[Treebase-guts] SF.net SVN: treebase:[572] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixConverter.java

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

Revision: 572
          http://treebase.svn.sourceforge.net/treebase/?rev=572&view=rev
Author:   rvos
Date:     2010-03-15 01:06:19 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Now calls getAnnotations() to let the object decide what metadata to add. Where we add metadata here, we use the URIs from the Constants class as opposed to hardcoding them here.

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	2010-03-15 01:04:39 UTC (rev 571)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2010-03-15 01:06:19 UTC (rev 572)
@@ -4,6 +4,7 @@
 import java.util.List;
 import java.util.Set;
 
+import org.cipres.treebase.Constants;
 import org.cipres.treebase.dao.jdbc.ContinuousMatrixElementJDBC;
 import org.cipres.treebase.dao.jdbc.ContinuousMatrixJDBC;
 import org.cipres.treebase.dao.jdbc.DiscreteMatrixElementJDBC;
@@ -179,9 +180,9 @@
 				if ( null != tbState.getDescription() ) {
 					xmlState.setLabel(tbState.getDescription());
 				}	
-				if ( null != tbState.getNotes() ) {
-					((Annotatable)xmlState).addAnnotationValue("dcterms:description", mDCURI, tbState.getNotes());
-				}
+//				if ( null != tbState.getNotes() ) {
+//					((Annotatable)xmlState).addAnnotationValue("dcterms:description", Constants.DCURI, tbState.getNotes());
+//				}
 				attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
 			}			
 			org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
@@ -222,7 +223,7 @@
 			org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
 			PhyloChar tbCharacter = tbColumn.getCharacter();
 			if ( null != tbCharacter.getDescription() && ! tbCharacter.getDescription().equals(tbDataType) ) {
-				((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", mDCURI, tbCharacter.getDescription());
+				((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);
@@ -245,7 +246,7 @@
 			org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter();
 			PhyloChar tbCharacter = tbColumn.getCharacter();
 			if ( null != tbCharacter.getDescription() ) {
-				((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", mDCURI, tbCharacter.getDescription());
+				((Annotatable)xmlCharacter).addAnnotationValue("dcterms:description", Constants.DCTermsURI, tbCharacter.getDescription());
 			}			
 			attachTreeBaseID((Annotatable)xmlCharacter,tbCharacter,PhyloChar.class);			
 		}		
@@ -275,10 +276,6 @@
 		}
 		xmlMatrix.setLabel(tbMatrix.getTitle());
 		attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix,Matrix.class);
-		((Annotatable)xmlMatrix).addAnnotationValue("tb:type.matrix", mTBTermsURI, tbMatrix.getDataType().getDescription());
-		((Annotatable)xmlMatrix).addAnnotationValue("tb:ntax.matrix", mTBTermsURI, tbMatrix.getnTax());
-		((Annotatable)xmlMatrix).addAnnotationValue("tb:nchar.matrix", mTBTermsURI, tbMatrix.getnChar());
-		((Annotatable)xmlMatrix).addAnnotationValue("tb:identifier.matrix", mTBTermsURI, tbMatrix.getId());
 		return xmlMatrix;
 	}
 
@@ -310,10 +307,10 @@
 					for ( RowSegment tbSegment : tbSegments ) {
 						if ( tbSegment.getStartIndex() <= charIndex && charIndex <= tbSegment.getEndIndex() ) {
 							if ( tbSegment.getSpecimenLabel().getLatitude() != null ) {
-								((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLatitude", mDwCURI, tbSegment.getSpecimenLabel().getLatitude());
+								((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLatitude", Constants.DwCURI, tbSegment.getSpecimenLabel().getLatitude());
 							}
 							if ( tbSegment.getSpecimenLabel().getLongitude() != null ) {
-								((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLongitude", mDwCURI, tbSegment.getSpecimenLabel().getLongitude());
+								((Annotatable)xmlCell).addAnnotationValue("DwC:DecimalLongitude", Constants.DwCURI, tbSegment.getSpecimenLabel().getLongitude());
 							}
 							/*
 							if ( tbSegment.getSpecimenLabel().getGenBankAccession() != null ) {


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