[Treebase-guts] SF.net SVN: treebase:[785] trunk/treebase-core/src/main/java/org/cipres/ treebase/domain/nexus/nexml/NexmlMatrixConverter.java

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

Revision: 785
          http://treebase.svn.sourceforge.net/treebase/?rev=785&view=rev
Author:   rvos
Date:     2011-04-19 10:49:22 +0000 (Tue, 19 Apr 2011)

Log Message:
-----------
Now setting the xml:base attribute on each matrix to <phylowsPurl>/matrix/TB2: so that we can use TreeBASE ID strings as XML IDs instead of doing the owl:sameAs stuff to attach identifiers.

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	2011-04-14 21:09:54 UTC (rev 784)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/nexus/nexml/NexmlMatrixConverter.java	2011-04-19 10:49:22 UTC (rev 785)
@@ -171,6 +171,7 @@
 	public CategoricalMatrix fromTreeBaseToXml(StandardMatrix tbMatrix) {
 		OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
 		CategoricalMatrix xmlMatrix = getDocument().createCategoricalMatrix(xmlOTUs);
+		xmlMatrix.setBaseURI(mMatrixBaseURI);
 		List<List<DiscreteCharState>> tbStateLabels = tbMatrix.getStateLabels();
 		List<MatrixColumn> tbColumns = tbMatrix.getColumnsReadOnly();
 		for ( int i = 0; i < tbColumns.size(); i++ ) {
@@ -219,6 +220,7 @@
 			xmlMatrix = getDocument().createMolecularMatrix(xmlOTUs, MolecularMatrix.Protein);
 			xmlStateSet = ((MolecularMatrix)xmlMatrix).getProteinCharacterStateSet();
 		}
+		xmlMatrix.setBaseURI(mMatrixBaseURI);
 		for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
 			org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter(xmlStateSet);
 			PhyloChar tbCharacter = tbColumn.getCharacter();
@@ -242,6 +244,7 @@
 	public org.nexml.model.ContinuousMatrix fromTreeBaseToXml(ContinuousMatrix tbMatrix) {
 		OTUs xmlOTUs = getOTUsById(tbMatrix.getTaxa().getId());
 		org.nexml.model.ContinuousMatrix xmlMatrix = getDocument().createContinuousMatrix(xmlOTUs);
+		xmlMatrix.setBaseURI(mMatrixBaseURI);
 		for ( MatrixColumn tbColumn : tbMatrix.getColumnsReadOnly() ) {
 			org.nexml.model.Character xmlCharacter = xmlMatrix.createCharacter();
 			PhyloChar tbCharacter = tbColumn.getCharacter();


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