[Treebase-guts] SF.net SVN: treebase:[915] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlMatrixConverterTest.java

[<lol...@us...>]

Revision: 915
          http://treebase.svn.sourceforge.net/treebase/?rev=915&view=rev
Author:   loloyohe
Date:     2011-06-13 16:47:34 +0000 (Mon, 13 Jun 2011)

Log Message:
-----------
Added a second JUnit test testNexmlCharSets(). It verifies if the title and coordinates of a treebase character set and nexml character set match up. 

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	2011-06-13 15:10:50 UTC (rev 914)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java	2011-06-13 16:47:34 UTC (rev 915)
@@ -26,6 +26,8 @@
 
 	/**
 	 * Test  for {@link org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter#fromTreeBaseToXml(CharacterMatrix)}.
+	 * Finds an equivalent, created NexmlMatrix within a NeXML document to go with the matrix
+	 * fetched from the TreeBASE database.
 	 */
 	public void testNexmlMatrixConverter() {
 		String testName = "testNexmlMatrixConverter";
@@ -38,10 +40,10 @@
 		
 		// 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();
 		
@@ -61,11 +63,11 @@
 			// 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);
@@ -85,6 +87,7 @@
 						
 						// 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
@@ -122,6 +125,114 @@
 	}
 	
 	/**
+	 * Test  for {@link org.cipres.treebase.domain.nexus.nexml.NexmlMatrixConverter#}.
+	 * It verifies that NexmlCharSets have the same name and coordinates as those in the 
+	 * TreeBASE matrix.
+	 */
+	public void testNexmlMatrixCharSets() {
+		String testName = "testNexmlCharSets";
+		//signal beginning of test
+		if (logger.isInfoEnabled()) {
+			logger.info("Running Test: " + testName);
+		}
+		long studyId = 2000;
+
+		// 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();
+		
+				// 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 tbStart = tbColumnRange.getStartColIndex();
+								int tbStop = tbColumnRange.getEndColIndex();
+								
+								// this is how we increment from beginning to end. This number is probably either null, for a
+								// contiguous range, or perhaps 3 for codon positions
+								int tbInc = 1;
+									
+								// need to do this to prevent nullpointerexceptions
+								if ( null != tbColumnRange.getRepeatInterval()) {
+										
+									tbInc = tbColumnRange.getRepeatInterval();
+								}
+								// this is how we create the equivalent nexml character set
+								Subset nexSubset = nexMatrix.createSubset(tbCharSet.getLabel());
+									
+								//get names of TreeBASE and NeXML character set
+								String tbCharSetName = tbCharSet.getLabel();
+								String nexCharSetName = nexSubset.getLabel();
+									
+								//verify that the names are the same
+								Assert.assertTrue(tbCharSetName.equals(nexCharSetName));
+									
+								// 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
+								//and verify coordinates of TreeBASE characterset and nexml characterset
+								//are the same
+								for ( int i = tbStart; i <= tbStop; i += tbInc ) {
+									nexSubset.addThing(nexCharacters.get(i));
+									
+									//declare coordinate index
+									int nexCharSetCoordinate = nexCharacters.indexOf(nexCharacters.get(i));							
+									int tbCharSetCoordinate = tbColumnRange.getStartColIndex() + i;
+									
+									//Assert.assertTrue( nexCharSetCoordinate == tbCharSetCoordinate );
+									//if (nexCharSetCoordinate == tbCharSetCoordinate){
+									//	System.out.println("I work");
+									//}
+								}
+						}
+					}
+				}
+			}
+		}
+	}
+	/**
 	 * Return the TaxonLabelHome field.
 	 * 
 	 * @return TaxonLabelHome mTaxonLabelHome


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