[MOBY-guts] biomoby commit
Paul Gordon
gordonp at dev.open-bio.org
Fri Jun 8 14:04:27 UTC 2007
gordonp
Fri Jun 8 10:04:27 EDT 2007
Update of /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util
In directory dev.open-bio.org:/tmp/cvs-serv28675/src/main/ca/ucalgary/seahawk/util
Modified Files:
HTMLUtils.java MobyUtils.java
Added Files:
DataRecorder.java MobyDataTransferable.java RegistryCache.java
SeahawkOptions.java
Log Message:
Commit of Seahawk 1.0 updates and associated core updates
moby-live/Java/src/main/ca/ucalgary/seahawk/util DataRecorder.java,NONE,1.1 MobyDataTransferable.java,NONE,1.1 RegistryCache.java,NONE,1.1 SeahawkOptions.java,NONE,1.1 HTMLUtils.java,1.2,1.3 MobyUtils.java,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/HTMLUtils.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/HTMLUtils.java 2007/04/26 15:15:45 1.2
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/HTMLUtils.java 2007/06/08 14:04:27 1.3
@@ -180,21 +180,25 @@
org.w3c.dom.Element data = db.parse(new ByteArrayInputStream(xmltext.getBytes())).getDocumentElement();
if(data.getLocalName().equals(MobyTags.MOBY)){
- content = MobyDataUtils.fromXMLDocument(data);
+ content = MobyDataUtils.fromXMLDocument(data, SeahawkOptions.getRegistry());
}
else if(data.getLocalName().equals(MobyTags.MOBYCONTENT)){
- content = new MobyContentInstance(data);
+ content = new MobyContentInstance(data, SeahawkOptions.getRegistry());
}
else if(data.getLocalName().equals(MobyTags.MOBYDATA)){
content = new MobyContentInstance();
- content.parseDataGroup(data);
+ content.parseDataGroup(data, SeahawkOptions.getRegistry());
}
else{
// Any other data can be processed by the base object class
- content = new MobyContentInstance(MobyDataObject.createInstanceFromDOM(data), "Drag 'n' Drop data");
+ content = new MobyContentInstance(MobyDataObject.createInstanceFromDOM(data, SeahawkOptions.getRegistry()),
+ "Drag 'n' Drop data");
}
} catch(Exception e){
e.printStackTrace();
+ System.err.println("This issue may be related to your choice of registry ("+
+ (SeahawkOptions.getRegistry() == null ? "MOBY default" : SeahawkOptions.getRegistry().getSynonym())
+ +")");
}
return content;
}
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyUtils.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyUtils.java 2007/04/18 15:55:18 1.6
+++ /home/repository/moby/moby-live/Java/src/main/ca/ucalgary/seahawk/util/MobyUtils.java 2007/06/08 14:04:27 1.7
@@ -4,10 +4,12 @@
import ca.ucalgary.seahawk.gui.MobyServicesGUI;
import ca.ucalgary.seahawk.services.MobyClient;
+import org.biomoby.registry.meta.Registry;
import org.biomoby.shared.data.*;
import org.biomoby.shared.MobyDataType;
import org.biomoby.shared.MobyNamespace;
+import java.awt.datatransfer.Transferable;
import java.io.ByteArrayOutputStream;
import java.io.InputStream;
import java.net.URL;
@@ -24,6 +26,10 @@
private static MobyContentGUI mobyContentGUI = null;
private static MobyServicesGUI mobyServicesGUI = null;
+
+ public static Transferable createTransferable(MobyContentInstance contents){
+ return null;
+ }
/**
* The purpose of this method is to create a MOBY document to encapsulate
@@ -47,20 +53,22 @@
// Find MOBY Objects in it
MobyDataObject[] foundObjects = client.getMobyObjects(bytes.toByteArray(),
- MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE));
+ MobyDataType.getDataType(MobyDataBytes.BASE64_DATATYPE,
+ SeahawkOptions.getRegistry()));
// Did we unambiguously find one binary object?
if(foundObjects != null && foundObjects.length == 1){
MobyContentInstance mci = new MobyContentInstance();
String[] dataName = url.getPath().split("/");
MobyDataJob job = new MobyDataJob();
job.put(dataName[dataName.length-1], foundObjects[0]);
+ System.err.println("Namespace of found object was " + foundObjects[0].getPrimaryNamespace().getName());
mci.put(dataName[dataName.length-1], job); // name the data by the last part of the URL path
return mci;
}
return null;
}
- public static MobyDataInstance[] convertStringToObjects(String data, boolean reverseSelected){
+ public static MobyDataInstance[] convertStringToObjects(String data){
if(data == null){
return new MobyDataInstance[0];
}
@@ -74,23 +82,13 @@
}
// Can always use the data as a string
- MobyDataString strObject = new MobyDataString(objectName, data);
+ MobyDataString strObject = new MobyDataString(objectName, data, SeahawkOptions.getRegistry());
strObject.setPrimaryNamespace(new MobyNamespace("seahawk"));
objects.add(strObject);
// See if it's sequence
MobyDataComposite mdc = createMobySequence(data, "user-selection");
if(mdc != null){
- // reverse complement DNA if necessary
- if(reverseSelected &&
- (mdc.getDataType() == MobyDataType.getDataType("DNASequence") ||
- mdc.getDataType() == MobyDataType.getDataType("RNASequence"))){
-
- MobyDataComposite nucObject = (MobyDataComposite) mdc;
- MobyDataString seq = (MobyDataString) nucObject.get("SequenceString");
- seq.setValue(Sequence.reverseComplement(seq.toString()));
- }
-
mdc.setName(objectName);
objects.add(mdc);
}
@@ -99,8 +97,9 @@
if(data.trim().matches("^[A-Za-z0-9_-]{3,35}$")){
objects.add(new MobyDataComposite("Global_Keyword",
"dummy_name",
- "seahawk",
- data.trim()));
+ "unknown",
+ data.trim(),
+ SeahawkOptions.getRegistry()));
}
}
@@ -163,19 +162,22 @@
sequence = new MobyDataComposite("DNASequence",
"dummy_name",
"seahawk",
- id);
+ id,
+ SeahawkOptions.getRegistry());
}
else if(Sequence.isRNA(sequenceData)){
sequence = new MobyDataComposite("RNASequence",
"dummy_name",
"seahawk",
- id);
+ id,
+ SeahawkOptions.getRegistry());
}
else if(Sequence.isProtein(sequenceData)){
sequence = new MobyDataComposite("AminoAcidSequence",
"dummy_name",
"seahawk",
- id);
+ id,
+ SeahawkOptions.getRegistry());
}
// Not a recognized type of sequence
else{
@@ -183,8 +185,8 @@
}
sequenceData = sequenceData.replaceAll("[ \t\r\n0-9]", ""); // strip whitespace and possible milestone digits
- sequence.put("SequenceString", new MobyDataString(sequenceData));
- sequence.put("Length", new MobyDataInt(sequenceData.length()));
+ sequence.put("SequenceString", new MobyDataString(sequenceData, SeahawkOptions.getRegistry()));
+ sequence.put("Length", new MobyDataInt(sequenceData.length(), SeahawkOptions.getRegistry()));
return sequence;
}
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