[Treebase-guts] SF.net SVN: treebase:[941] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixConverter.java

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

Revision: 941
          http://treebase.svn.sourceforge.net/treebase/?rev=941&view=rev
Author:   rvos
Date:     2011-08-25 13:59:02 +0000 (Thu, 25 Aug 2011)
Log Message:
-----------
Actually, in order to be valid xsi:type subclasses, they should spell out all possible states for dna/rna/protein, not just the ones we've seen in the database

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	2011-08-25 13:57:44 UTC (rev 940)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2011-08-25 13:59:02 UTC (rev 941)
@@ -229,8 +229,7 @@
 		// attach base uri
 		xmlMatrix.setBaseURI(mMatrixBaseURI);
 		
-		// lookup the equivalent state in tb and attach identifiers, only keep those in matrix
-		Set<CharacterState> seenStates = new HashSet<CharacterState>();
+		// lookup the equivalent state in tb and attach identifiers
 		for(StateSet tbStateSet : tbMatrix.getStateSets() ) {
 			for (DiscreteCharState tbState : tbStateSet.getStates() ) {
 				String tbSymbol = tbState.getSymbol().toString().toUpperCase();
@@ -239,10 +238,8 @@
 					xmlState = xmlStateSet.createCharacterState(tbSymbol);
 				}
 				attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
-				seenStates.add(xmlState);
 			}
 		}
-		xmlStateSet.setCharacterStates(seenStates);
 		
 		// create columns and attach identifiers
 		for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {

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