[Treebase-guts] SF.net SVN: treebase:[900] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlMatrixConverterTest.java

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

Revision: 900
          http://treebase.svn.sourceforge.net/treebase/?rev=900&view=rev
Author:   rvos
Date:     2011-06-06 14:18:19 +0000 (Mon, 06 Jun 2011)

Log Message:
-----------
This is pretty much how to convert treebase matrices to nexml ones.

Modified Paths:
--------------
    trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java

Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java	2011-06-04 03:36:27 UTC (rev 899)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java	2011-06-06 14:18:19 UTC (rev 900)
@@ -1,18 +1,20 @@
 package org.cipres.treebase.domain.nexus;
 
+import java.util.List;
+
 import junit.framework.Assert;
 
 import org.cipres.treebase.dao.AbstractDAOTest;
 import org.cipres.treebase.domain.matrix.CharacterMatrix;
-import org.cipres.treebase.domain.matrix.Matrix;
-import org.cipres.treebase.domain.matrix.StandardMatrix;
-import org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter;
 import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
-import org.cipres.treebase.domain.nexus.NexusDataSet;
 import org.cipres.treebase.domain.study.Study;
 import org.cipres.treebase.domain.taxon.TaxonLabelHome;
+import org.nexml.model.CategoricalMatrix;
+import org.nexml.model.ContinuousMatrix;
 import org.nexml.model.DocumentFactory;
 import org.nexml.model.Document;
+import org.nexml.model.Matrix;
+import org.nexml.model.MolecularMatrix;
 
 public class NexmlMatrixConverterTest extends AbstractDAOTest {
 	private TaxonLabelHome mTaxonLabelHome;
@@ -29,30 +31,26 @@
 		
 		long studyId = 1787;
 		Study study = (Study)loadObject(Study.class, studyId);
-		NexusDataSet nexusDataSet = new NexusDataSet();
 		
 		Document doc = DocumentFactory.safeCreateDocument();
 		NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),doc);
-		NexmlMatrixConverter nmc = new NexmlMatrixConverter (study,getTaxonLabelHome(),ndc.fromTreeBaseToXml(study));
-		nexusDataSet = ndc.fromXmlToTreeBase(doc);
-		nexusDataSet.setNexmlProject(doc);
-		
-		for (org.cipres.treebase.domain.matrix.Matrix matrix : nexusDataSet.getMatrices() ) {
-			if ( matrix instanceof CharacterMatrix ) {
-				//fromTreeBaseToXml(CharacterMatrix) is main method being tested here--it uses populateXmlMatrix() function
-				String xml = ((Document) nmc.fromTreeBaseToXml((CharacterMatrix)matrix)).getXmlString();
-				System.out.println(xml);
-				Assert.assertNotNull(xml);
+		Document document = ndc.fromTreeBaseToXml(study);
+		List<Matrix<?>> matrices = document.getMatrices();
+		Assert.assertTrue(matrices.size() != 0 );
+		for ( Matrix<?> matrix : matrices ) {
+			if ( matrix instanceof MolecularMatrix ) {
+				System.out.println(matrix.getId() + " is a molecular character state matrix");
 			}
+			else if ( matrix instanceof ContinuousMatrix ) {
+				System.out.println(matrix.getId() + " is a continuous-valued character matrix");
+			}
+			else if ( matrix instanceof CategoricalMatrix ) {
+				System.out.println(matrix.getId() + " is a categorical character state matrix");
+			}
 			else {
-				System.out.println("im not working");
+				System.out.println("This should not ever happen.");
 			}
 		}
-		
-		//signal that test is over
-		if (logger.isInfoEnabled()) {
-			logger.info(testName + " - end ");
-		}
 	}
 	
 	/**


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.