[Treebase-guts] SF.net SVN: treebase:[1026] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixWriter.java

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

Revision: 1026
          http://treebase.svn.sourceforge.net/treebase/?rev=1026&view=rev
Author:   rvos
Date:     2012-01-31 21:23:29 +0000 (Tue, 31 Jan 2012)
Log Message:
-----------
Apparently, missing and gap state sets aren't considered states that a DicreteMatrix would return in its set of sets. We will just have to hardcode them in.

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

Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java	2012-01-31 21:10:45 UTC (rev 1025)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java	2012-01-31 21:23:29 UTC (rev 1026)
@@ -82,31 +82,24 @@
 		
 		// then create the single state set out of the map, assigning all non-missing characters to missing
 		Set<CharacterState> xmlMissingStates = new HashSet<CharacterState>();
-		UncertainCharacterState missing = null;
 		for ( Character symbol : stateForSymbol.keySet() ) {
-			char sym = symbol.charValue();
-			CharacterState xmlState = null;
-			String symString = symbol.toString();
-			if ( sym == '-' ) {
-				xmlState = xmlStateSet.createUncertainCharacterState(symString, new HashSet<CharacterState>());
+			char sym = symbol.charValue();			
+			if ( sym != '-' && sym != '?' ) {
+				String symString = symbol.toString();
+				CharacterState xmlState = xmlStateSet.createCharacterState(symString);
 				xmlMissingStates.add(xmlState);
-			}
-			else if ( sym == '?' ) {
-				xmlState = xmlStateSet.createUncertainCharacterState(symString, new HashSet<CharacterState>());
-				missing = (UncertainCharacterState) xmlState;
-			}
-			else {
-				xmlState = xmlStateSet.createCharacterState(symString);
-				xmlMissingStates.add(xmlState);
+				DiscreteCharState tbState = stateForSymbol.get(symbol);
+				xmlState.setLabel(symString);
+				attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);				
 			}				
-			DiscreteCharState tbState = stateForSymbol.get(symbol);
-			xmlState.setLabel(symString);
-			attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
 		}
-		if ( null != missing ) {
-			missing.setStates(xmlMissingStates);
-		}
 		
+		UncertainCharacterState gap = xmlStateSet.createUncertainCharacterState("-", new HashSet<CharacterState>());
+		gap.setLabel("-");
+		xmlMissingStates.add(gap);
+		UncertainCharacterState missing = xmlStateSet.createUncertainCharacterState("?", xmlMissingStates);
+		missing.setLabel("?");
+		
 		// then create the XML characters, assigning them all the same state set
 		List<MatrixColumn> tbColumns = tbMatrix.getColumnsReadOnly();
 		for ( int i = 0; i < tbColumns.size(); i++ ) {

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