[Treebase-guts] SF.net SVN: treebase:[1056] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixWriter.java

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

Revision: 1056
          http://treebase.svn.sourceforge.net/treebase/?rev=1056&view=rev
Author:   rvos
Date:     2012-02-05 19:24:29 +0000 (Sun, 05 Feb 2012)
Log Message:
-----------
Now attaches MatrixRow IDs to <row> elements

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	2012-02-05 15:23:09 UTC (rev 1055)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixWriter.java	2012-02-05 19:24:29 UTC (rev 1056)
@@ -353,10 +353,11 @@
 					}
 				}
 				xmlMatrix.setSeq(seq,xmlOTU);
+				org.nexml.model.MatrixRow<CharacterState> xmlRow = xmlMatrix.getRowObject(xmlOTU);
+				attachTreeBaseID(xmlRow, tbRow, MatrixRow.class);
 				
 				// this often only happens once, when the row has only 1 segment
-				for ( RowSegment tbSegment : tbSegments ) {
-					org.nexml.model.MatrixRow<CharacterState> xmlRow = xmlMatrix.getRowObject(xmlOTU);
+				for ( RowSegment tbSegment : tbSegments ) {					
 					Annotation xmlSegment = xmlRow.addAnnotationValue("tb:rowSegment", Constants.TBTermsURI, new String());
 					xmlSegment.addAnnotationValue("tb:startIndex", Constants.TBTermsURI, tbSegment.getStartIndex());
 					xmlSegment.addAnnotationValue("tb:endIndex", Constants.TBTermsURI, tbSegment.getEndIndex());
@@ -427,8 +428,9 @@
 				xmlMatrix.setSeq(seq,xmlOTU);
 			}
 			Set<RowSegment> tbSegments = tbRow.getSegmentsReadOnly();
-			for ( RowSegment tbSegment : tbSegments ) {
-				org.nexml.model.MatrixRow<Double> xmlRow = xmlMatrix.getRowObject(xmlOTU);
+			org.nexml.model.MatrixRow<Double> xmlRow = xmlMatrix.getRowObject(xmlOTU);
+			attachTreeBaseID(xmlRow, tbRow, MatrixRow.class);
+			for ( RowSegment tbSegment : tbSegments ) {				
 				Annotation xmlSegment = xmlRow.addAnnotationValue("tb:rowSegment", Constants.TBTermsURI, new String());
 				xmlSegment.addAnnotationValue("tb:startIndex", Constants.TBTermsURI, tbSegment.getStartIndex());
 				xmlSegment.addAnnotationValue("tb:endIndex", Constants.TBTermsURI, tbSegment.getEndIndex());				

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