[Treebase-guts] SF.net SVN: treebase:[1036] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixWriter.java

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

Revision: 1036
          http://treebase.svn.sourceforge.net/treebase/?rev=1036&view=rev
Author:   rvos
Date:     2012-02-01 21:40:44 +0000 (Wed, 01 Feb 2012)
Log Message:
-----------
Now generates character state sequences that only contain schema-valid IUPAC single character symbols like N, not constructs like {ACGT}, for indicating uncertainty.

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	2012-02-01 21:33:34 UTC (rev 1035)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java	2012-02-01 21:40:44 UTC (rev 1036)
@@ -308,7 +308,7 @@
 			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();
+					String seq = tbRow.getNormalizedSymbolString();
 					xmlMatrix.setSeq(seq, xmlOTU);
 					org.nexml.model.Character xmlCharacter = characterList.get(charIndex);
 					MatrixCell<CharacterState> xmlCell = xmlMatrix.getCell(xmlOTU, xmlCharacter);							
@@ -428,7 +428,7 @@
 				}
 			}
 			else {
-				String seq = tbRow.buildElementAsString();
+				String seq = tbRow.getNormalizedSymbolString();
 				if ( tbMatrix.getDataType().getDescription().equals(MatrixDataType.MATRIX_DATATYPE_STANDARD) ) {
 					StringBuilder sb = new StringBuilder();
 					for ( int i = 0; i < seq.length(); i++ ) {

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