From kawas at dev.open-bio.org  Thu Aug  5 10:50:31 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 10:50:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051450.o75EoVIP015362@dev.open-bio.org>


kawas
Thu Aug  5 10:50:31 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv15327/src/main/org/biomoby/shared/test

Modified Files:
	MobyNamespaceTestCase.java 
Log Message:
updated the test registry
moby-live/Java/src/main/org/biomoby/shared/test MobyNamespaceTestCase.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/MobyNamespaceTestCase.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/test/MobyNamespaceTestCase.java	2008/07/16 20:34:54	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/MobyNamespaceTestCase.java	2010/08/05 14:50:31	1.2
@@ -11,8 +11,8 @@
 
     private final static String BIOMOBY_NAMESPACE_VALID = "NCBI_gi";
     private final static String BIOMOBY_NAMESPACE_INVALID = "ThisNamespaceShouldntExistInMobyCentral";
-    private final static String BIOMOBY_TEST_REGISTRY_URL = "http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl";
-    private final static String BIOMOBY_TEST_REGISTRY_NS = "http://bioinfo.icapture.ubc.ca/MOBY/Central";
+    private final static String BIOMOBY_TEST_REGISTRY_URL = "http://mobytest.biordf.net/MOBY-Central.pl";
+    private final static String BIOMOBY_TEST_REGISTRY_NS = "http://mobytest.biordf.net/MOBY/Central";
 
     public MobyNamespaceTestCase(String name){
 	super(name);


From kawas at dev.open-bio.org  Thu Aug  5 10:53:58 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 10:53:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051453.o75Erw2G015426@dev.open-bio.org>


kawas
Thu Aug  5 10:53:58 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv15391/src/main/org/biomoby/client

Modified Files:
	CentralDigestCachedSimpleImpl.java 
Log Message:

moby-live/Java/src/main/org/biomoby/client CentralDigestCachedSimpleImpl.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.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/client/CentralDigestCachedSimpleImpl.java	2009/08/13 21:26:26	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.java	2010/08/05 14:53:58	1.6
@@ -324,7 +324,6 @@
 	    fileout =
 		new PrintWriter (new BufferedOutputStream (new FileOutputStream (outputFile)));
 	    fileout.write (data);
-	    fileout.close();
 	} catch (IOException e) {
 	    throw new MobyException ("Cannot write to '" + outputFile.getAbsolutePath() + ". " + e.toString());
 	} finally {
@@ -363,13 +362,12 @@
 
 	} catch (Throwable e) {     // be prepare for "out-of-memory" error
 	    throw new MobyException ("Serious error when reading from cache. " + e.toString());
-
 	} finally {
-	    if (in != null)
-		try {
-		    in.close();
-		} catch (IOException e) {}
-	}
+            try {
+                if (in != null)
+                    in.close();
+            } catch (IOException e) {}
+        }
     }
 
     /**************************************************************************


From kawas at dev.open-bio.org  Thu Aug  5 12:01:54 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 12:01:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051601.o75G1sUn016542@dev.open-bio.org>


kawas
Thu Aug  5 12:01:53 EDT 2010
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv16511/xmls

Added Files:
	tavernaBuild.xml 
Log Message:
build file for the biomoby plugin. excludes the branch ca/* because taverna is meant to be used with java 1.5
moby-live/Java/xmls tavernaBuild.xml,NONE,1.1

From kawas at dev.open-bio.org  Thu Aug  5 12:02:31 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 12:02:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051602.o75G2Vw6016585@dev.open-bio.org>


kawas
Thu Aug  5 12:02:31 EDT 2010
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv16550

Modified Files:
	build.xml 
Log Message:
added tavernaBuild.xml to the build file
moby-live/Java build.xml,1.84,1.85
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -r1.84 -r1.85
--- /home/repository/moby/moby-live/Java/build.xml	2010/01/09 16:10:29	1.84
+++ /home/repository/moby/moby-live/Java/build.xml	2010/08/05 16:02:31	1.85
@@ -16,6 +16,7 @@
   <!ENTITY mobysyncBuild  SYSTEM "xmls/mobysyncBuild.xml">
   <!ENTITY featureClientBuild  SYSTEM "xmls/featureClientBuild.xml">
   <!ENTITY inbMoby  SYSTEM "xmls/inbMoby.xml">
+  <!ENTITY tavernaBuild  SYSTEM "xmls/tavernaBuild.xml">
 ]>
 
 <!-- =================== Build for jMoby =================== -->
@@ -158,6 +159,7 @@
   &mobysyncBuild;   <!-- MobySync targets -->
   &featureClientBuild; <!-- Featureclient targets -->
   &inbMoby; <!-- INB jMOBY code -->
+  &tavernaBuild; <!-- jmoby for taverna plugin -->
   
   <!-- ================================================================== -->
   <!--                            Maven                                   -->


From drepchevski at dev.open-bio.org  Tue Aug 31 11:22:47 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 11:22:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311522.o7VFMlkB027500@dev.open-bio.org>


drepchevski
Tue Aug 31 11:22:47 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/model
In directory dev.open-bio.org:/tmp/cvs-serv27447/model

Modified Files:
	DatatypesModel.java 
Log Message:
minor visual fix in MobyGenerator
moby-live/Java/src/main/org/inb/biomoby/central/model DatatypesModel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/model/DatatypesModel.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/inb/biomoby/central/model/DatatypesModel.java	2009/12/16 15:24:36	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/model/DatatypesModel.java	2010/08/31 15:22:46	1.2
@@ -135,7 +135,7 @@
         throw new UnsupportedOperationException("Not supported yet.");
     }
 
-    private void stop()
+    private synchronized void stop()
     {
         if (thread != null)
         {


From drepchevski at dev.open-bio.org  Tue Aug 31 11:22:46 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 11:22:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311522.o7VFMkcV027482@dev.open-bio.org>


drepchevski
Tue Aug 31 11:22:46 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui
In directory dev.open-bio.org:/tmp/cvs-serv27447/gui

Modified Files:
	AbstractEntityTreePanel.java 
Log Message:
minor visual fix in MobyGenerator
moby-live/Java/src/main/org/inb/biomoby/central/gui AbstractEntityTreePanel.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/AbstractEntityTreePanel.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/inb/biomoby/central/gui/AbstractEntityTreePanel.java	2010/05/27 12:17:58	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/AbstractEntityTreePanel.java	2010/08/31 15:22:46	1.3
@@ -10,8 +10,6 @@
 
 package org.inb.biomoby.central.gui;
 
-import java.awt.Component;
-import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.Point;
 import java.awt.image.BufferedImage;
@@ -22,10 +20,11 @@
 import javax.swing.ToolTipManager;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
+import javax.swing.event.TreeModelEvent;
+import javax.swing.event.TreeModelListener;
 import javax.swing.tree.DefaultMutableTreeNode;
 import javax.swing.tree.TreePath;
 import org.inb.biomoby.central.MobyCentral;
-import org.inb.biomoby.central.model.MobyCentralModel;
 import org.inb.biomoby.central.model.ModelListener;
 import org.inb.biomoby.central.gui.renderer.EntityTreeCellRenderer;
 import org.inb.swing.DecoratedJScrollPane;
@@ -38,7 +37,7 @@
  */
 
 public abstract class AbstractEntityTreePanel extends JLayeredPane
-        implements ChangeListener, ModelListener<MobyCentral>
+        implements TreeModelListener, ChangeListener, ModelListener<MobyCentral>
 {
     protected final JTree tree;
     protected final JPanel control;
@@ -64,7 +63,7 @@
         add(scroll, JLayeredPane.DEFAULT_LAYER);
         add(control, JLayeredPane.PALETTE_LAYER);
 
-        MobyCentralModel.instance().addListener(this);
+        tree.getModel().addTreeModelListener(this);
     }
 
     protected void setBackgroundImage(BufferedImage logo)
@@ -117,30 +116,26 @@
         control.setBounds(Math.max(3, width - bPaneSize.width - 3), Math.max(3, 3), bPaneSize.width, bPaneSize.height);
     }
 
-    private void setEnabled(Container parent, boolean isEnabled)
-    {
-        parent.setEnabled(isEnabled);
+    public void treeNodesChanged(TreeModelEvent e) {}
+    public void treeNodesRemoved(TreeModelEvent e) {}
 
-        for (Component child : parent.getComponents())
+    public void treeNodesInserted(TreeModelEvent e)
+    {
+        if (!tree.isExpanded(0))
         {
-            if (child instanceof Container)
-            {
-                setEnabled((Container)child,isEnabled);
-            }
-            else
-            {
-                child.setEnabled(isEnabled);
-            }
+            tree.expandRow(0);
         }
     }
 
-    @Override
-    public void modelCleared()
-    {   
-        MobyCentral central = MobyCentralModel.instance().getSelectedCentral();
-        setEnabled(this, central != null);
+    public void treeStructureChanged(TreeModelEvent e)
+    {
+        if (!tree.isExpanded(0))
+        {
+            tree.expandRow(0);
+        }
     }
 
+    @Override public void modelCleared() {}
     @Override public void modelObjectInserted(MobyCentral central) {}
     @Override public void modelObjectRemoved(MobyCentral central) {}
     @Override public void modelObjectChanged(MobyCentral central1, MobyCentral central2) {}


From drepchevski at dev.open-bio.org  Tue Aug 31 11:23:00 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 11:23:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311523.o7VFN0TA027568@dev.open-bio.org>


drepchevski
Tue Aug 31 11:23:00 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/model
In directory dev.open-bio.org:/tmp/cvs-serv27533/model

Modified Files:
	DataTypesTreeModel.java 
Log Message:
minor visual fix in MobyGenerator
moby-live/Java/src/main/org/inb/biomoby/central/gui/model DataTypesTreeModel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/model/DataTypesTreeModel.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/inb/biomoby/central/gui/model/DataTypesTreeModel.java	2009/12/17 11:40:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/model/DataTypesTreeModel.java	2010/08/31 15:23:00	1.2
@@ -36,7 +36,8 @@
 
     public DataTypesTreeModel()
     {
-        super(new DefaultMutableTreeNode(new ObjectType("Object")));
+        //super(new DefaultMutableTreeNode(new ObjectType("Object")));
+        super(new DefaultMutableTreeNode());
 
         orphans = new LinkedList<ObjectType>();
     }
@@ -274,12 +275,12 @@
         String name = element.getName();
 
         DefaultMutableTreeNode raiz = getRoot();
-        ObjectType object = (ObjectType)raiz.getUserObject();
-
-        if (name.equals(object.getName()))
-        {
-            return raiz;
-        }
+//        ObjectType object = (ObjectType)raiz.getUserObject();
+//
+//        if (name.equals(object.getName()))
+//        {
+//            return raiz;
+//        }
 
         Enumeration nodes = raiz.depthFirstEnumeration();
 
@@ -289,7 +290,7 @@
 
             ObjectType objectType = (ObjectType)node.getUserObject();
 
-            if (name.equals(objectType.getName()))
+            if (objectType != null && name.equals(objectType.getName()))
             {
                 return node;
             }
@@ -320,6 +321,15 @@
             return new ObjectType("Object");
         }
 
+        DefaultMutableTreeNode raiz = getRoot();
+        
+        if (raiz.getUserObject() == null)
+        {
+            raiz.setUserObject(element);
+
+            checkOrphans(raiz);
+        }
+
         return null;
     }
 


From drepchevski at dev.open-bio.org  Tue Aug 31 12:15:44 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 12:15:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311615.o7VGFiih028391@dev.open-bio.org>


drepchevski
Tue Aug 31 12:15:44 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby
In directory dev.open-bio.org:/tmp/cvs-serv28356/biomoby

Modified Files:
	MobyMessageContext.java 
Log Message:

moby-live/Java/src/main/org/inb/biomoby MobyMessageContext.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/MobyMessageContext.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/inb/biomoby/MobyMessageContext.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/MobyMessageContext.java	2010/08/31 16:15:44	1.2
@@ -35,7 +35,13 @@
     private static JAXBIntrospector introspector;
     
     private MobyMessageContext() {}
-    
+
+    /**
+     * Method that returns a cached JAXB context for BioMoby elements
+     *
+     * @return - a JAXB context
+     * @throws JAXBException
+     */
     public static synchronized JAXBContext getContext() throws JAXBException
     {
         if (jc == null)
@@ -46,6 +52,13 @@
         return jc;
     }
 
+    /**
+     * An utility method that returns a BioMoby "name" of a given BioMOby Object.
+     *
+     * @param mobyObject - an object we get a name for (for instance MobyString)
+     * @return - BioMoby name for a given BioMoby object
+     * @throws JAXBException - if the object was not found in a JAXBContext
+     */
     public static synchronized String getMobyName(AbstractMobyObject mobyObject) throws JAXBException
     {
         if (mobyObject instanceof AnyMobyObject)
@@ -69,6 +82,14 @@
         return name.getLocalPart();
     }
 
+    /**
+     * An utility method that encode a JAXB object into an XML string
+     *
+     * @param message - BioMoby element to be encoded
+     * @return - an XML string representation of given BioMOby element
+     *
+     * @throws JAXBException - when privided object is not known to a JAXBContext
+     */
     public static String marshall(Object message) throws JAXBException
     {
         if (message == null)


From drepchevski at dev.open-bio.org  Tue Aug 31 12:15:44 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 12:15:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311615.o7VGFiBm028413@dev.open-bio.org>


drepchevski
Tue Aug 31 12:15:44 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv28356/biomoby/client

Modified Files:
	MobyDispatch.java 
Log Message:

moby-live/Java/src/main/org/inb/biomoby/client MobyDispatch.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.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/inb/biomoby/client/MobyDispatch.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java	2010/08/31 16:15:44	1.2
@@ -76,7 +76,7 @@
     
     private final String user;
     private final String password;
-    
+
     public MobyDispatch(org.inb.biomoby.shared.registry.Service mobyService)
     {
         this(mobyService, null, null);
@@ -97,7 +97,7 @@
     }
 
     /**
-     * Method to synchronously invoke BioMoby service (provided in constructor)
+     * Method to synchronously invoke BioMoby service (provided in the constructor)
      *
      * @param message - message to be sent.
      * @return message sent by the service.
@@ -153,8 +153,7 @@
         
         if (user != null)
         {
-            //dispatch.getRequestContext().put(Context.SECURITY_AUTHENTICATION, "none");
-
+//            dispatch.getRequestContext().put(Context.SECURITY_AUTHENTICATION, "none");
 //            dispatch.getRequestContext().put(BindingProvider.USERNAME_PROPERTY, "pepino");
 //            dispatch.getRequestContext().put(BindingProvider.PASSWORD_PROPERTY, "password");
         }
@@ -219,7 +218,7 @@
 
         dispatch.getRequestContext().put(BindingProvider.SOAPACTION_USE_PROPERTY, Boolean.TRUE); //use SOAPAction!
         dispatch.getRequestContext().put(BindingProvider.SOAPACTION_URI_PROPERTY, service.getServiceName().getNamespaceURI() + '#' + mobyService.getName() + "_submit");
-        
+
         SOAPMessage responseMessage = dispatch.invoke(request);
 
         JAXBContext ctx = MobyMessageContext.getContext();
@@ -265,9 +264,8 @@
         sElement.setEncodingStyle("http://schemas.xmlsoap.org/soap/encoding/");
 
         SOAPElement aElement = sElement.addChildElement("arg0", "nsl");
-        
-        aElement.addNamespaceDeclaration("soapenc", "http://schemas.xmlsoap.org/soap/encoding/");
-        aElement.setAttribute("xsi:type", "soapenc:string");
+
+        aElement.setAttribute("xsi:type", "xsd:string");
 
         if (object != null)
         {


From drepchevski at dev.open-bio.org  Tue Aug 31 12:15:45 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 12:15:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311615.o7VGFjeK028439@dev.open-bio.org>


drepchevski
Tue Aug 31 12:15:45 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui
In directory dev.open-bio.org:/tmp/cvs-serv28356/biomoby/generator/gui

Modified Files:
	AbstractServiceModelPanel.java DatatypesGeneratorPanel.java 
Log Message:

moby-live/Java/src/main/org/inb/biomoby/generator/gui AbstractServiceModelPanel.java,1.1,1.2 DatatypesGeneratorPanel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/AbstractServiceModelPanel.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/inb/biomoby/generator/gui/AbstractServiceModelPanel.java	2009/12/17 14:06:03	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/AbstractServiceModelPanel.java	2010/08/31 16:15:44	1.2
@@ -19,6 +19,7 @@
 import javax.swing.ImageIcon;
 import javax.swing.JFileChooser;
 import javax.swing.SwingWorker;
+import javax.swing.event.TreeModelEvent;
 import javax.swing.event.TreeSelectionEvent;
 import javax.swing.event.TreeSelectionListener;
 import javax.swing.tree.TreePath;
@@ -26,7 +27,6 @@
 import org.inb.biomoby.central.model.MobyCentralModel;
 import org.inb.biomoby.central.model.ServicesModel;
 import org.inb.biomoby.central.gui.AbstractMobyServicesTreePanel;
-import org.inb.biomoby.central.gui.renderer.EntityTreeCellRenderer;
 import org.inb.biomoby.shared.registry.Service;
 import org.inb.swing.ImageLoader;
 import org.inb.swing.LabelButton;
@@ -45,7 +45,6 @@
 
     public AbstractServiceModelPanel()
     {
-        tree.setCellRenderer(new EntityTreeCellRenderer());
         tree.addTreeSelectionListener(this);
 
         reloadButton = new LabelButton(new ImageIcon(ImageLoader.read("images/reload.png")));
@@ -120,6 +119,42 @@
     }
 
     @Override
+    public void treeNodesInserted(TreeModelEvent e)
+    {
+        super.treeNodesInserted(e);
+
+        if (!reloadButton.isEnabled())
+        {
+           reloadButton.setEnabled(true);
+        }
+    }
+
+    @Override
+    public void treeNodesRemoved(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (reloadButton != null &&
+            generateButton != null &&
+            tree.getRowCount() < 1)
+        {
+            reloadButton.setEnabled(false);
+            generateButton.setEnabled(false);
+        }
+    }
+
+    @Override
+    public void treeStructureChanged(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (reloadButton != null && reloadButton.isEnabled() != (tree.getRowCount() > 0))
+        {
+            reloadButton.setEnabled(!reloadButton.isEnabled());
+        }
+    }
+
+    @Override
     public void propertyChange(PropertyChangeEvent evt)
     {
         Object value = evt.getNewValue();

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/DatatypesGeneratorPanel.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/inb/biomoby/generator/gui/DatatypesGeneratorPanel.java	2009/12/17 14:06:03	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/DatatypesGeneratorPanel.java	2010/08/31 16:15:44	1.2
@@ -19,6 +19,7 @@
 import javax.swing.ImageIcon;
 import javax.swing.JFileChooser;
 import javax.swing.SwingWorker;
+import javax.swing.event.TreeModelEvent;
 import javax.swing.filechooser.FileNameExtensionFilter;
 import org.inb.biomoby.central.model.DatatypesModel;
 import org.inb.biomoby.central.gui.AbstractMobyDatatypesTreePanel;
@@ -124,6 +125,45 @@
     }
 
     @Override
+    public void treeNodesInserted(TreeModelEvent e)
+    {
+        super.treeNodesInserted(e);
+
+        if (!reloadButton.isEnabled())
+        {
+           reloadButton.setEnabled(true);
+        }
+
+        if (!generateButton.isEnabled())
+        {
+           generateButton.setEnabled(true);
+        }
+    }
+
+    @Override
+    public void treeNodesRemoved(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (tree.getRowCount() < 1)
+        {
+            reloadButton.setEnabled(false);
+            generateButton.setEnabled(false);
+        }
+    }
+
+    @Override
+    public void treeStructureChanged(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (reloadButton.isEnabled() != (tree.getRowCount() > 0))
+        {
+            reloadButton.setEnabled(!reloadButton.isEnabled());
+        }
+    }
+
+    @Override
     public void propertyChange(PropertyChangeEvent evt)
     {
         Object value = evt.getNewValue();


From kawas at dev.open-bio.org  Thu Aug  5 14:50:31 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 10:50:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051450.o75EoVIP015362@dev.open-bio.org>


kawas
Thu Aug  5 10:50:31 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test
In directory dev.open-bio.org:/tmp/cvs-serv15327/src/main/org/biomoby/shared/test

Modified Files:
	MobyNamespaceTestCase.java 
Log Message:
updated the test registry
moby-live/Java/src/main/org/biomoby/shared/test MobyNamespaceTestCase.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/MobyNamespaceTestCase.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/test/MobyNamespaceTestCase.java	2008/07/16 20:34:54	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/shared/test/MobyNamespaceTestCase.java	2010/08/05 14:50:31	1.2
@@ -11,8 +11,8 @@
 
     private final static String BIOMOBY_NAMESPACE_VALID = "NCBI_gi";
     private final static String BIOMOBY_NAMESPACE_INVALID = "ThisNamespaceShouldntExistInMobyCentral";
-    private final static String BIOMOBY_TEST_REGISTRY_URL = "http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl";
-    private final static String BIOMOBY_TEST_REGISTRY_NS = "http://bioinfo.icapture.ubc.ca/MOBY/Central";
+    private final static String BIOMOBY_TEST_REGISTRY_URL = "http://mobytest.biordf.net/MOBY-Central.pl";
+    private final static String BIOMOBY_TEST_REGISTRY_NS = "http://mobytest.biordf.net/MOBY/Central";
 
     public MobyNamespaceTestCase(String name){
 	super(name);



From kawas at dev.open-bio.org  Thu Aug  5 14:53:58 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 10:53:58 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051453.o75Erw2G015426@dev.open-bio.org>


kawas
Thu Aug  5 10:53:58 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv15391/src/main/org/biomoby/client

Modified Files:
	CentralDigestCachedSimpleImpl.java 
Log Message:

moby-live/Java/src/main/org/biomoby/client CentralDigestCachedSimpleImpl.java,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.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/client/CentralDigestCachedSimpleImpl.java	2009/08/13 21:26:26	1.5
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/client/CentralDigestCachedSimpleImpl.java	2010/08/05 14:53:58	1.6
@@ -324,7 +324,6 @@
 	    fileout =
 		new PrintWriter (new BufferedOutputStream (new FileOutputStream (outputFile)));
 	    fileout.write (data);
-	    fileout.close();
 	} catch (IOException e) {
 	    throw new MobyException ("Cannot write to '" + outputFile.getAbsolutePath() + ". " + e.toString());
 	} finally {
@@ -363,13 +362,12 @@
 
 	} catch (Throwable e) {     // be prepare for "out-of-memory" error
 	    throw new MobyException ("Serious error when reading from cache. " + e.toString());
-
 	} finally {
-	    if (in != null)
-		try {
-		    in.close();
-		} catch (IOException e) {}
-	}
+            try {
+                if (in != null)
+                    in.close();
+            } catch (IOException e) {}
+        }
     }
 
     /**************************************************************************



From kawas at dev.open-bio.org  Thu Aug  5 16:01:54 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 12:01:54 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051601.o75G1sUn016542@dev.open-bio.org>


kawas
Thu Aug  5 12:01:53 EDT 2010
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv16511/xmls

Added Files:
	tavernaBuild.xml 
Log Message:
build file for the biomoby plugin. excludes the branch ca/* because taverna is meant to be used with java 1.5
moby-live/Java/xmls tavernaBuild.xml,NONE,1.1


From kawas at dev.open-bio.org  Thu Aug  5 16:02:31 2010
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 5 Aug 2010 12:02:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008051602.o75G2Vw6016585@dev.open-bio.org>


kawas
Thu Aug  5 12:02:31 EDT 2010
Update of /home/repository/moby/moby-live/Java
In directory dev.open-bio.org:/tmp/cvs-serv16550

Modified Files:
	build.xml 
Log Message:
added tavernaBuild.xml to the build file
moby-live/Java build.xml,1.84,1.85
===================================================================
RCS file: /home/repository/moby/moby-live/Java/build.xml,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -r1.84 -r1.85
--- /home/repository/moby/moby-live/Java/build.xml	2010/01/09 16:10:29	1.84
+++ /home/repository/moby/moby-live/Java/build.xml	2010/08/05 16:02:31	1.85
@@ -16,6 +16,7 @@
   <!ENTITY mobysyncBuild  SYSTEM "xmls/mobysyncBuild.xml">
   <!ENTITY featureClientBuild  SYSTEM "xmls/featureClientBuild.xml">
   <!ENTITY inbMoby  SYSTEM "xmls/inbMoby.xml">
+  <!ENTITY tavernaBuild  SYSTEM "xmls/tavernaBuild.xml">
 ]>
 
 <!-- =================== Build for jMoby =================== -->
@@ -158,6 +159,7 @@
   &mobysyncBuild;   <!-- MobySync targets -->
   &featureClientBuild; <!-- Featureclient targets -->
   &inbMoby; <!-- INB jMOBY code -->
+  &tavernaBuild; <!-- jmoby for taverna plugin -->
   
   <!-- ================================================================== -->
   <!--                            Maven                                   -->



From drepchevski at dev.open-bio.org  Tue Aug 31 15:22:47 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 11:22:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311522.o7VFMlkB027500@dev.open-bio.org>


drepchevski
Tue Aug 31 11:22:47 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/model
In directory dev.open-bio.org:/tmp/cvs-serv27447/model

Modified Files:
	DatatypesModel.java 
Log Message:
minor visual fix in MobyGenerator
moby-live/Java/src/main/org/inb/biomoby/central/model DatatypesModel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/model/DatatypesModel.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/inb/biomoby/central/model/DatatypesModel.java	2009/12/16 15:24:36	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/model/DatatypesModel.java	2010/08/31 15:22:46	1.2
@@ -135,7 +135,7 @@
         throw new UnsupportedOperationException("Not supported yet.");
     }
 
-    private void stop()
+    private synchronized void stop()
     {
         if (thread != null)
         {



From drepchevski at dev.open-bio.org  Tue Aug 31 15:22:46 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 11:22:46 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311522.o7VFMkcV027482@dev.open-bio.org>


drepchevski
Tue Aug 31 11:22:46 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui
In directory dev.open-bio.org:/tmp/cvs-serv27447/gui

Modified Files:
	AbstractEntityTreePanel.java 
Log Message:
minor visual fix in MobyGenerator
moby-live/Java/src/main/org/inb/biomoby/central/gui AbstractEntityTreePanel.java,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/AbstractEntityTreePanel.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/inb/biomoby/central/gui/AbstractEntityTreePanel.java	2010/05/27 12:17:58	1.2
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/AbstractEntityTreePanel.java	2010/08/31 15:22:46	1.3
@@ -10,8 +10,6 @@
 
 package org.inb.biomoby.central.gui;
 
-import java.awt.Component;
-import java.awt.Container;
 import java.awt.Dimension;
 import java.awt.Point;
 import java.awt.image.BufferedImage;
@@ -22,10 +20,11 @@
 import javax.swing.ToolTipManager;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
+import javax.swing.event.TreeModelEvent;
+import javax.swing.event.TreeModelListener;
 import javax.swing.tree.DefaultMutableTreeNode;
 import javax.swing.tree.TreePath;
 import org.inb.biomoby.central.MobyCentral;
-import org.inb.biomoby.central.model.MobyCentralModel;
 import org.inb.biomoby.central.model.ModelListener;
 import org.inb.biomoby.central.gui.renderer.EntityTreeCellRenderer;
 import org.inb.swing.DecoratedJScrollPane;
@@ -38,7 +37,7 @@
  */
 
 public abstract class AbstractEntityTreePanel extends JLayeredPane
-        implements ChangeListener, ModelListener<MobyCentral>
+        implements TreeModelListener, ChangeListener, ModelListener<MobyCentral>
 {
     protected final JTree tree;
     protected final JPanel control;
@@ -64,7 +63,7 @@
         add(scroll, JLayeredPane.DEFAULT_LAYER);
         add(control, JLayeredPane.PALETTE_LAYER);
 
-        MobyCentralModel.instance().addListener(this);
+        tree.getModel().addTreeModelListener(this);
     }
 
     protected void setBackgroundImage(BufferedImage logo)
@@ -117,30 +116,26 @@
         control.setBounds(Math.max(3, width - bPaneSize.width - 3), Math.max(3, 3), bPaneSize.width, bPaneSize.height);
     }
 
-    private void setEnabled(Container parent, boolean isEnabled)
-    {
-        parent.setEnabled(isEnabled);
+    public void treeNodesChanged(TreeModelEvent e) {}
+    public void treeNodesRemoved(TreeModelEvent e) {}
 
-        for (Component child : parent.getComponents())
+    public void treeNodesInserted(TreeModelEvent e)
+    {
+        if (!tree.isExpanded(0))
         {
-            if (child instanceof Container)
-            {
-                setEnabled((Container)child,isEnabled);
-            }
-            else
-            {
-                child.setEnabled(isEnabled);
-            }
+            tree.expandRow(0);
         }
     }
 
-    @Override
-    public void modelCleared()
-    {   
-        MobyCentral central = MobyCentralModel.instance().getSelectedCentral();
-        setEnabled(this, central != null);
+    public void treeStructureChanged(TreeModelEvent e)
+    {
+        if (!tree.isExpanded(0))
+        {
+            tree.expandRow(0);
+        }
     }
 
+    @Override public void modelCleared() {}
     @Override public void modelObjectInserted(MobyCentral central) {}
     @Override public void modelObjectRemoved(MobyCentral central) {}
     @Override public void modelObjectChanged(MobyCentral central1, MobyCentral central2) {}



From drepchevski at dev.open-bio.org  Tue Aug 31 15:23:00 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 11:23:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311523.o7VFN0TA027568@dev.open-bio.org>


drepchevski
Tue Aug 31 11:23:00 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/model
In directory dev.open-bio.org:/tmp/cvs-serv27533/model

Modified Files:
	DataTypesTreeModel.java 
Log Message:
minor visual fix in MobyGenerator
moby-live/Java/src/main/org/inb/biomoby/central/gui/model DataTypesTreeModel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/model/DataTypesTreeModel.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/inb/biomoby/central/gui/model/DataTypesTreeModel.java	2009/12/17 11:40:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/central/gui/model/DataTypesTreeModel.java	2010/08/31 15:23:00	1.2
@@ -36,7 +36,8 @@
 
     public DataTypesTreeModel()
     {
-        super(new DefaultMutableTreeNode(new ObjectType("Object")));
+        //super(new DefaultMutableTreeNode(new ObjectType("Object")));
+        super(new DefaultMutableTreeNode());
 
         orphans = new LinkedList<ObjectType>();
     }
@@ -274,12 +275,12 @@
         String name = element.getName();
 
         DefaultMutableTreeNode raiz = getRoot();
-        ObjectType object = (ObjectType)raiz.getUserObject();
-
-        if (name.equals(object.getName()))
-        {
-            return raiz;
-        }
+//        ObjectType object = (ObjectType)raiz.getUserObject();
+//
+//        if (name.equals(object.getName()))
+//        {
+//            return raiz;
+//        }
 
         Enumeration nodes = raiz.depthFirstEnumeration();
 
@@ -289,7 +290,7 @@
 
             ObjectType objectType = (ObjectType)node.getUserObject();
 
-            if (name.equals(objectType.getName()))
+            if (objectType != null && name.equals(objectType.getName()))
             {
                 return node;
             }
@@ -320,6 +321,15 @@
             return new ObjectType("Object");
         }
 
+        DefaultMutableTreeNode raiz = getRoot();
+        
+        if (raiz.getUserObject() == null)
+        {
+            raiz.setUserObject(element);
+
+            checkOrphans(raiz);
+        }
+
         return null;
     }
 



From drepchevski at dev.open-bio.org  Tue Aug 31 16:15:44 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 12:15:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311615.o7VGFiih028391@dev.open-bio.org>


drepchevski
Tue Aug 31 12:15:44 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby
In directory dev.open-bio.org:/tmp/cvs-serv28356/biomoby

Modified Files:
	MobyMessageContext.java 
Log Message:

moby-live/Java/src/main/org/inb/biomoby MobyMessageContext.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/MobyMessageContext.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/inb/biomoby/MobyMessageContext.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/MobyMessageContext.java	2010/08/31 16:15:44	1.2
@@ -35,7 +35,13 @@
     private static JAXBIntrospector introspector;
     
     private MobyMessageContext() {}
-    
+
+    /**
+     * Method that returns a cached JAXB context for BioMoby elements
+     *
+     * @return - a JAXB context
+     * @throws JAXBException
+     */
     public static synchronized JAXBContext getContext() throws JAXBException
     {
         if (jc == null)
@@ -46,6 +52,13 @@
         return jc;
     }
 
+    /**
+     * An utility method that returns a BioMoby "name" of a given BioMOby Object.
+     *
+     * @param mobyObject - an object we get a name for (for instance MobyString)
+     * @return - BioMoby name for a given BioMoby object
+     * @throws JAXBException - if the object was not found in a JAXBContext
+     */
     public static synchronized String getMobyName(AbstractMobyObject mobyObject) throws JAXBException
     {
         if (mobyObject instanceof AnyMobyObject)
@@ -69,6 +82,14 @@
         return name.getLocalPart();
     }
 
+    /**
+     * An utility method that encode a JAXB object into an XML string
+     *
+     * @param message - BioMoby element to be encoded
+     * @return - an XML string representation of given BioMOby element
+     *
+     * @throws JAXBException - when privided object is not known to a JAXBContext
+     */
     public static String marshall(Object message) throws JAXBException
     {
         if (message == null)



From drepchevski at dev.open-bio.org  Tue Aug 31 16:15:44 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 12:15:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311615.o7VGFiBm028413@dev.open-bio.org>


drepchevski
Tue Aug 31 12:15:44 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client
In directory dev.open-bio.org:/tmp/cvs-serv28356/biomoby/client

Modified Files:
	MobyDispatch.java 
Log Message:

moby-live/Java/src/main/org/inb/biomoby/client MobyDispatch.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.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/inb/biomoby/client/MobyDispatch.java	2009/09/09 19:47:48	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/client/MobyDispatch.java	2010/08/31 16:15:44	1.2
@@ -76,7 +76,7 @@
     
     private final String user;
     private final String password;
-    
+
     public MobyDispatch(org.inb.biomoby.shared.registry.Service mobyService)
     {
         this(mobyService, null, null);
@@ -97,7 +97,7 @@
     }
 
     /**
-     * Method to synchronously invoke BioMoby service (provided in constructor)
+     * Method to synchronously invoke BioMoby service (provided in the constructor)
      *
      * @param message - message to be sent.
      * @return message sent by the service.
@@ -153,8 +153,7 @@
         
         if (user != null)
         {
-            //dispatch.getRequestContext().put(Context.SECURITY_AUTHENTICATION, "none");
-
+//            dispatch.getRequestContext().put(Context.SECURITY_AUTHENTICATION, "none");
 //            dispatch.getRequestContext().put(BindingProvider.USERNAME_PROPERTY, "pepino");
 //            dispatch.getRequestContext().put(BindingProvider.PASSWORD_PROPERTY, "password");
         }
@@ -219,7 +218,7 @@
 
         dispatch.getRequestContext().put(BindingProvider.SOAPACTION_USE_PROPERTY, Boolean.TRUE); //use SOAPAction!
         dispatch.getRequestContext().put(BindingProvider.SOAPACTION_URI_PROPERTY, service.getServiceName().getNamespaceURI() + '#' + mobyService.getName() + "_submit");
-        
+
         SOAPMessage responseMessage = dispatch.invoke(request);
 
         JAXBContext ctx = MobyMessageContext.getContext();
@@ -265,9 +264,8 @@
         sElement.setEncodingStyle("http://schemas.xmlsoap.org/soap/encoding/");
 
         SOAPElement aElement = sElement.addChildElement("arg0", "nsl");
-        
-        aElement.addNamespaceDeclaration("soapenc", "http://schemas.xmlsoap.org/soap/encoding/");
-        aElement.setAttribute("xsi:type", "soapenc:string");
+
+        aElement.setAttribute("xsi:type", "xsd:string");
 
         if (object != null)
         {



From drepchevski at dev.open-bio.org  Tue Aug 31 16:15:45 2010
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Tue, 31 Aug 2010 12:15:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <201008311615.o7VGFjeK028439@dev.open-bio.org>


drepchevski
Tue Aug 31 12:15:45 EDT 2010
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui
In directory dev.open-bio.org:/tmp/cvs-serv28356/biomoby/generator/gui

Modified Files:
	AbstractServiceModelPanel.java DatatypesGeneratorPanel.java 
Log Message:

moby-live/Java/src/main/org/inb/biomoby/generator/gui AbstractServiceModelPanel.java,1.1,1.2 DatatypesGeneratorPanel.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/AbstractServiceModelPanel.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/inb/biomoby/generator/gui/AbstractServiceModelPanel.java	2009/12/17 14:06:03	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/AbstractServiceModelPanel.java	2010/08/31 16:15:44	1.2
@@ -19,6 +19,7 @@
 import javax.swing.ImageIcon;
 import javax.swing.JFileChooser;
 import javax.swing.SwingWorker;
+import javax.swing.event.TreeModelEvent;
 import javax.swing.event.TreeSelectionEvent;
 import javax.swing.event.TreeSelectionListener;
 import javax.swing.tree.TreePath;
@@ -26,7 +27,6 @@
 import org.inb.biomoby.central.model.MobyCentralModel;
 import org.inb.biomoby.central.model.ServicesModel;
 import org.inb.biomoby.central.gui.AbstractMobyServicesTreePanel;
-import org.inb.biomoby.central.gui.renderer.EntityTreeCellRenderer;
 import org.inb.biomoby.shared.registry.Service;
 import org.inb.swing.ImageLoader;
 import org.inb.swing.LabelButton;
@@ -45,7 +45,6 @@
 
     public AbstractServiceModelPanel()
     {
-        tree.setCellRenderer(new EntityTreeCellRenderer());
         tree.addTreeSelectionListener(this);
 
         reloadButton = new LabelButton(new ImageIcon(ImageLoader.read("images/reload.png")));
@@ -120,6 +119,42 @@
     }
 
     @Override
+    public void treeNodesInserted(TreeModelEvent e)
+    {
+        super.treeNodesInserted(e);
+
+        if (!reloadButton.isEnabled())
+        {
+           reloadButton.setEnabled(true);
+        }
+    }
+
+    @Override
+    public void treeNodesRemoved(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (reloadButton != null &&
+            generateButton != null &&
+            tree.getRowCount() < 1)
+        {
+            reloadButton.setEnabled(false);
+            generateButton.setEnabled(false);
+        }
+    }
+
+    @Override
+    public void treeStructureChanged(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (reloadButton != null && reloadButton.isEnabled() != (tree.getRowCount() > 0))
+        {
+            reloadButton.setEnabled(!reloadButton.isEnabled());
+        }
+    }
+
+    @Override
     public void propertyChange(PropertyChangeEvent evt)
     {
         Object value = evt.getNewValue();

===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/DatatypesGeneratorPanel.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/inb/biomoby/generator/gui/DatatypesGeneratorPanel.java	2009/12/17 14:06:03	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/generator/gui/DatatypesGeneratorPanel.java	2010/08/31 16:15:44	1.2
@@ -19,6 +19,7 @@
 import javax.swing.ImageIcon;
 import javax.swing.JFileChooser;
 import javax.swing.SwingWorker;
+import javax.swing.event.TreeModelEvent;
 import javax.swing.filechooser.FileNameExtensionFilter;
 import org.inb.biomoby.central.model.DatatypesModel;
 import org.inb.biomoby.central.gui.AbstractMobyDatatypesTreePanel;
@@ -124,6 +125,45 @@
     }
 
     @Override
+    public void treeNodesInserted(TreeModelEvent e)
+    {
+        super.treeNodesInserted(e);
+
+        if (!reloadButton.isEnabled())
+        {
+           reloadButton.setEnabled(true);
+        }
+
+        if (!generateButton.isEnabled())
+        {
+           generateButton.setEnabled(true);
+        }
+    }
+
+    @Override
+    public void treeNodesRemoved(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (tree.getRowCount() < 1)
+        {
+            reloadButton.setEnabled(false);
+            generateButton.setEnabled(false);
+        }
+    }
+
+    @Override
+    public void treeStructureChanged(TreeModelEvent e)
+    {
+        super.treeStructureChanged(e);
+
+        if (reloadButton.isEnabled() != (tree.getRowCount() > 0))
+        {
+            reloadButton.setEnabled(!reloadButton.isEnabled());
+        }
+    }
+
+    @Override
     public void propertyChange(PropertyChangeEvent evt)
     {
         Object value = evt.getNewValue();