[Treebase-guts] SF.net SVN: treebase:[952] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixConverter.java

[<lol...@us...>]

Revision: 952
          http://treebase.svn.sourceforge.net/treebase/?rev=952&view=rev
Author:   loloyohe
Date:     2011-09-12 07:10:22 +0000 (Mon, 12 Sep 2011)
Log Message:
-----------
Added code starting at line 388 that fixes bug #3303002, in which some studies were not printing the matrix in NeXML. I have commented out the original code with the bug in case the new code does not work for some reason. 

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	2011-09-01 18:31:45 UTC (rev 951)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2011-09-12 07:10:22 UTC (rev 952)
@@ -384,6 +384,17 @@
 			OTU xmlOTU = getOTUById(xmlOTUs, tbRow.getTaxonLabel().getId());
 			int charIndex = 0;
 			if ( characterList.size() <= MAX_GRANULAR_NCHAR && xmlOTUs.getAllOTUs().size() <= MAX_GRANULAR_NTAX ) {
+				for ( MatrixColumn tbColumn : ((CharacterMatrix)tbMatrix).getColumns() ) {
+					String seq = tbRow.buildElementAsString();
+					xmlMatrix.setSeq(seq, xmlOTU);
+					org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
+					MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);							
+		
+					attachTreeBaseID ((Annotatable) xmlCell,  tbColumn , DiscreteMatrixElement.class);
+				
+				//The following is commented out as tbRow.getElements() does not work directly and crashes the loop. 
+				//The above for loop fixes this issue. 
+				/*
 				for ( MatrixElement tbCell : tbRow.getElements() ) {
 					org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
 					MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);				
@@ -392,6 +403,8 @@
 					CharacterState xmlState = xmlCharacter.getCharacterStateSet().lookupCharacterStateBySymbol(tbSymbolString);								
 					xmlCell.setValue(xmlState);								
 					attachTreeBaseID((Annotatable)xmlCell,tbCell,DiscreteMatrixElement.class);
+				*/
+					
 					for ( RowSegment tbSegment : tbSegments ) {
 						if ( tbSegment.getStartIndex() <= charIndex && charIndex <= tbSegment.getEndIndex() ) {
 							//declare variables for row-segment annotations

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