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[Treebase-guts] SF.net SVN: treebase:[921] trunk/treebase-core/src/test/java/org/cipres/ treebase/domain/nexus/NexmlMatrixConverterTest.java
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From: <rv...@us...> - 2011-06-17 14:00:51
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Revision: 921
http://treebase.svn.sourceforge.net/treebase/?rev=921&view=rev
Author: rvos
Date: 2011-06-17 14:00:40 +0000 (Fri, 17 Jun 2011)
Log Message:
-----------
If the NexmlMatrixConverter (so NOT this test class) functions correctly, it must have now implemented the logic from testNexmlMatrixConverter so that the tests in testNexmlMatrixCharSets.
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 2011-06-17 02:28:54 UTC (rev 920)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexmlMatrixConverterTest.java 2011-06-17 14:00:40 UTC (rev 921)
@@ -10,6 +10,7 @@
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.matrix.PhyloChar;
import org.cipres.treebase.domain.nexus.nexml.NexmlDocumentConverter;
import org.cipres.treebase.domain.study.Study;
import org.cipres.treebase.domain.taxon.TaxonLabelHome;
@@ -135,7 +136,7 @@
if (logger.isInfoEnabled()) {
logger.info("Running Test: " + testName);
}
- long studyId = 1787;
+ long studyId = 794;
// this is the full study as it is stored by the database
Study tbStudy = (Study)loadObject(Study.class, studyId);
@@ -174,9 +175,18 @@
// we have to coerce the tbMatrix into a character matrix to get its character sets
CharacterMatrix tbCharacterMatrix = (CharacterMatrix)tbMatrix;
Set<CharSet> tbCharSets = tbCharacterMatrix.getCharSets();
+
+ // NexmlMatrixConverter must have assigned character objects to zero or more subsets. Here we get the full list of characters
+ List<org.nexml.model.Character> nexCharacters = nexMatrix.getCharacters();
+ Assert.assertEquals("The number of characters in the NeXML matrix must match that of the TreeBASE matrix", (Integer)tbMatrix.getnChar(), (Integer)nexCharacters.size());
+
if (tbCharSets.isEmpty() != true) {
// a treebase matrix has zero or more character sets, we must iterate over them
for ( CharSet tbCharSet : tbCharSets ) {
+
+ // this is how we fetch the equivalent nexml character set
+ Subset nexSubset = nexMatrix.getSubset(tbCharSet.getLabel());
+ Assert.assertNotNull("If NexmlMatrixConverter works correctly, a Subset is returned", nexSubset);
// the coordinates of the character set are defined by a collection of column ranges that we iterate over
Collection<ColumnRange> tbColumnRanges = tbCharSet.getColumns(tbCharacterMatrix);
@@ -196,30 +206,35 @@
tbInc = tbColumnRange.getRepeatInterval();
}
- // this is how we create the equivalent nexml character set
- Subset nexSubset = nexMatrix.createSubset(tbCharSet.getLabel());
+
+ // The NexmlMatrixConverter should have created a Subset for each tbCharSet
+ if ( null != nexSubset ) {
- //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 = i;
- Assert.assertTrue( nexCharSetCoordinate == tbCharSetCoordinate );
+ //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("The NeXML character set must have copied the label of the TreeBASE character set",tbCharSetName.equals(nexCharSetName));
+
+ // now we iterate over the coordinates in this column range
+ //and verify whether correct character objects are returned
+ for ( int i = tbStart; i <= tbStop; i += tbInc ) {
+
+ // get the nexml character that should have been created
+ org.nexml.model.Character nexCharacter = nexCharacters.get(i);
+ Assert.assertNotNull("The NeXML Character should not be null if there as an index into it in this set", nexCharacter);
+ Assert.assertTrue("The Subset should contain the character at index i", nexSubset.containsThing(nexCharacter));
+
+ //get the treebase character for the index in this column range
+ PhyloChar tbCharacter = tbCharacterMatrix.getCharacter(i);
+ Assert.assertNotNull("The TreeBASE PhyloChar should not be null if there as an index into it in this set", tbCharacter);
+ Assert.assertEquals("If the TreeBASE character has a label, then the NeXML character's label should match it", tbCharacter.getLabel(), nexCharacter.getLabel());
+ }
}
+ else {
+ System.out.println("NexmlMatrixConverter failed to create a Subset");
+ }
}
}
}
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