[Treebase-guts] SF.net SVN: treebase:[1023] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixWriter.java

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

Revision: 1023
          http://treebase.svn.sourceforge.net/treebase/?rev=1023&view=rev
Author:   rvos
Date:     2012-01-31 20:21:36 +0000 (Tue, 31 Jan 2012)
Log Message:
-----------
Re-ordered state set generation so that "missing" is populated with all other states. Also, set the assignment of the XML id before any annotations are added, this so that the about attribute is updated correctly.

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 19:53:12 UTC (rev 1022)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java	2012-01-31 20:21:36 UTC (rev 1023)
@@ -79,27 +79,23 @@
 				stateForSymbol.put(symbol, state);			
 			}
 		}
-		UncertainCharacterState missing = xmlStateSet.createUncertainCharacterState("?", new HashSet<CharacterState>());
-		UncertainCharacterState gap = xmlStateSet.createUncertainCharacterState("-", new HashSet<CharacterState>());
-		missing.getStates().add(gap);
 		
-		// then create the single state set out of the map, assigning all non-gap characters to missing
+		// then create the single state set out of the map, assigning all non-missing characters to missing
+		Set<CharacterState> xmlMissingStates = new HashSet<CharacterState>();
 		for ( Character symbol : stateForSymbol.keySet() ) {
-			CharacterState xmlState = null;
-			if ( symbol.charValue() == '?' ) {
-				xmlState = missing;
+			if ( symbol.charValue() != '?' && symbol.charValue() != '-' ) {
+				CharacterState xmlState = xmlStateSet.createCharacterState(symbol.toString());
+				DiscreteCharState tbState = stateForSymbol.get(symbol);
+				xmlState.setLabel(tbState.getLabel());
+				attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
+				xmlMissingStates.add(xmlState);
 			}
-			else if ( symbol.charValue() == '-' ) {
-				xmlState = gap;
-			}
-			else {
-				xmlState = xmlStateSet.createCharacterState(symbol.toString());
-				missing.getStates().add(xmlState);
-			}
-			DiscreteCharState tbState = stateForSymbol.get(symbol);
-			xmlState.setLabel(tbState.getLabel());
-			attachTreeBaseID((Annotatable)xmlState,tbState,DiscreteCharState.class);
-		}
+		}		
+		UncertainCharacterState gap = xmlStateSet.createUncertainCharacterState("-", new HashSet<CharacterState>());
+		xmlMissingStates.add(gap);
+		UncertainCharacterState missing = xmlStateSet.createUncertainCharacterState("?", xmlMissingStates);
+		missing.setLabel("?");
+		gap.setLabel("-");		
 		
 		// then create the XML characters, assigning them all the same state set
 		List<MatrixColumn> tbColumns = tbMatrix.getColumnsReadOnly();
@@ -120,16 +116,16 @@
 	}
 
 	private void setMatrixAttributes(org.nexml.model.Matrix<?> xmlMatrix,CharacterMatrix tbMatrix) {
-		xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");
-		xmlMatrix.setBaseURI(mMatrixBaseURI);
-		xmlMatrix.setLabel(tbMatrix.getLabel());
-		
 		// attach matrix identifiers
 		attachTreeBaseID((Annotatable)xmlMatrix, tbMatrix,Matrix.class);
 		String tb1MatrixID = tbMatrix.getTB1MatrixID();
 		if ( null != tb1MatrixID ) {
 			((Annotatable)xmlMatrix).addAnnotationValue("tb:identifier.matrix.tb1", Constants.TBTermsURI, tb1MatrixID);
 		}		
+		
+		xmlMatrix.addAnnotationValue("skos:historyNote", Constants.SKOSURI, "Mapped from TreeBASE schema using "+this.toString()+" $Rev$");
+		xmlMatrix.setBaseURI(mMatrixBaseURI);
+		xmlMatrix.setLabel(tbMatrix.getLabel());				
 	}	
 	
 	/**

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