[Treebase-guts] SF.net SVN: treebase:[937] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixConverter.java

[<rv...@us...>]

Revision: 937
          http://treebase.svn.sourceforge.net/treebase/?rev=937&view=rev
Author:   rvos
Date:     2011-08-25 09:08:48 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
TreeBASE uses singleton PhyloChar objects for matrices (as a space-saving hack), so it is no good to use the PhyloChar.id to create PhyloWS URIs. Instead, we should use MatrixColumn identifiers.

Modified Paths:
--------------
    trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2011-08-11 19:44:41 UTC (rev 936)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2011-08-25 09:08:48 UTC (rev 937)
@@ -195,7 +195,7 @@
 			if ( null != tbCharacter.getDescription() ) {
 				xmlCharacter.setLabel(tbCharacter.getDescription());
 			}			
-			attachTreeBaseID((Annotatable)xmlCharacter,tbCharacter,PhyloChar.class);
+			attachTreeBaseID((Annotatable)xmlCharacter,tbColumns.get(i),MatrixColumn.class);
 		}		
 		return xmlMatrix;
 	}
@@ -233,10 +233,8 @@
 			}
 			if ( null != tbCharacter.getDescription() && ! tbCharacter.getDescription().equals(tbDataType) ) {
 				((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", Constants.DCTermsURI, tbCharacter.getDescription());
-			}			
-			if ( null != tbCharacter.getId() && tbCharacter.getId() != 2 ) { // XXX is PhyloChar.id 2 some sort of magic number?
-				attachTreeBaseID((Annotatable)xmlCharacter,tbCharacter,PhyloChar.class);
 			}
+			attachTreeBaseID((Annotatable)xmlCharacter,tbColumn,MatrixColumn.class);
 		}
 		return xmlMatrix;
 	}
@@ -259,7 +257,7 @@
 				xmlCharacter.setLabel(tbCharacter.getDescription());
 				((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", Constants.DCTermsURI, tbCharacter.getDescription());
 			}			
-			attachTreeBaseID((Annotatable)xmlCharacter,tbCharacter,PhyloChar.class);
+			attachTreeBaseID((Annotatable)xmlCharacter,tbColumn,MatrixColumn.class);
 			
 			//coerce the tbMatrix into a character matrix to get its character sets
 			CharacterMatrix tbCharacterMatrix = (CharacterMatrix)tbMatrix;

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