) return (Map) cache.get("retrieveServiceNames"); String result = (String)doCall ("retrieveServiceNames", @@ -515,8 +536,11 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("serviceName"); for (int i = 0; i < list.getLength(); i++) { @@ -526,7 +550,7 @@ } // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveServiceNames", results); return results; } @@ -543,16 +567,19 @@ throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveServiceProviders")) - return (String[]) cache.get("retrieveServiceProviders"); + if (useCache && cache.containsKey ("retrieveServiceProviders")) + return (String[]) cache.get ("retrieveServiceProviders"); String result = (String)doCall ("retrieveServiceProviders", new Object[] {}); // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("serviceProvider"); String[] results = new String [list.getLength()]; @@ -560,7 +587,7 @@ results[i] = ((Element)list.item (i)).getAttribute ("name"); // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveServiceProviders", results); return results; } @@ -579,7 +606,7 @@ public Map getServiceTypes() throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveServiceTypes")) + if (useCache && cache.containsKey ("retrieveServiceTypes")) return (Map) cache.get("retrieveServiceTypes"); String result = (String)doCall ("retrieveServiceTypes", @@ -588,7 +615,8 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} + try { + document = docBuilder.parse(new StringBufferInputStream(result));} catch(Exception e){throw new MobyException(e.toString());} NodeList list = document.getElementsByTagName ("serviceType"); @@ -634,31 +662,33 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getDocumentElement().getElementsByTagName ("Namespace"); - if(list == null || list.getLength() == 0){ - throw new MobyException("Could not find Namespace children of response root node " + - document.getDocumentElement()); + if (list == null || list.getLength() == 0) { + throw new MobyException ("Could not find Namespace children of response root node " + + document.getDocumentElement()); } int length = list.getLength(); for (int i = 0; i < length; i++) { Element elem = (Element)list.item (i); NodeList children = elem.getElementsByTagName("Description"); - if(children.item(0).hasChildNodes()){ + if (children.item(0).hasChildNodes()) { children.item(0).normalize(); results.put (elem.getAttribute ("name"), children.item(0).getFirstChild().getNodeValue()); - } - else{ + } else { // No description provided results.put (elem.getAttribute ("name"), ""); } } - + // Add this data to the cache in case we get called again - if(useCache) + if (useCache) cache.put("retrieveNamespaces", results); return results; } @@ -677,7 +707,7 @@ public Map getDataTypeNames() throws MobyException { // First, see if we have the values cached from a previous call in this instance - if(useCache && cache.containsKey("retrieveObjectNames")) + if (useCache && cache.containsKey("retrieveObjectNames")) return (Map) cache.get("retrieveObjectNames"); String result = (String)doCall ("retrieveObjectNames", @@ -686,8 +716,11 @@ // parse returned XML Map results = new HashMap(); Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("Object"); for (int i = 0; i < list.getLength(); i++) { @@ -702,7 +735,7 @@ } } - if(useCache) + if (useCache) cache.put("retrieveObjectNames", results); return results; } @@ -723,6 +756,10 @@ * urn:lsid:biomoby.org:objectclass:string * urn:lsid:biomoby.org:objectclass:string * + * + * urn:lsid:biomoby.org:objectclass:string + * urn:lsid:biomoby.org:objectclass:string + * * * *************************************************************************/ @@ -730,9 +767,9 @@ throws MobyException, NoSuccessException { // See if we've already retrieved the DataType and cached it - if(cache.containsKey("retrieveObjectDefinition"+dataTypeName)) - return (MobyDataType) cache.get("retrieveObjectDefinition"+dataTypeName); - + if (cache.containsKey("retrieveObjectDefinition" + dataTypeName)) + return (MobyDataType) cache.get("retrieveObjectDefinition" + dataTypeName); + String result = (String)doCall ("retrieveObjectDefinition", new Object[] { @@ -743,18 +780,21 @@ // parse returned XML Document document = null; - try{document=docBuilder.parse(new StringBufferInputStream(result));} - catch(Exception e){throw new MobyException(e.toString());} + try { + document = docBuilder.parse(new StringBufferInputStream(result)); + } catch (Exception e) { + throw new MobyException(e.toString()); + } NodeList list = document.getElementsByTagName ("retrieveObjectDefinition"); if (list == null || list.getLength() == 0) - throw new NoSuccessException ("Data Type name was not founnd.", + throw new NoSuccessException ("Data Type name was not found.", dataTypeName); MobyDataType data = null; Element elem = (Element)list.item (0); NodeList children = elem.getChildNodes(); - // first find the "real" data type name + // first find the "real" (LSID-ized) data type name for (int j = 0; j < children.getLength(); j++) { String nodeName = children.item (j).getNodeName(); if (nodeName.equals ("objectType")) { @@ -792,7 +832,18 @@ for (int k = 0; k < belows.getLength(); k++) { if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), - belows.item (k).getFirstChild().getNodeValue() ); + belows.item (k).getFirstChild().getNodeValue(), + MobyRelationship.HASA ); + } + } + } else if (relationshipType.endsWith ("has")) { + + NodeList belows = children.item (j).getChildNodes(); + for (int k = 0; k < belows.getLength(); k++) { + if (belows.item (k).getNodeName().equals ("objectType")) { + data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), + belows.item (k).getFirstChild().getNodeValue(), + MobyRelationship.HAS ); } } } @@ -804,42 +855,6 @@ /************************************************************************** * B - * - * - * ]]> - * - * - * ... - * ... - * - * - *************************************************************************/ -// public String getDataType (String dataTypeName) -// throws MobyException, NoSuccessException { -// String result = -// (String)doCall ("retrieveObjectSchema", -// new Object[] { -// "" + -// "" + dataTypeName + "" + -// "" -// }); - -// // parse returned XML (hack: taking blindly everything in the Schema tag) -// String xsd = ""; -// int pos = result.indexOf (""); -// if (pos == 1) -// throw new NoSuccessException ("Data Type name was not founnd.", -// dataTypeName); -// int pos2 = result.indexOf (""); -// if (pos2 < pos) -// throw new NoSuccessException ("Something wrong with the returned XML.", -// result); -// return result.substring (pos + 8, pos2); -// } - - /************************************************************************** - * B *************************************************************************/ public String getServiceWSDL (String serviceName) throws MobyException, NoSuccessException { @@ -889,7 +904,7 @@ } /************************************************************************* - * B + * *************************************************************************/ public void registerDataType (MobyDataType dataType) throws MobyException, NoSuccessException, PendingCurationException { @@ -904,16 +919,24 @@ buf.append ("\n"); } - // build the HASA tag (expressing containment of data types) - Hashtable children = dataType.getChildren(); - StringBuffer buf2 = new StringBuffer(); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { - String name = (String)en.nextElement(); - buf2.append (""); - buf2.append (children.get (name)); - buf2.append (""); + // build the HASA/HAS tags (expressing containments of data types) + MobyRelationship[] children = dataType.getChildren(); + StringBuffer buf2 = new StringBuffer(); // for HASA + StringBuffer buf3 = new StringBuffer(); // for HAS + for (int i = 0; i < children.length; i++) { + if (children[i].getRelationshipType() == MobyRelationship.HASA) { + buf2.append (""); + buf2.append (children[i].getDataTypeName()); + buf2.append (""); + } else if (children[i].getRelationshipType() == MobyRelationship.HAS) { + buf3.append (""); + buf3.append (children[i].getDataTypeName()); + buf3.append (""); + } } String result = @@ -927,30 +950,15 @@ "" + "" + new String (buf2) + "" + + "" + new String (buf3) + + "" + "" + dataType.getAuthority() + "" + "" + dataType.getEmailContact() + "" + "" }); - dataType.setId (checkRegistration (result, dataType)); + dataType.setId (checkRegistration (result, dataType)[0]); } -// -// NewObjectType -// -// -// -// ExistingObjectType -// ... -// ... -// -// ... -// ... -// Your.URI.here -// You at your.address.com -// - /************************************************************************* * B *************************************************************************/ @@ -995,7 +1003,7 @@ "" + "" }); - serviceType.setId (checkRegistration (result, serviceType)); + serviceType.setId (checkRegistration (result, serviceType)[0]); } // @@ -1042,7 +1050,7 @@ "" + "" }); - namespace.setId (checkRegistration (result, namespace)); + namespace.setId (checkRegistration (result, namespace)[0]); } /************************************************************************* @@ -1074,6 +1082,7 @@ "" + service.getName() + "" + "" + service.getType() + "" + "" + service.getAuthority() + "" + + "" + service.getSignatureURL() + "" + "" + service.getURL() + "" + "" + service.getEmailContact() + "" + "" + (service.isAuthoritative() ? "1" : "0") + "" + @@ -1084,7 +1093,22 @@ buildOutputTag (service) + "" }); - service.setId (checkRegistration (result, service)); + String[] registered = checkRegistration (result, service); + service.setId (registered [0]); + service.setRDF (registered [1]); + String pathToRDF = service.getPathToRDF(); + if ( ! pathToRDF.equals ("") ) { + File fileRDF = new File (pathToRDF); + try { + PrintStream fileout = new PrintStream (new FileOutputStream (fileRDF)); + fileout.println (registered [1]); + fileout.close(); + } catch (IOException e) { + throw new MobyException ("Failed to save RDF in '" + fileRDF.getAbsolutePath() + "'. " + + e.toString() + + "\nReturned RDF:\n" + registered [1]); + } + } } /************************************************************************* @@ -1390,11 +1414,13 @@ } /** - * By default, caching is enabled to reduce network traffic and XML parsing. Setting - * this to false will clear the cache, and not cache any further calls unless it is - * set to true again. - * - * @param shouldCache whether retrieveXXX call results should be cached in case they are called again (i.e. don't requery MobyCentral every time) + * By default, caching is enabled to reduce network traffic. + * Setting this to false will clear the cache, and not cache any + * further calls unless it is set to true again.

+ * + * @param shouldCache whether retrieveXXX call results should be + * cached in case they are called again (i.e. don't requery + * MobyCentral every time) */ public void setCacheMode(boolean shouldCache){ useCache = shouldCache; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2003/11/25 13:18:10 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/22 21:11:17 1.3 @@ -6,11 +6,14 @@ package org.biomoby.client; -import org.biomoby.shared.*; - -import java.net.*; -import java.util.*; -import java.io.*; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.Properties; + +import org.biomoby.shared.MobyDataType; +import org.biomoby.shared.MobyRelationship; +import org.biomoby.shared.MobyServiceType; +import org.biomoby.shared.Utils; /** * A utility class that understands how to create @@ -134,15 +137,15 @@ buf.append (trName (name)); buf.append (";\n"); } - Hashtable children = type.getChildren(); - if (children.size() > 0) { + MobyRelationship[] children = type.getChildren(); + if (children.length > 0) { String dummyName = trName (name) + "_HASA"; buf.append ("\t" + trName (name) + " -> " + dummyName); buf.append (" [style=dotted,dir=forward,arrowhead=none,arrowtail=ediamond];\n"); StringBuffer hasaBuf = new StringBuffer(); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { - String childName = (String)en.nextElement(); - String childType = Utils.pureName ((String)children.get (childName)); + for (int i = 0; i < children.length; i++) { + String childName = Utils.pureName (children[i].getName()); + String childType = Utils.pureName (children[i].getDataTypeName()); if (childType == null) childType = "n/a"; // should not happen I guess hasaBuf.append (" | {" + childType + "|" + childName + "}"); From senger at pub.open-bio.org Wed Sep 22 21:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBH8l015617@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv15476/src/support Modified Files: README _README.FIRST_ Log Message: new registration procedure, etc. moby-live/Java/src/support README,1.3,1.4 _README.FIRST_,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/README,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/support/README 2003/11/08 00:27:24 1.3 +++ /home/repository/moby/moby-live/Java/src/support/README 2004/09/22 21:11:17 1.4 @@ -1,5 +1,5 @@ This directory contains Moby clients in Java, ready to be used and to -communicate with a real Moby server. More documentation is available +communicate with a real Moby registry. More documentation is available in the 'docs' directory. A full distribution with sources is available from the BioMoby home page http://biomoby.org. @@ -8,9 +8,10 @@ Invoke available clients using provided (and very simple) scripts (use those ending with '.bat' for Windows OS): - sh ./run-cmdline-client -help - sh ./run-testing-central - sh ./run-graphs-client -help + sh ./run/run-cmdline-client -help + sh ./run/run-testing-central + sh ./run/run-graphs-client -help + etc. Or, on Unix platforms, use chmod to make the scripts above executable and call them without 'sh' (note that this small inconvenience is due =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/_README.FIRST_,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/support/_README.FIRST_ 2003/09/25 02:35:02 1.1 +++ /home/repository/moby/moby-live/Java/src/support/_README.FIRST_ 2004/09/22 21:11:17 1.2 @@ -1,6 +1,6 @@ Files in this directory are used as templates when creating a binary distribution. They are not intended to be used per se. For invoking -various clients, use scripts available in the main directory above. +various clients, use scripts available in the build/run directory. -------------------------------------------------------------------- Comments to the biomoby mailing lists, or directly to Martin Senger From senger at pub.open-bio.org Wed Sep 22 21:11:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 17:11:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222111.i8MLBHe1015594@pub.open-bio.org> senger Wed Sep 22 17:11:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv15476/src/main/org/biomoby/shared Modified Files: MobyDataType.java MobyPrimaryDataSimple.java MobyService.java Added Files: MobyRelationship.java Log Message: new registration procedure, etc. moby-live/Java/src/main/org/biomoby/shared MobyRelationship.java,NONE,1.1 MobyDataType.java,1.2,1.3 MobyPrimaryDataSimple.java,1.1,1.2 MobyService.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/03/09 00:20:13 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/22 21:11:17 1.3 @@ -11,15 +11,14 @@ /** - * A container representing a data type used in the Moby registry. - * The Moby data types are used to specify what types of inputs and - * outputs are needed or produced by Moby services. - *

+ * A container representing a data type used in the Moby registry (in + * the BioMoby speak it is called "Object Class"). The Moby data + * types are used to specify what types of inputs and outputs are + * needed or produced by Moby services.

* - * This container is used mainly to register a new data type in a + * This container is used mainly to register a new data type into a * Moby registry, and to find services with this particular input or - * output data type. - *

+ * output data type.

* * @author Martin Senger * @version $Id$ @@ -32,12 +31,18 @@ protected String emailContact = ""; protected String description = ""; protected String[] parentNames = new String[] { }; - protected Hashtable children = new Hashtable(); + protected MobyRelationship[] children = new MobyRelationship[] { }; protected String id = null; /************************************************************************** - * Default constructor. Other characteristics are empty - which is usually - * wrong - therefore use 'set' method to fill them. + * Default constructor. Other characteristics are empty - which is + * usually wrong - you should use 'set' methods to fill them + * before using this instance.

+ * + * @param name of this data type (e.g. GenericSequence, or + * String). The name can be either a simple string (e.g. Object), + * or a full-blown LSID + * (e.g. urn:lsid:biomoby.org:objectclass:Object). *************************************************************************/ public MobyDataType (String name) { this.name = name; @@ -47,34 +52,76 @@ return name; } + /** + * Return an ID that is given to this data type during its + * registration. The ID seems to be used only for de-registration + * of this data type; you are not supposed to fill it when you + * create an instance of this object. + */ public String getId() { return id; } + + /** + * @see #getId + */ public void setId (String value) { id = value; } + /** + * Return an authority for this data type. The authority is an URI + * of this data type provider. Very often empty. + */ public String getAuthority() { return authority; } + /** + * @see #getAuthority + */ public void setAuthority (String value) { authority = (value == null ? "" : value); } + /** + * Return a contact email. The purpose of this field is still a + * bit obscure - but I think that the intention is to use it in + * the process of de-registration of this data type. + */ public String getEmailContact() { return emailContact; } + /** + * @see #getEmailContact + */ public void setEmailContact (String value) { emailContact = (value == null ? "" : value); } + /** + * Return a (usually) human readable description of this data + * type. + */ public String getDescription() { return description; } + /** + * @see #getDescription + */ public void setDescription (String value) { description = (value == null ? "" : value); } + /** + * Return names of all parental data types (as stored in the + * BioMoby class ontology). Note, however, that the current + * BioMoby API (0.8) does not expect (probably even does not + * allow) multiple-inheritance.

+ * + * @return (at the moment) none (for the root data type) or one + * name. The name is an LSID + * (e.g. urn:lsid:biomoby.org:objectclass:Object). + */ public String[] getParentNames() { synchronized (parentNames) { String[] names = new String [parentNames.length]; @@ -82,6 +129,12 @@ return names; } } + /** + * @see #getParentNames + * @param value is a set of parent names (usually just one name, + * however). If it is null all parents set previously are + * forgotten. + */ public void setParentNames (String[] value) { synchronized (parentNames) { if (value == null) @@ -92,6 +145,13 @@ } } } + /** + * Add one parent of this data type.

+ * + * @see #getParentNames + * @param value is a name of a parental data type. A null value is + * ignored. + */ public void addParentName (String value) { if (value != null) { synchronized (parentNames) { @@ -105,53 +165,90 @@ } /** - * Describes what children this data type has (expressing ontology - * term HAS-A). The returned value is a hashtable with: - *

    - *
  • key is a (unique) name of this child a data type - *
  • value is a name of a data type representing this child - *
+ * Return children of this data type, and the way how they are + * ontologically related to this data type. The returned elements + * are containers, each of them defining the child data type, + * under what name it is used here (the BioMoby API calls this + * name an "article name"), and what relationship it has to this + * data type (HAS, HASA).

+ * + * Note that it does not return children that belong to the parent + * types - in other words it does not go up through the whole + * ontology tree to find all children.

+ * + * @see MobyRelationship.HAS + * @see MobyRelationship.HASA */ - public Hashtable getChildren() { + public MobyRelationship[] getChildren() { return children; } - public void setChildren (Hashtable value) { - children = (value == null ? new Hashtable() : value); + /** + * @see #getChildren + * @param value is an array of children. If it is null all + * children set previously are forgotten. + */ + public void setChildren (MobyRelationship[] value) { + children = (value == null ? new MobyRelationship[] {} : value); } /** - * 'name' is a name given to this child (attribute) - * 'typeName' is a name of a type represented by this child + * @see #getChildren + * @param child a new child to be added. If null it is ignored. */ - public void addChild (String name, String typeName) { + public void addChild (MobyRelationship child) { + if (child != null) { + synchronized (children) { + int len = children.length + 1; + MobyRelationship[] newChildren = new MobyRelationship [len]; + System.arraycopy (children, 0, newChildren, 0, len-1); + newChildren [len - 1] = child; + setChildren (newChildren); + } + } + } + /** + * Create a {@link MobyRelationship MobyRelationship} object from + * given parameters and add it as a new child.

+ * + * @see #getChildren + * @param name is a name how the new child is known to this data + * type (an "article name" in the BioMoby speak), + * e.g. 'length'. Because of the backward compatibility it accepts + * also a null or empty string here - but according to the BioMoby + * API (0.8) this name should be always given. + * @param typeName is a name of the child data type, + * e.g. 'Integer'. If null it is ignored. + * @param relationshipType is either {@link MobyRelationship.HASA + * HASA} or {@link MobyRelationship.HAS HAS}. If it is something + * else it is silenty changed to {@link MobyRelationship.HASA + * HASA}. + */ + public void addChild (String name, String typeName, int relationshipType) { if (typeName != null) { - if (name == null || name.equals ("")) - name = typeName; -// children.put (typeName, name); - children.put (name, typeName); + if (name == null) name = ""; + if (relationshipType != MobyRelationship.HASA && + relationshipType != MobyRelationship.HAS) + relationshipType = MobyRelationship.HASA; + addChild (new MobyRelationship (name, typeName, relationshipType)); } } - public String toString() { StringBuffer buf = new StringBuffer(); buf.append ("Name: " + name + "\n"); buf.append ("Auth: " + authority + "\n"); buf.append ("Desc: " + description + "\n"); buf.append ("Contact: " + emailContact + "\n"); - buf.append ("ID: " + id + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); buf.append ("Parents:\n"); for (int i = 0 ; i < parentNames.length; i++) { buf.append (Utils.format (null, 1)); buf.append (parentNames [i]); buf.append ("\n"); } - buf.append ("Children:\n"); - for (Enumeration en = children.keys(); en.hasMoreElements(); ) { + buf.append ("Children (only those registered here):\n"); + for (int i = 0 ; i < children.length; i++) { buf.append (Utils.format (null, 1)); - String key = (String)en.nextElement(); - buf.append (key); - buf.append (" => "); - buf.append (children.get (key)); + buf.append (children[i].toString()); buf.append ("\n"); } return new String (buf); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2003/09/24 14:33:37 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyPrimaryDataSimple.java 2004/09/22 21:11:17 1.2 @@ -104,7 +104,7 @@ buf.append (name); buf.append ("\">\n"); buf.append (""); - buf.append (dataType.getName()); + if (dataType != null) buf.append (dataType.getName()); buf.append ("\n"); if (namespaces.size() > 0) { for (Enumeration en = namespaces.elements(); en.hasMoreElements(); ) { @@ -121,7 +121,7 @@ public String toString() { StringBuffer buf = new StringBuffer(); buf.append ("Name: " + name + "\n"); - buf.append ("ID: " + id + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); if (dataType != null) buf.append ("Data Type:\n" + dataType.format (1)); buf.append ("Namespaces:\n"); =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2004/04/01 23:24:27 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyService.java 2004/09/22 21:11:17 1.3 @@ -10,12 +10,12 @@ import java.util.*; /** - * A container representing a service. - *

+ * A container representing a service. But do not be too excited - + * this is not a real service but only its definition as it appears in + * the BioMoby regustry.

* * This container is used mainly to register a new service in a - * Moby registry, and to find registered services later. - *

+ * Moby registry, and to find registered services later.

* * @author Martin Senger * @version $Id$ @@ -30,6 +30,9 @@ protected String type = ""; protected String description = ""; protected String url = ""; + protected String signatureURL = ""; + protected String rdf = ""; + protected String pathToRDF = ""; protected boolean authoritativeService = true; protected String id = null; @@ -39,8 +42,9 @@ protected Vector primaryOutputs = new Vector(); /************************************************************************** - * Default constructor. Other characteristics are empty - which is usually - * wrong - therefore use 'set' method to fill them. + * Default constructor. Other characteristics are empty - which is + * usually wrong - therefore use 'set' methods to fill them before + * using this instance. *************************************************************************/ public MobyService (String name) { this.name = name; @@ -50,9 +54,21 @@ return name; } + /** + * Return an ID that is given to this service instance during its + * registration. The ID is used only for de-registration of this + * service instance (you are not supposed to fill it when you + * create an instance of this object). But it soon becomes + * obsolete anyway because of the new way of registering services + * (see {@link #getSignatureURL}).

+ */ public String getId() { return id; } + /** + * Don't use it. + * @see #getId + */ public void setId (String value) { id = value; } @@ -99,13 +115,89 @@ type = (value == null ? "" : value); } + /** + * Return a URL where this service is being served from. It is a + * URL where the clients of this service are going when they want + * to use it.

+ * + * Note that there is nothing in the BioMoby registry remembering + * (registering) a namespace of your service. Therefore, your + * service is supposed to use always the namespace + * http://biomoby.org.

+ */ public String getURL() { return url; } + /** + * @see #getURL + */ public void setURL (String value) { url = (value == null ? "" : value); } + /** + * Return a URL pointing to an RDF document that contains this + * service description (signature). Note that this RDF document + * can include also other things, such as other service + * signatures.

+ * + * This is how it works: + *

    + * + *
  1. When you register a service (using an instance of this + * class) you put here (by calling {@link #setSignatureURL}) a + * URL pointing to your HTTP space, to an RDF + * document. But this document does not need to exist yet. + * + *
  2. After a successful registration this instance will have + * an RDF document with this service signature. You can obtain + * it by calling {@link #getRDF}. + * + *
  3. You are expected to copy this RDF document to the place + * that you had suggested in step 1. Failing to do it will + * result in de-registrating your service automatically + * sometimes later. Therefore, if your service is only a testing + * one, do not copy RDF anywhere and the service will disappear. + * + *
  4. Some implementations of the {@link Central} interface + * (such as its default implementation {@link + * org.biomoby.client.CentralImpl CentralImpl} can copy the RDF + * document for you if you put here a fully qualified path to + * the file where the RDF document should be put (by calling + * {@link #setPathToRDF}). + * + *
+ */ + public String getSignatureURL() { + return signatureURL; + } + /** + * @see #getSignatureURL + */ + public void setSignatureURL (String value) { + signatureURL = (value == null ? "" : value); + } + + /** + * @see #getSignatureURL + */ + public String getPathToRDF() { + return pathToRDF; + } + public void setPathToRDF (String value) { + pathToRDF = (value == null ? "" : value); + } + + /** + * @see #getSignatureURL + */ + public String getRDF() { + return rdf; + } + public void setRDF (String value) { + rdf = (value == null ? "" : value); + } + public void setInputs (MobyData[] value) { if (value == null) { primaryInputs.clear(); @@ -176,14 +268,16 @@ public String toString() { StringBuffer buf = new StringBuffer(); - buf.append ("Name: " + name + "\n"); - buf.append ("Type: " + type + "\n"); - buf.append ("Category: " + category + "\n"); - buf.append ("Auth: " + authority + "\n"); - buf.append ("Desc: " + description + "\n"); - buf.append ("URL: " + url + "\n"); - buf.append ("Contact: " + emailContact + "\n"); - buf.append ("ID: " + id + "\n"); + buf.append ("Name: " + name + "\n"); + buf.append ("Type: " + type + "\n"); + buf.append ("Category: " + category + "\n"); + buf.append ("Auth: " + authority + "\n"); + buf.append ("Desc: " + description + "\n"); + buf.append ("URL: " + url + "\n"); + buf.append ("Contact: " + emailContact + "\n"); + buf.append ("Signature URL: " + signatureURL + "\n"); + buf.append ("Path to RDF: " + pathToRDF + "\n"); + if (id != null) buf.append ("ID: " + id + "\n"); buf.append ("\nPrimary inputs:\n"); for (Enumeration en = primaryInputs.elements(); en.hasMoreElements(); ) From senger at pub.open-bio.org Wed Sep 22 23:20:17 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 19:20:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409222320.i8MNKHtJ015938@pub.open-bio.org> senger Wed Sep 22 19:20:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv15920/src/config Log Message: Directory /home/repository/moby/moby-live/Java/src/config added to the repository moby-live/Java/src/config - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/config/RCS/directory,v: No such file or directory From senger at pub.open-bio.org Thu Sep 23 00:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1B1016161@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs/API In directory pub.open-bio.org:/tmp/cvs-serv16113/docs/API Modified Files: .cvsignore.template Log Message: enhanced build.xml to support other subprojects moby-live/Java/docs/API .cvsignore.template,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2003/09/25 12:27:47 1.2 +++ /home/repository/moby/moby-live/Java/docs/API/.cvsignore.template 2004/09/23 00:18:01 1.3 @@ -4,4 +4,4 @@ *-list class-use org - +resources From senger at pub.open-bio.org Thu Sep 23 00:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1dB016176@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/config In directory pub.open-bio.org:/tmp/cvs-serv16113/src/config Added Files: run-any-client run-any-client.bat run-cmdline-client run-cmdline-client.bat run-graphs-client run-graphs-client.bat run-testing-central run-testing-central.bat source.me.csh source.me.sh Log Message: enhanced build.xml to support other subprojects moby-live/Java/src/config run-any-client,NONE,1.1 run-any-client.bat,NONE,1.1 run-cmdline-client,NONE,1.1 run-cmdline-client.bat,NONE,1.1 run-graphs-client,NONE,1.1 run-graphs-client.bat,NONE,1.1 run-testing-central,NONE,1.1 run-testing-central.bat,NONE,1.1 source.me.csh,NONE,1.1 source.me.sh,NONE,1.1 From senger at pub.open-bio.org Thu Sep 23 00:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I1gA016142@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java In directory pub.open-bio.org:/tmp/cvs-serv16113 Modified Files: build.xml Removed Files: run-any-client run-any-client.bat run-cmdline-client run-cmdline-client.bat run-graphs-client run-graphs-client.bat run-testing-central run-testing-central.bat Log Message: enhanced build.xml to support other subprojects moby-live/Java build.xml,1.6,1.7 run-any-client,1.1,NONE run-any-client.bat,1.1,NONE run-cmdline-client,1.2,NONE run-cmdline-client.bat,1.2,NONE run-graphs-client,1.1,NONE run-graphs-client.bat,1.1,NONE run-testing-central,1.2,NONE run-testing-central.bat,1.2,NONE =================================================================== RCS file: /home/repository/moby/moby-live/Java/build.xml,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/build.xml 2003/11/09 01:05:02 1.6 +++ /home/repository/moby/moby-live/Java/build.xml 2004/09/23 00:18:00 1.7 @@ -22,6 +22,7 @@ + @@ -43,6 +44,7 @@ + @@ -79,6 +81,18 @@ + + + + + + + + + + + + @@ -115,6 +129,20 @@ + + + + + + + + + + + + + + @@ -135,6 +163,7 @@ + @@ -156,6 +185,19 @@ + + + + + + + + + + + + + @@ -209,12 +251,24 @@ + + + + + + + + + + + + - Missing one or more third-party libraries. @@ -240,6 +294,18 @@ + + + + + + + + + + + @@ -407,6 +473,20 @@ + + + + + + + + + + + + + + rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-any-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-any-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-cmdline-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-cmdline-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-graphs-client,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-graphs-client.bat,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-testing-central,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/RCS/run-testing-central.bat,v: No such file or directory From senger at pub.open-bio.org Thu Sep 23 00:18:01 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Wed, 22 Sep 2004 20:18:01 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409230018.i8N0I15k016197@pub.open-bio.org> senger Wed Sep 22 20:18:01 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/support In directory pub.open-bio.org:/tmp/cvs-serv16113/src/support Modified Files: README Log Message: enhanced build.xml to support other subprojects moby-live/Java/src/support README,1.4,1.5 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/support/README,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- /home/repository/moby/moby-live/Java/src/support/README 2004/09/22 21:11:17 1.4 +++ /home/repository/moby/moby-live/Java/src/support/README 2004/09/23 00:18:01 1.5 @@ -8,9 +8,9 @@ Invoke available clients using provided (and very simple) scripts (use those ending with '.bat' for Windows OS): - sh ./run/run-cmdline-client -help - sh ./run/run-testing-central - sh ./run/run-graphs-client -help + sh ./run-cmdline-client -help + sh ./run-testing-central + sh ./run-graphs-client -help etc. Or, on Unix platforms, use chmod to make the scripts above executable From senger at pub.open-bio.org Thu Sep 23 10:20:29 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKTMn017972@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients In directory pub.open-bio.org:/tmp/cvs-serv17926/src/Clients Modified Files: MobyCmdLineClient.java PopulateLocalCentralForTesting.java TestingCentral.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/Clients MobyCmdLineClient.java,1.5,1.6 PopulateLocalCentralForTesting.java,1.2,1.3 TestingCentral.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/22 21:11:17 1.5 +++ /home/repository/moby/moby-live/Java/src/Clients/MobyCmdLineClient.java 2004/09/23 10:20:29 1.6 @@ -221,11 +221,11 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i], MobyRelationship.HASA); + data.addChild (null, hasas [i], Central.iHASA); } else if (pos == hasas[i].length() - 1) { - data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HASA); + data.addChild (hasas [i].substring (0, pos), null, Central.iHASA); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HASA); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), Central.iHASA); } } } @@ -234,11 +234,11 @@ for (int i = 0; i < hasas.length; i++) { int pos = hasas[i].indexOf (":"); if (pos == -1) { - data.addChild (null, hasas [i], MobyRelationship.HAS); + data.addChild (null, hasas [i], Central.iHAS); } else if (pos == hasas[i].length() - 1) { - data.addChild (hasas [i].substring (0, pos), null, MobyRelationship.HAS); + data.addChild (hasas [i].substring (0, pos), null, Central.iHAS); } else { - data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), MobyRelationship.HAS); + data.addChild (hasas[i].substring (0, pos), hasas[i].substring (pos+1), Central.iHAS); } } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/22 21:11:17 1.2 +++ /home/repository/moby/moby-live/Java/src/Clients/PopulateLocalCentralForTesting.java 2004/09/23 10:20:29 1.3 @@ -240,10 +240,10 @@ protected MobyDataType[] createAllDataTypes() { MobyDataType data1 = createDataType (dataType_1); data1.addParentName ("Object"); - data1.addChild ("address", "string", MobyRelationship.HASA); - data1.addChild ("age", "integer", MobyRelationship.HASA); - data1.addChild ("salary", "float", MobyRelationship.HASA); - data1.addChild ("born", "datetime", MobyRelationship.HASA); + data1.addChild ("address", "string", Central.iHASA); + data1.addChild ("age", "integer", Central.iHASA); + data1.addChild ("salary", "float", Central.iHASA); + data1.addChild ("born", "datetime", Central.iHASA); MobyDataType data2 = createDataType (dataType_2); data2.addParentName ("Object"); MobyDataType data3 = createDataType (dataType_3); @@ -253,8 +253,8 @@ MobyDataType data5 = createDataType (dataType_5); data5.addParentName (dataType_3); data5.addParentName (dataType_2); - data5.addChild ("range_min", "integer", MobyRelationship.HAS); - data5.addChild ("range_max", "integer", MobyRelationship.HAS); + data5.addChild ("range_min", "integer", Central.iHAS); + data5.addChild ("range_max", "integer", Central.iHAS); return new MobyDataType [] { data1, data2, data3, data4, data5 }; } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/TestingCentral.java 2004/09/23 10:20:29 1.4 @@ -247,9 +247,9 @@ try { start ("registerDataType - 2"); data2.addParentName (data1.getName()); - data2.addChild ("len", "Integer", MobyRelationship.HASA); - data2.addChild ("sub", "String", MobyRelationship.HAS); - data2.addChild ("real_type", data3.getName(), MobyRelationship.HASA); + data2.addChild ("len", "Integer", Central.iHASA); + data2.addChild ("sub", "String", Central.iHAS); + data2.addChild ("real_type", data3.getName(), Central.iHASA); worker.registerDataType (data2); ok(); } catch (MobyException e) { error (e); From senger at pub.open-bio.org Thu Sep 23 10:20:29 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:29 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKT07017945@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv17926/docs Modified Files: ChangeLog Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/docs ChangeLog,1.18,1.19 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/22 21:11:17 1.18 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/23 10:20:29 1.19 @@ -1,3 +1,8 @@ +2004-09-23 Martin Senger + + * Moved constants ISA, HAS, HASA from MobyRelationship to Central + (as iHAS, iHASA and iISA). + 2004-09-22 Martin Senger * Fixed option -rs-out in MobyCmdLineClient. From senger at pub.open-bio.org Thu Sep 23 10:20:30 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKUR8017992@pub.open-bio.org> senger Thu Sep 23 06:20:29 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv17926/src/main/org/biomoby/client Modified Files: CentralImpl.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.14,1.15 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/22 21:11:17 1.14 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/23 10:20:29 1.15 @@ -833,7 +833,7 @@ if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), belows.item (k).getFirstChild().getNodeValue(), - MobyRelationship.HASA ); + Central.iHASA ); } } } else if (relationshipType.endsWith ("has")) { @@ -843,7 +843,7 @@ if (belows.item (k).getNodeName().equals ("objectType")) { data.addChild ( ((Element)belows.item (k)).getAttribute ("articleName"), belows.item (k).getFirstChild().getNodeValue(), - MobyRelationship.HAS ); + Central.iHAS ); } } } @@ -924,13 +924,13 @@ StringBuffer buf2 = new StringBuffer(); // for HASA StringBuffer buf3 = new StringBuffer(); // for HAS for (int i = 0; i < children.length; i++) { - if (children[i].getRelationshipType() == MobyRelationship.HASA) { + if (children[i].getRelationshipType() == Central.iHASA) { buf2.append (""); buf2.append (children[i].getDataTypeName()); buf2.append (""); - } else if (children[i].getRelationshipType() == MobyRelationship.HAS) { + } else if (children[i].getRelationshipType() == Central.iHAS) { buf3.append (""); From senger at pub.open-bio.org Thu Sep 23 10:20:30 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Thu, 23 Sep 2004 06:20:30 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231020.i8NAKUIn018025@pub.open-bio.org> senger Thu Sep 23 06:20:30 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv17926/src/main/org/biomoby/shared Modified Files: Central.java MobyDataSimpleInstance.java MobyDataType.java MobyRelationship.java Log Message: some constants moved from MobyRelationship to Central interface moby-live/Java/src/main/org/biomoby/shared Central.java,1.5,1.6 MobyDataSimpleInstance.java,1.2,1.3 MobyDataType.java,1.3,1.4 MobyRelationship.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/05/18 10:13:17 1.5 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/23 10:20:29 1.6 @@ -48,15 +48,38 @@ public interface Central { - /** A name for the relationship type "is a". */ + /** A relationship type expressing a straight inheritance (as + * string). If Object_A ISA Object_B then all attributes of + * Object_B are guaranteed to be present in Object_A. + */ static final String ISA = "ISA"; - /** A name for the relationship type "has a". */ + /** A relationship type expressing a contaiment (as string). If + * Object_A HASA Object_B then Object_B is an object inside of + * Object_A in one copy only. */ static final String HASA = "HASA"; - /** A name for the relationship type "has". */ + /** A relationship type expressing a contaiment (as string). If + * Object_A HAS Object_B then Object_B is an object inside of + * Object_A in one or more copies. */ static final String HAS = "HAS"; + /** A relationship type expressing a straight inheritance (as + * integer). If Object_A ISA Object_B then all attributes of + * Object_B are guaranteed to be present in Object_A. + */ + static final int iISA = 1; + + /** A relationship type expressing a contaiment (as integer). If + * Object_A HASA Object_B then Object_B is an object inside of + * Object_A in one copy only. */ + static final int iHASA = 2; + + /** A relationship type expressing a contaiment (as integer). If + * Object_A HAS Object_B then Object_B is an object inside of + * Object_A in one or more copies. */ + static final int iHAS = 3; + /************************************************************************** * Get a (redundant) list of all registered service names. *

@@ -309,7 +332,7 @@ /************************************************************************** * Find service matching both all non-empty fields in the 'pattern' and - * the 'keywords', and take into account also the whole ontology tree: + * the 'keywords', and take into account also the whole ontology tree. *

* @param includeChildrenServiceTypes - if true (which is default) * then it discovers also services that are child types (more @@ -351,4 +374,12 @@ * Reports whether server responses are being cached or not. *************************************************************************/ boolean getCacheMode(); + + + // Work in progress: +// http://biomoby.org/RESOURCES/MOBY-S/Objects +// http://biomoby.org/RESOURCES/MOBY-S/Services +// http://biomoby.org/RESOURCES/MOBY-S/Namespaces +// http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances + } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/03 20:28:16 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataSimpleInstance.java 2004/09/23 10:20:29 1.3 @@ -140,7 +140,7 @@ } /** - * Used to set the data instance value based on a ID string (i.e. just an Object) + * Used to set the data instance value based on an ID string. E.i. just an Object. */ public void setId(String value){ super.setId(value); @@ -214,7 +214,7 @@ * a template for use in MOBY Central services, or a Simple element for use in calling a service * instance. * - * @returns the MOBY XML representation of the data instance + * @return the MOBY XML representation of the data instance */ public String toXML(){ if(xmlMode == SERVICE_XML_MODE) =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyDataType.java 2004/09/23 10:20:29 1.4 @@ -176,8 +176,8 @@ * types - in other words it does not go up through the whole * ontology tree to find all children.

* - * @see MobyRelationship.HAS - * @see MobyRelationship.HASA + * @see Central#iHAS + * @see Central#iHASA */ public MobyRelationship[] getChildren() { return children; @@ -216,18 +216,18 @@ * also a null or empty string here - but according to the BioMoby * API (0.8) this name should be always given. * @param typeName is a name of the child data type, - * e.g. 'Integer'. If null it is ignored. - * @param relationshipType is either {@link MobyRelationship.HASA - * HASA} or {@link MobyRelationship.HAS HAS}. If it is something - * else it is silenty changed to {@link MobyRelationship.HASA + * e.g. 'Integer'. If it is null it is ignored. + * @param relationshipType is either {@link Central#iHASA + * HASA} or {@link Central#iHAS HAS}. If it is something + * else it is silenty changed to {@link Central#iHASA * HASA}. */ public void addChild (String name, String typeName, int relationshipType) { if (typeName != null) { if (name == null) name = ""; - if (relationshipType != MobyRelationship.HASA && - relationshipType != MobyRelationship.HAS) - relationshipType = MobyRelationship.HASA; + if (relationshipType != Central.iHASA && + relationshipType != Central.iHAS) + relationshipType = Central.iHASA; addChild (new MobyRelationship (name, typeName, relationshipType)); } } =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java 2004/09/22 21:11:17 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/MobyRelationship.java 2004/09/23 10:20:29 1.2 @@ -20,25 +20,9 @@ public class MobyRelationship { - /** A relationship type expressing a straight inheritance. If - * Object_A ISA Object_B then all attributes of Object_B are - * guaranteed to be present in Object_A. - */ - public static final int ISA = 1; - - /** A relationship type expressing a contaiment. If Object_A HASA - * Object_B then Object_B is an object inside of Object_A in one - * copy only. */ - public static final int HASA = 2; - - /** A relationship type expressing a contaiment. If Object_A HAS - * Object_B then Object_B is an object inside of Object_A in one - * or more copies. */ - public static final int HAS = 3; - protected String name; // articleName protected String dataTypeName; - protected int relationshipType = HASA; + protected int relationshipType = Central.iHASA; /************************************************************************** * Default (and only) constructor.

@@ -50,15 +34,15 @@ * should be always given. * @param dataTypeName is a name of a data type that is defined by * this relationship, e.g. 'Integer'. - * @param relationshipType is either {@link #HASA} or {@link - * #HAS}. If it is something else it is silently changed to {@link - * #HASA}. + * @param relationshipType is either {@link Central#iHASA HASA} or {@link + * Central#iHAS HAS}. If it is something else it is silently changed to {@link + * Central#iHASA HASA}. *************************************************************************/ public MobyRelationship (String name, String dataTypeName, int relationshipType) { this.name = name; this.dataTypeName = dataTypeName; - if (relationshipType != HASA && relationshipType != HAS) - relationshipType = HASA; + if (relationshipType != Central.iHASA && relationshipType != Central.iHAS) + relationshipType = Central.iHASA; this.relationshipType = relationshipType; } @@ -78,8 +62,8 @@ } /** - * Return type of this relationship. It is either {@link #HASA} or - * {@link #HAS}. + * Return type of this relationship. It is either {@link Central#iHASA HASA} or + * {@link Central#iHAS HAS}. */ public int getRelationshipType() { return relationshipType; @@ -93,9 +77,9 @@ */ public static String type2str (int relationshipType) { switch (relationshipType) { - case HASA: return "HASA"; - case HAS: return "HAS"; - case ISA: return "ISA"; + case Central.iHASA: return Central.HASA; + case Central.iHAS: return Central.HAS; + case Central.iISA: return Central.ISA; default: return "unknown"; } } From kawas at pub.open-bio.org Thu Sep 23 14:27:08 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Thu, 23 Sep 2004 10:27:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409231427.i8NER8aO019251@pub.open-bio.org> kawas Thu Sep 23 10:27:08 EDT 2004 Update of /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets In directory pub.open-bio.org:/tmp/cvs-serv19222 Removed Files: Untitled-2.htm index-old.html index.htm service-app.jar service.html service.jar tree-app.jar tree.jar Log Message: removed the files and will commit them to their proper packages. part 3 (i missed a few) moby-live/Accessories/ObjectCreationTool/Applets Untitled-2.htm,1.1,NONE index-old.html,1.1,NONE index.htm,1.2,NONE service-app.jar,1.1,NONE service.html,1.1,NONE service.jar,1.1,NONE tree-app.jar,1.2,NONE tree.jar,1.2,NONE rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/Untitled-2.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/index-old.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/index.htm,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service-app.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service.html,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/service.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/tree-app.jar,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Accessories/ObjectCreationTool/Applets/RCS/tree.jar,v: No such file or directory From senger at pub.open-bio.org Fri Sep 24 19:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquZ7032093@pub.open-bio.org> senger Fri Sep 24 15:52:55 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/Clients/help In directory pub.open-bio.org:/tmp/cvs-serv32055/src/Clients/help Modified Files: MobyGraphs_usage.txt Log Message: signatureURL was missing in service response object moby-live/Java/src/Clients/help MobyGraphs_usage.txt,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2003/11/25 13:18:10 1.3 +++ /home/repository/moby/moby-live/Java/src/Clients/help/MobyGraphs_usage.txt 2004/09/24 19:52:55 1.4 @@ -1,12 +1,23 @@ Usage: java MobyGraphs -h[elp] - java MobyGraphs + java MobyGraphs [] - -q ... quiet mode +where specify what Moby registry to connect to: - -d ... graph showing data types - -s ... graph showing service instances - -t ... graph showing service types + -e + ia an endpoint of a Moby registry + (default: http://mobycentral.cbr.nrc.ca/cgi-bin/MOBY-Central.pl) + -uri + is a URI defining Moby registry's namespace + (default: http://mobycentral.cbr.nrc.ca/MOBY/Central) + +where are: + + -q ... quiet mode + + -d ... make graph showing data types + -s ... make graph showing service instances + -t ... make graph showing service types output format: -dot ... (this is default) From senger at pub.open-bio.org Fri Sep 24 19:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquwd032118@pub.open-bio.org> senger Fri Sep 24 15:52:56 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client In directory pub.open-bio.org:/tmp/cvs-serv32055/src/main/org/biomoby/client Modified Files: CentralImpl.java Graphviz.java Log Message: signatureURL was missing in service response object moby-live/Java/src/main/org/biomoby/client CentralImpl.java,1.15,1.16 Graphviz.java,1.3,1.4 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/23 10:20:29 1.15 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralImpl.java 2004/09/24 19:52:55 1.16 @@ -407,8 +407,9 @@ * * Service_Ontology_Term * moby - * http://service.endpoint.here/scriptname * your at email.addy.here + * http://service.RDF.here + * http://service.endpoint.here/scriptname * 1 * * @@ -453,6 +454,8 @@ service.setCategory (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("URL")) { service.setURL (children.item (j).getFirstChild().getNodeValue()); + } else if (nodeName.equals ("signatureURL")) { + service.setSignatureURL (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("contactEmail")) { service.setEmailContact (children.item (j).getFirstChild().getNodeValue()); } else if (nodeName.equals ("serviceType")) { =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/22 21:11:17 1.3 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/Graphviz.java 2004/09/24 19:52:56 1.4 @@ -93,8 +93,8 @@ edgeAttrs.append ("]"); } buf.append ("\t" + - edge.sourceService.getName() + " -> " + - edge.targetService.getName() + + quoteIt (edge.sourceService.getName()) + " -> " + + quoteIt (edge.targetService.getName()) + new String (edgeAttrs) + "\n"); } } @@ -132,15 +132,15 @@ String[] parents = type.getParentNames(); for (int i = 0; i < parents.length; i++) { buf.append ("\t"); - buf.append (trName (Utils.pureName (parents[i]))); + buf.append (quoteIt (trName (Utils.pureName (parents[i])))); buf.append (" -> "); - buf.append (trName (name)); + buf.append (quoteIt (trName (name))); buf.append (";\n"); } MobyRelationship[] children = type.getChildren(); if (children.length > 0) { String dummyName = trName (name) + "_HASA"; - buf.append ("\t" + trName (name) + " -> " + dummyName); + buf.append ("\t" + quoteIt (trName (name)) + " -> " + quoteIt (dummyName)); buf.append (" [style=dotted,dir=forward,arrowhead=none,arrowtail=ediamond];\n"); StringBuffer hasaBuf = new StringBuffer(); for (int i = 0; i < children.length; i++) { @@ -150,7 +150,7 @@ childType = "n/a"; // should not happen I guess hasaBuf.append (" | {" + childType + "|" + childName + "}"); } - buf.append ("\t" + dummyName + " [shape=record, label=\"HAS[A]"); + buf.append ("\t" + quoteIt (dummyName) + " [shape=record, label=\"HAS[A]"); buf.append (hasaBuf); buf.append ("\"];\n"); } @@ -187,9 +187,9 @@ String[] parents = type.getParentNames(); for (int i = 0; i < parents.length; i++) { buf.append ("\t"); - buf.append (trName (Utils.pureName (parents[i])).toLowerCase()); + buf.append (quoteIt (trName (Utils.pureName (parents[i])).toLowerCase())); buf.append (" -> "); - buf.append (trName (name).toLowerCase()); + buf.append (quoteIt (trName (name).toLowerCase())); buf.append (";\n"); } } @@ -219,4 +219,16 @@ return name.replace ('-', '_'); } + /************************************************************************* + * Surround given text by quotes. This will prevent errors + * encoutered by 'dot' when names have whitespaces or when they + * are identical to the 'dot's keywords (such as 'edge'). + * + * @param name to be quoted + * @return changed 'name' + *************************************************************************/ + public static String quoteIt (String name) { + return "\"" + name + "\""; + } + } From senger at pub.open-bio.org Fri Sep 24 19:52:56 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:56 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJquf9032137@pub.open-bio.org> senger Fri Sep 24 15:52:56 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared In directory pub.open-bio.org:/tmp/cvs-serv32055/src/main/org/biomoby/shared Modified Files: Central.java Log Message: signatureURL was missing in service response object moby-live/Java/src/main/org/biomoby/shared Central.java,1.6,1.7 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/23 10:20:29 1.6 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/Central.java 2004/09/24 19:52:56 1.7 @@ -381,5 +381,6 @@ // http://biomoby.org/RESOURCES/MOBY-S/Services // http://biomoby.org/RESOURCES/MOBY-S/Namespaces // http://biomoby.org/RESOURCES/MOBY-S/ServiceInstances +// http://biomoby.org/RESOURCES/MOBY-S/FULL } From senger at pub.open-bio.org Fri Sep 24 19:52:55 2004 From: senger at pub.open-bio.org (senger@ebi.ac.uk) Date: Fri, 24 Sep 2004 15:52:55 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409241952.i8OJqt8S032074@pub.open-bio.org> senger Fri Sep 24 15:52:55 EDT 2004 Update of /home/repository/moby/moby-live/Java/docs In directory pub.open-bio.org:/tmp/cvs-serv32055/docs Modified Files: ChangeLog Log Message: signatureURL was missing in service response object moby-live/Java/docs ChangeLog,1.19,1.20 =================================================================== RCS file: /home/repository/moby/moby-live/Java/docs/ChangeLog,v retrieving revision 1.19 retrieving revision 1.20 diff -u -r1.19 -r1.20 --- /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/23 10:20:29 1.19 +++ /home/repository/moby/moby-live/Java/docs/ChangeLog 2004/09/24 19:52:55 1.20 @@ -1,3 +1,7 @@ +2004-09-24 Martin Senger + + * Fixed signatureURL in service response object. + 2004-09-23 Martin Senger * Moved constants ISA, HAS, HASA from MobyRelationship to Central From kawas at pub.open-bio.org Mon Sep 27 20:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPQa019481@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIP3o019502@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/development Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIP4h019445@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui added to the repository moby-live/Java/src/main/org/biomoby/client/gui - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPR2019463@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPCb019520@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/general Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:25 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:25 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIPO0019539@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/media Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQo0019584@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/table Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQsK019606@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/text Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQqn019624@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/serviceTypeCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQhh019647@pub.open-bio.org> kawas Mon Sep 27 16:18:26 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/util Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util added to the repository moby-live/Java/src/main/org/biomoby/client/util - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:26 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:26 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIQ9d019557@pub.open-bio.org> kawas Mon Sep 27 16:18:25 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv19421/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation added to the repository moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 20:18:37 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIbV7019697@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/general Added Files: Remove24.gif Save16.gif SaveAs24.gif AlignTop16.gif Refresh24.gif TipOfTheDay24.gif Paste24.gif PageSetup24.gif Export24.gif Import24.gif AlignBottom16.gif Stop24.gif FindAgain16.gif Stop16.gif ZoomIn16.gif AlignRight16.gif SaveAll24.gif Delete16.gif Zoom24.gif SaveAll16.gif Properties24.gif SendMail24.gif Paste16.gif Refresh16.gif Open16.gif Cut24.gif PrintPreview16.gif ComposeMail16.gif History16.gif About24.gif Edit24.gif SaveAs16.gif AlignCenter24.gif Search16.gif AlignTop24.gif AlignJustifyHorizontal24.gif Information24.gif Copy16.gif Help16.gif ZoomOut16.gif PageSetup16.gif AlignJustifyVertical24.gif Import16.gif AlignRight24.gif Redo16.gif Save24.gif Add16.gif AlignJustifyVertical16.gif Cut16.gif Find24.gif Remove16.gif Properties16.gif Undo16.gif TipOfTheDay16.gif History24.gif ZoomIn24.gif AlignJustifyHorizontal16.gif About16.gif Undo24.gif ContextualHelp24.gif Export16.gif Print24.gif Redo24.gif SendMail16.gif Add24.gif ComposeMail24.gif ZoomOut24.gif Replace16.gif Help24.gif Delete24.gif Edit16.gif New24.gif Preferences16.gif Zoom16.gif Find16.gif AlignCenter16.gif New16.gif AlignBottom24.gif Copy24.gif AlignLeft16.gif Information16.gif Bookmarks24.gif Preferences24.gif ContextualHelp16.gif Open24.gif FindAgain24.gif Bookmarks16.gif PrintPreview24.gif Replace24.gif AlignLeft24.gif Print16.gif Search24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/general Remove24.gif,NONE,1.1 Save16.gif,NONE,1.1 SaveAs24.gif,NONE,1.1 AlignTop16.gif,NONE,1.1 Refresh24.gif,NONE,1.1 TipOfTheDay24.gif,NONE,1.1 Paste24.gif,NONE,1.1 PageSetup24.gif,NONE,1.1 Export24.gif,NONE,1.1 Import24.gif,NONE,1.1 AlignBottom16.gif,NONE,1.1 Stop24.gif,NONE,1.1 FindAgain16.gif,NONE,1.1 Stop16.gif,NONE,1.1 ZoomIn16.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 SaveAll24.gif,NONE,1.1 Delete16.gif,NONE,1.1 Zoom24.gif,NONE,1.1 SaveAll16.gif,NONE,1.1 Properties24.gif,NONE,1.1 SendMail24.gif,NONE,1.1 Paste16.gif,NONE,1.1 Refresh16.gif,NONE,1.1 Open16.gif,NONE,1.1 Cut24.gif,NONE,1.1 PrintPreview16.gif,NONE,1.1 ComposeMail16.gif,NONE,1.1 History16.gif,NONE,1.1 About24.gif,NONE,1.1 Edit24.gif,NONE,1.1 SaveAs16.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 Search16.gif,NONE,1.1 AlignTop24.gif,NONE,1.1 AlignJustifyHorizontal24.gif,NONE,1.1 Information24.gif,NONE,1.1 Copy16.gif,NONE,1.1 Help16.gif,NONE,1.1 ! ZoomOut16.gif,NONE,1.1 PageSetup16.gif,NONE,1.1 AlignJustifyVertical24.gif,NONE,1.1 Import16.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Redo16.gif,NONE,1.1 Save24.gif,NONE,1.1 Add16.gif,NONE,1.1 AlignJustifyVertical16.gif,NONE,1.1 Cut16.gif,NONE,1.1 Find24.gif,NONE,1.1 Remove16.gif,NONE,1.1 Properties16.gif,NONE,1.1 Undo16.gif,NONE,1.1 TipOfTheDay16.gif,NONE,1.1 History24.gif,NONE,1.1 ZoomIn24.gif,NONE,1.1 AlignJustifyHorizontal16.gif,NONE,1.1 About16.gif,NONE,1.1 Undo24.gif,NONE,1.1 ContextualHelp24.gif,NONE,1.1 Export16.gif,NONE,1.1 Print24.gif,NONE,1.1 Redo24.gif,NONE,1.1 SendMail16.gif,NONE,1.1 Add24.gif,NONE,1.1 ComposeMail24.gif,NONE,1.1 ZoomOut24.gif,NONE,1.1 Replace16.gif,NONE,1.1 Help24.gif,NONE,1.1 Delete24.gif,NONE,1.1 Edit16.gif,NONE,1.1 New24.gif,NONE,1.1 Preferences16.gif,NONE,1.1 Zoom16.gif,NONE,1.1 Find16.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 New16.gif,NONE,1.1 AlignBottom24.gif,NONE,1.1 Copy24.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Information16.gif,NONE,1.1 Bo! okmarks24.gif,NONE,1.1 Preferences24.gif,NONE,1.1 ContextualH! elp16.gif,NONE,1.1 Open24.gif,NONE,1.1 FindAgain24.gif,NONE,1.1 Bookmarks16.gif,NONE,1.1 PrintPreview24.gif,NONE,1.1 Replace24.gif,NONE,1.1 AlignLeft24.gif,NONE,1.1 Print16.gif,NONE,1.1 Search24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcvj019800@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Added Files: Back24.gif Back16.gif Down16.gif Home24.gif Up24.gif Forward16.gif Up16.gif Home16.gif Forward24.gif Down24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/navigation Back24.gif,NONE,1.1 Back16.gif,NONE,1.1 Down16.gif,NONE,1.1 Home24.gif,NONE,1.1 Up24.gif,NONE,1.1 Forward16.gif,NONE,1.1 Up16.gif,NONE,1.1 Home16.gif,NONE,1.1 Forward24.gif,NONE,1.1 Down24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIc6e019818@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img Added Files: LICENSE moby_small.gif middle.gif java.gif MOBY-S.jpeg left.gif bio.gif moby1.gif moby.gif right.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img LICENSE,NONE,1.1 moby_small.gif,NONE,1.1 middle.gif,NONE,1.1 java.gif,NONE,1.1 MOBY-S.jpeg,NONE,1.1 left.gif,NONE,1.1 bio.gif,NONE,1.1 moby1.gif,NONE,1.1 moby.gif,NONE,1.1 right.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcS2019782@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/table Added Files: ColumnInsertAfter16.gif RowInsertAfter24.gif RowInsertBefore16.gif RowDelete16.gif RowDelete24.gif RowInsertAfter16.gif ColumnInsertAfter24.gif ColumnDelete16.gif ColumnInsertBefore16.gif RowInsertBefore24.gif ColumnInsertBefore24.gif ColumnDelete24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/table ColumnInsertAfter16.gif,NONE,1.1 RowInsertAfter24.gif,NONE,1.1 RowInsertBefore16.gif,NONE,1.1 RowDelete16.gif,NONE,1.1 RowDelete24.gif,NONE,1.1 RowInsertAfter16.gif,NONE,1.1 ColumnInsertAfter24.gif,NONE,1.1 ColumnDelete16.gif,NONE,1.1 ColumnInsertBefore16.gif,NONE,1.1 RowInsertBefore24.gif,NONE,1.1 ColumnInsertBefore24.gif,NONE,1.1 ColumnDelete24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcsS019834@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/text Added Files: AlignLeft24.gif AlignCenter16.gif Underline16.gif AlignLeft16.gif Normal16.gif Bold24.gif AlignRight24.gif Normal24.gif Italic24.gif Underline24.gif AlignRight16.gif Italic16.gif AlignCenter24.gif AlignJustify16.gif AlignJustify24.gif Bold16.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/text AlignLeft24.gif,NONE,1.1 AlignCenter16.gif,NONE,1.1 Underline16.gif,NONE,1.1 AlignLeft16.gif,NONE,1.1 Normal16.gif,NONE,1.1 Bold24.gif,NONE,1.1 AlignRight24.gif,NONE,1.1 Normal24.gif,NONE,1.1 Italic24.gif,NONE,1.1 Underline24.gif,NONE,1.1 AlignRight16.gif,NONE,1.1 Italic16.gif,NONE,1.1 AlignCenter24.gif,NONE,1.1 AlignJustify16.gif,NONE,1.1 AlignJustify24.gif,NONE,1.1 Bold16.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcru019764@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/serviceTypeCreationTool Added Files: ServiceTypeApplet.java README Household.java Construct.java MobyTree.java Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,NONE,1.1 README,NONE,1.1 Household.java,NONE,1.1 Construct.java,NONE,1.1 MobyTree.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIct2019729@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/development Added Files: JarAdd24.gif War16.gif EnterpriseJavaBeanJar16.gif WebComponentAdd16.gif WebComponent24.gif Host24.gif J2EEApplicationClient16.gif EnterpriseJavaBean24.gif J2EEServer16.gif Server16.gif J2EEApplicationClientAdd16.gif J2EEApplication24.gif War24.gif ApplicationDeploy16.gif Host16.gif Application16.gif J2EEApplication16.gif J2EEServer24.gif ApplicationDeploy24.gif Server24.gif BeanAdd24.gif Bean24.gif Jar24.gif Applet24.gif Jar16.gif BeanAdd16.gif WebComponent16.gif EnterpriseJavaBean16.gif Bean16.gif Applet16.gif Application24.gif J2EEApplicationClientAdd24.gif J2EEApplicationClient24.gif WarAdd24.gif WarAdd16.gif EnterpriseJavaBeanJar24.gif JarAdd16.gif WebComponentAdd24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/development JarAdd24.gif,NONE,1.1 War16.gif,NONE,1.1 EnterpriseJavaBeanJar16.gif,NONE,1.1 WebComponentAdd16.gif,NONE,1.1 WebComponent24.gif,NONE,1.1 Host24.gif,NONE,1.1 J2EEApplicationClient16.gif,NONE,1.1 EnterpriseJavaBean24.gif,NONE,1.1 J2EEServer16.gif,NONE,1.1 Server16.gif,NONE,1.1 J2EEApplicationClientAdd16.gif,NONE,1.1 J2EEApplication24.gif,NONE,1.1 War24.gif,NONE,1.1 ApplicationDeploy16.gif,NONE,1.1 Host16.gif,NONE,1.1 Application16.gif,NONE,1.1 J2EEApplication16.gif,NONE,1.1 J2EEServer24.gif,NONE,1.1 ApplicationDeploy24.gif,NONE,1.1 Server24.gif,NONE,1.1 BeanAdd24.gif,NONE,1.1 Bean24.gif,NONE,1.1 Jar24.gif,NONE,1.1 Applet24.gif,NONE,1.1 Jar16.gif,NONE,1.1 BeanAdd16.gif,NONE,1.1 WebComponent16.gif,NONE,1.1 EnterpriseJavaBean16.gif,NONE,1.1 Bean16.gif,NONE,1.1 Applet16.gif,NONE,1.1 Application24.gif,NONE,1.1 J2EEApplicationClientAdd24.gif,NONE,1.1 J2EEApplicationClient24.gif,NONE,1.1 WarAdd24.gif! ,NONE,1.1 WarAdd16.gif,NONE,1.1 EnterpriseJavaBeanJar24.gif,NONE,1.1 JarAdd16.gif,NONE,1.1 WebComponentAdd24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:38 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:38 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIcg6019746@pub.open-bio.org> kawas Mon Sep 27 16:18:38 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/util Added Files: TreeLoaderThread.java REGEXP.java Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/util TreeLoaderThread.java,NONE,1.1 REGEXP.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 20:18:37 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 16:18:37 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272018.i8RKIbgL019712@pub.open-bio.org> kawas Mon Sep 27 16:18:37 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media In directory pub.open-bio.org:/tmp/cvs-serv19676/org/biomoby/client/gui/img/toolbarButtonGraphics/media Added Files: Play16.gif StepForward16.gif Movie16.gif StepBack24.gif Rewind16.gif Volume24.gif Stop16.gif Pause16.gif Play24.gif Volume16.gif FastForward24.gif FastForward16.gif StepForward24.gif Pause24.gif StepBack16.gif Rewind24.gif Stop24.gif Movie24.gif Log Message: ServiceTypeBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/img/toolbarButtonGraphics/media Play16.gif,NONE,1.1 StepForward16.gif,NONE,1.1 Movie16.gif,NONE,1.1 StepBack24.gif,NONE,1.1 Rewind16.gif,NONE,1.1 Volume24.gif,NONE,1.1 Stop16.gif,NONE,1.1 Pause16.gif,NONE,1.1 Play24.gif,NONE,1.1 Volume16.gif,NONE,1.1 FastForward24.gif,NONE,1.1 FastForward16.gif,NONE,1.1 StepForward24.gif,NONE,1.1 Pause24.gif,NONE,1.1 StepBack16.gif,NONE,1.1 Rewind24.gif,NONE,1.1 Stop24.gif,NONE,1.1 Movie24.gif,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 21:02:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:02:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272102.i8RL26T2020147@pub.open-bio.org> kawas Mon Sep 27 17:02:06 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20123/org/biomoby/client/gui/util Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util added to the repository moby-live/Java/src/main/org/biomoby/client/gui/util - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 21:02:09 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:02:09 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272102.i8RL29Ak020181@pub.open-bio.org> kawas Mon Sep 27 17:02:09 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20160/org/biomoby/client/gui/util Added Files: REGEXP.java TreeLoaderThread.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,NONE,1.1 TreeLoaderThread.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 21:06:17 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:06:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272106.i8RL6HA6020232@pub.open-bio.org> kawas Mon Sep 27 17:06:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20203/org/biomoby/client/gui/util Modified Files: REGEXP.java TreeLoaderThread.java Log Message: fixed some imports and ensured that code is in the gui package moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.1,1.2 TreeLoaderThread.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:02:09 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:06:17 1.2 @@ -1,4 +1,4 @@ -package org.biomoby.client.util; +package org.biomoby.client.gui.util; import java.util.regex.Matcher; import java.util.regex.Pattern; =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:02:09 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:06:17 1.2 @@ -1,4 +1,4 @@ -package org.biomoby.client.util; +package org.biomoby.client.gui.util; import javax.swing.SwingUtilities; /** From kawas at pub.open-bio.org Mon Sep 27 21:06:17 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:06:17 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272106.i8RL6HGO020251@pub.open-bio.org> kawas Mon Sep 27 17:06:17 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20203/org/biomoby/client/gui/serviceTypeCreationTool Modified Files: ServiceTypeApplet.java Log Message: fixed some imports and ensured that code is in the gui package moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool ServiceTypeApplet.java,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 20:18:38 1.1 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceTypeCreationTool/ServiceTypeApplet.java 2004/09/27 21:06:17 1.2 @@ -26,8 +26,8 @@ import javax.swing.tree.TreePath; import org.biomoby.client.CentralImpl; -import org.biomoby.client.util.REGEXP; -import org.biomoby.client.util.TreeLoaderThread; +import org.biomoby.client.gui.util.REGEXP; +import org.biomoby.client.gui.util.TreeLoaderThread; import org.biomoby.shared.Central; import org.biomoby.shared.MobyException; import org.biomoby.shared.MobyServiceType; From kawas at pub.open-bio.org Mon Sep 27 21:26:54 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:26:54 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272126.i8RLQsHn020435@pub.open-bio.org> kawas Mon Sep 27 17:26:54 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20410/org/biomoby/client/gui/util Modified Files: REGEXP.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util REGEXP.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/REGEXP.java 2004/09/27 21:26:54 1.3 @@ -5,62 +5,56 @@ /** * - * @author Edward Kawas - *

- * This class provides the methods necessary to validate email - * addresses, - *

- * URLs, and URIs. + * @author Eddie Kawas + *

Created for the Biomoby Project + *

This class was created to provide the necessary methods to validate email addresses + *

URLs, and URIs. + *

For questions, comments, or bugs + *

email me at edward.kawas at gmail.com */ - public class REGEXP { - /* - * regular expressions used for validation. - */ - private final static String EMAIL = "(^[\\w]+\\+?\\w*(\\.[\\w]+)*@[\\w]{2,}\\.[\\w]{2,}(\\.[\\w]{2,})*$)"; - - private final static String URI = - //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; - //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per - // rfc 2396 appendix a. - "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; - - private final static String URL = "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; - - /** - * - * @param address - - * the string to validate. - * @return true is address is a valid email address, false otherwise. - */ - public static boolean isValidEmailAddress(String address) { - Pattern p = Pattern.compile(EMAIL); - Matcher m = p.matcher(address); - return m.matches(); - } - - /** - * - * @param uri - - * the string to validate. - * @return true if the uri is a valid uri, false otherwise. - */ - public static boolean isValidURI(String uri) { - Pattern p = Pattern.compile(URI); - Matcher m = p.matcher(uri); - return m.matches(); - } - - /** - * - * @param url - - * the string to validate. - * @return true if url is a valid URL, false otherwise. - */ - public static boolean isValidURL(String url) { - Pattern p = Pattern.compile(URL); - Matcher m = p.matcher(url); - return m.matches(); - } + /* + * regular expressions used for validation. + */ + private final static String EMAIL = "(^[\\w]+\\+?\\w*(\\.[\\w]+)*@[\\w]{2,}\\.[\\w]{2,}(\\.[\\w]{2,})*$)"; + private final static String URI = + //"(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|www\\.|http:\\/\\/|HTTP:\\/\\/)?[\\w]+\\.[\\w].*\\w$)"; + //"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?"; // as per rfc 2396 appendix a. + "^([\\w]+\\.[\\w]+(\\.[\\w]+)*)$"; + private final static String URL = + "(^(http:\\/\\/www\\.|HTTP:\\/\\/www\\.|http:\\/\\/|HTTP:\\/\\/)[\\w]+\\.[\\w].*(\\/\\w+(\\.{1}\\w+)*)$)"; + + /** + * + * @param address - the string to validate. + * @return true is address is a valid email address, false otherwise. + */ + public static boolean isValidEmailAddress(String address) { + Pattern p = Pattern.compile(EMAIL); + Matcher m = p.matcher(address); + return m.matches(); + } + + /** + * + * @param uri - the string to validate. + * @return true if the uri is a valid uri, false otherwise. + */ + public static boolean isValidURI(String uri) { + Pattern p = Pattern.compile(URI); + Matcher m = p.matcher(uri); + return m.matches(); + } + + /** + * + * @param url - the string to validate. + * @return true if url is a valid URL, false otherwise. + */ + public static boolean isValidURL(String url) { + Pattern p = Pattern.compile(URL); + Matcher m = p.matcher(url); + return m.matches(); + } } \ No newline at end of file From kawas at pub.open-bio.org Mon Sep 27 21:27:04 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:27:04 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272127.i8RLR4J3020465@pub.open-bio.org> kawas Mon Sep 27 17:27:04 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util In directory pub.open-bio.org:/tmp/cvs-serv20440/org/biomoby/client/gui/util Modified Files: TreeLoaderThread.java Log Message: moby-live/Java/src/main/org/biomoby/client/gui/util TreeLoaderThread.java,1.2,1.3 =================================================================== RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:06:17 1.2 +++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/util/TreeLoaderThread.java 2004/09/27 21:27:04 1.3 @@ -2,17 +2,14 @@ import javax.swing.SwingUtilities; /** - * This is the 3rd version of SwingWorker (also known as - * SwingWorker 3), an abstract class that you subclass to - * perform GUI-related work in a dedicated thread. For - * instructions on and examples of using this class, see: - * - * http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html - * - * Note that the API changed slightly in the 3rd version: - * You must now invoke start() on the SwingWorker after - * creating it. + * @author Sun Micro Systems + *

This class was created to provide an abstract class that you subclass to + *

perform GUI-related work in a dedicated thread. + * @see http://java.sun.com/docs/books/tutorial/uiswing/misc/threads.html + *

For questions, comments, or bugs + *

email me at edward.kawas at gmail.com */ + public abstract class TreeLoaderThread { private Object value; // see getValue(), setValue() From kawas at pub.open-bio.org Mon Sep 27 21:29:08 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:29:08 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLT8YU020499@pub.open-bio.org> kawas Mon Sep 27 17:29:08 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20475/org/biomoby/client/gui/serviceInstanceCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 21:29:15 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:29:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLTFxU020541@pub.open-bio.org> kawas Mon Sep 27 17:29:15 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool In directory pub.open-bio.org:/tmp/cvs-serv20520/org/biomoby/client/gui/serviceInstanceCreationTool Added Files: MobyCollection.java MobyUtilities.java NamespaceListener.java Construct.java NamespaceTree.java Pair.java MobyTree.java README Household.java TreeListener.java HelpActionListener.java ServiceCreationTool.java InputOutputActionListener.java ServiceInstancePanelFactory.java Service.java ButtonBeautifier.java ServiceActionListener.java InputOutputFocusListener.java MobyInputOutputData.java ServiceFocusListener.java ServiceTypeTree.java Log Message: ServiceInstanceBuilder initial commit moby-live/Java/src/main/org/biomoby/client/gui/serviceInstanceCreationTool MobyCollection.java,NONE,1.1 MobyUtilities.java,NONE,1.1 NamespaceListener.java,NONE,1.1 Construct.java,NONE,1.1 NamespaceTree.java,NONE,1.1 Pair.java,NONE,1.1 MobyTree.java,NONE,1.1 README,NONE,1.1 Household.java,NONE,1.1 TreeListener.java,NONE,1.1 HelpActionListener.java,NONE,1.1 ServiceCreationTool.java,NONE,1.1 InputOutputActionListener.java,NONE,1.1 ServiceInstancePanelFactory.java,NONE,1.1 Service.java,NONE,1.1 ButtonBeautifier.java,NONE,1.1 ServiceActionListener.java,NONE,1.1 InputOutputFocusListener.java,NONE,1.1 MobyInputOutputData.java,NONE,1.1 ServiceFocusListener.java,NONE,1.1 ServiceTypeTree.java,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 21:29:15 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 17:29:15 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272129.i8RLTFwG020556@pub.open-bio.org> kawas Mon Sep 27 17:29:15 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main In directory pub.open-bio.org:/tmp/cvs-serv20520 Added Files: .cvsignore Log Message: ServiceInstanceBuilder initial commit moby-live/Java/src/main .cvsignore,NONE,1.1 From kawas at pub.open-bio.org Mon Sep 27 22:07:12 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 18:07:12 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272207.i8RM7Ctp021120@pub.open-bio.org> kawas Mon Sep 27 18:07:12 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util In directory pub.open-bio.org:/tmp/cvs-serv21097 Removed Files: REGEXP.java TreeLoaderThread.java Log Message: no message moby-live/Java/src/main/org/biomoby/client/util REGEXP.java,1.1,NONE TreeLoaderThread.java,1.1,NONE rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/REGEXP.java,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/util/RCS/TreeLoaderThread.java,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 22:10:06 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 18:10:06 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272210.i8RMA6nZ021205@pub.open-bio.org> kawas Mon Sep 27 18:10:06 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv21181/org/biomoby/client/gui/objectCreationTool Log Message: Directory /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool added to the repository moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool - New directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/-,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/New,v: No such file or directory rcsdiff: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool/RCS/directory,v: No such file or directory From kawas at pub.open-bio.org Mon Sep 27 22:15:13 2004 From: kawas at pub.open-bio.org (Eddie Kawas) Date: Mon, 27 Sep 2004 18:15:13 -0400 Subject: [MOBY-guts] biomoby commit Message-ID: <200409272215.i8RMFDkX021327@pub.open-bio.org> kawas Mon Sep 27 18:15:13 EDT 2004 Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool In directory pub.open-bio.org:/tmp/cvs-serv21306/org/biomoby/client/gui/objectCreationTool Added Files: ButtonBeautifier.java MobyUtilities.java TreeListener.java MobyUserPanel.java Construct.java FieldFocusListeners.java FieldKeyListener.java Pair.java MobyXML.java ButtonActions.java PanelFactory.java MobyTree.java Household.java Registration.java ObjectCreationTool.java MobyPlainText.java Log Message: ObjectCreationTool initial commit moby-live/Java/src/main/org/biomoby/client/gui/objectCreationTool ButtonBeautifier.java,NONE,1.1 MobyUtilities.java,NONE,1.1 TreeListener.java,NONE,1.1 MobyUserPanel.java,NONE,1.1 Construct.java,NONE,1.1 FieldFocusListeners.java,NONE,1.1 FieldKeyListener.java,NONE,1.1 Pair.java,NONE,1.1 MobyXML.java,NONE,1.1 ButtonActions.java,NONE,1.1 PanelFactory.java,NONE,1.1 MobyTree.java,NONE,1.1 Household.java,NONE,1.1 Registration.java,NONE,1.1 ObjectCreationTool.java,NONE,1.1 MobyPlainText.java,NONE,1.1