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[Treebase-guts] SF.net SVN: treebase:[903] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlMatrixConverterTest.java
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From: <rv...@us...> - 2011-06-08 14:02:59
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Revision: 903
http://treebase.svn.sourceforge.net/treebase/?rev=903&view=rev
Author: rvos
Date: 2011-06-08 14:02:50 +0000 (Wed, 08 Jun 2011)
Log Message:
-----------
Updated this to demonstrate how char set creation should work.
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 2011-06-08 14:01:38 UTC (rev 902)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-06-08 14:02:50 UTC (rev 903)
@@ -1,11 +1,15 @@
package org.cipres.treebase.domain.nexus;
+import java.util.Collection;
import java.util.List;
+import java.util.Set;
import junit.framework.Assert;
import org.cipres.treebase.dao.AbstractDAOTest;
+import org.cipres.treebase.domain.matrix.CharSet;
import org.cipres.treebase.domain.matrix.CharacterMatrix;
+import org.cipres.treebase.domain.matrix.ColumnRange;
import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -15,6 +19,7 @@
import org.nexml.model.Document;
import org.nexml.model.Matrix;
import org.nexml.model.MolecularMatrix;
+import org.nexml.model.Subset;
public class NexmlMatrixConverterTest extends AbstractDAOTest {
private TaxonLabelHome mTaxonLabelHome;
@@ -26,30 +31,85 @@
String testName = "testNexmlMatrixConverter";
//signal beginning of test
if (logger.isInfoEnabled()) {
- logger.info("\n\t\tRunning Test: " + testName);
+ logger.info("Running Test: " + testName);
}
long studyId = 1787;
- Study study = (Study)loadObject(Study.class, studyId);
- Document doc = DocumentFactory.safeCreateDocument();
- NexmlDocumentConverter ndc = new NexmlDocumentConverter(study,getTaxonLabelHome(),doc);
- 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");
+ // this is the full study as it is stored by the database
+ Study tbStudy = (Study)loadObject(Study.class, studyId);
+
+ // these are the character state matrices that are part of the study
+ Set<org.cipres.treebase.domain.matrix.Matrix> tbMatrices = tbStudy.getMatrices();
+
+ // this is an object representation of a NeXML document
+ Document nexDoc = DocumentFactory.safeCreateDocument();
+
+ // the converter populates the NeXML document with the contents of the treebase study
+ NexmlDocumentConverter ndc = new NexmlDocumentConverter(tbStudy,getTaxonLabelHome(),nexDoc);
+ ndc.fromTreeBaseToXml(tbStudy); // here is where the conversion happens
+
+ // these are the NeXML matrices that were created from the study
+ List<Matrix<?>> nexMatrices = nexDoc.getMatrices();
+
+ // there most be more than zero matrices because every treebase study has at least one matrix
+ Assert.assertTrue(nexMatrices.size() != 0 );
+
+ // now we're going to match up the NeXML matrices with their equivalent treebase ones
+ for ( Matrix<?> nexMatrix : nexMatrices ) {
+
+ // the xml id is the same as the primary key of the equivalent matrix stored by treebase
+ String nexId = nexMatrix.getId();
+ boolean foundEquivalentMatrix = false;
+
+ // iterate over all treebase matrices for the study
+ for ( org.cipres.treebase.domain.matrix.Matrix tbMatrix : tbMatrices ) {
+ String tbId = "M" + tbMatrix.getId();
+
+ // although there is a class DistanceMatrix, it is my belief that we don't actually have
+ // any distance matrices stored, nor can we convert them to NeXML
+ Assert.assertTrue("TreeBASE matrix "+tbId+" must be a character matrix, not a distance matrix", tbMatrix instanceof CharacterMatrix);
+
+ // if true, the matrices are equivalent
+ if ( nexId.equals(tbId) ) {
+ foundEquivalentMatrix = true;
+ Assert.assertTrue("NeXML matrix "+nexId+ " is one of the known subclasses",
+ nexMatrix instanceof CategoricalMatrix || nexMatrix instanceof MolecularMatrix || nexMatrix instanceof ContinuousMatrix);
+
+ // we have to coerce the tbMatrix into a character matrix to get its character sets
+ CharacterMatrix tbCharacterMatrix = (CharacterMatrix)tbMatrix;
+ Set<CharSet> tbCharSets = tbCharacterMatrix.getCharSets();
+
+ // a treebase matrix has zero or more character sets, we must iterate over them
+ for ( CharSet tbCharSet : tbCharSets ) {
+
+ // the coordinates of the character set are defined by a collection of column ranges that we iterate over
+ Collection<ColumnRange> tbColumnRanges = tbCharSet.getColumns(tbCharacterMatrix);
+ for ( ColumnRange tbColumnRange : tbColumnRanges ) {
+
+ // these are the beginning and end of the range
+ int start = tbColumnRange.getStartColIndex();
+ int stop = tbColumnRange.getEndColIndex();
+
+ // this is how we increment from beginning to end. This number is probably either 1, for a
+ // contiguous range, or 3 for codon positions
+ int inc = tbColumnRange.getRepeatInterval();
+
+ // this is how we create the equivalent nexml character set
+ Subset nexSubset = nexMatrix.createSubset(tbCharSet.getLabel());
+
+ // we have to assign character objects to the subset. Here we get the full list
+ List<org.nexml.model.Character> nexCharacters = nexMatrix.getCharacters();
+
+ // now we iterate over the coordinates and assign the nexml characters to the set
+ for ( int i = start; i <= stop; i += inc ) {
+ nexSubset.addThing(nexCharacters.get(i));
+ }
+ }
+ }
+ }
}
- 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("This should not ever happen.");
- }
+ Assert.assertTrue("Searched for equivalent to NeXML matrix "+nexId, foundEquivalentMatrix);
}
}
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