Adding tests for matrix row implementation

Author: rvosa

test/org/nexml/model/TestAnnotationTypes.java

@@ -105,7 +105,7 @@ public void testXsdType () {
 	public void parseMetaTypes() {
 		String nexmlRoot = System.getenv("NEXML_ROOT");
 		if ( nexmlRoot == null ) {
-			nexmlRoot = "/Users/rvosa/Documents/workspace/nexml/trunk/nexml";
+			nexmlRoot = "/Users/rvosa/Dropbox/documents/projects/current/nexml/src/nexml/trunk/nexml";
 		}
 		File file = new File(nexmlRoot+"/examples/meta_types.xml");
 		Document doc = null;

test/org/nexml/model/TestFileParse.java

@@ -21,9 +21,9 @@ public class TestFileParse {
 	public void parseCharacters() {
 		String nexmlRoot = System.getenv("NEXML_ROOT");
 		if ( nexmlRoot == null ) {
-			nexmlRoot = "/Users/rvosa/Documents/workspace/nexml/trunk/nexml";
+			nexmlRoot = "/Users/rvosa/Dropbox/documents/projects/current/nexml/src/nexml/trunk/nexml";
 		}
-		File file = new File(nexmlRoot+"/examples/trees.xml");
+		File file = new File(nexmlRoot+"/examples/characters.xml");
 		Document doc = null;
 		try {
 			doc = DocumentFactory.parse(file);

test/org/nexml/model/TestMatrixRows.java

@@ -0,0 +1,52 @@
+package org.nexml.model;
+
+import java.net.URI;
+
+import org.junit.Test;
+
+
+public class TestMatrixRows {
+	URI tbTermsUri = URI.create("http://purl.org/phylo/treebase/2.0/terms#");
+
+	@Test
+	public void testCreateDNAMatrix () {
+		
+		// create a document
+		Document doc = DocumentFactory.safeCreateDocument();
+        
+        // create a taxa block with 5 taxa
+        OTUs otus = doc.createOTUs();
+        for ( int i = 1; i <= 5; i++ ) {
+        	OTU otu = otus.createOTU();
+        	otu.setLabel("Taxon_"+i);
+        }		
+        
+        // create a DNA matrix for the taxa
+        MolecularMatrix matrix = doc.createMolecularMatrix(otus, MolecularMatrix.DNA);
+        CharacterStateSet stateSet = matrix.getCharacterStateSet();
+      
+        
+        // populate
+        String[] symbols = { "A", "C", "G", "T" };
+        for ( OTU otu : otus.getAllOTUs() ) {
+        	StringBuffer sb = new StringBuffer();
+        	
+        	for ( int i = 0; i <= 9; i++ ) {
+        		Long l = new Long(Math.round(Math.random()*(symbols.length-1)));
+        		sb.append(symbols[l.intValue()]);
+        		matrix.createCharacter(stateSet);
+        	}
+        	MatrixRow<CharacterState> row = matrix.getRowObject(otu);
+        	Annotation annotation = row.addAnnotationValue("tb:rowSegment", tbTermsUri,new String());
+        	annotation.addAnnotationValue("tb:segmentStart", tbTermsUri, 1);
+        	annotation.addAnnotationValue("tb:segmentEnd", tbTermsUri, 10);
+        	annotation.addAnnotationValue("tb:accession", tbTermsUri, "DC567254");
+        	row.setSeq(sb.toString());
+        }
+        
+        // print document
+        System.out.println(doc.getXmlString());
+
+	}
+	
+}

test/org/nexml/model/TestParseTrees.java

@@ -18,7 +18,7 @@ public class TestParseTrees {
 	public void parseFloatTree() throws Throwable {
 		String nexmlRoot = System.getenv("NEXML_ROOT");
 		if ( nexmlRoot == null ) {
-			nexmlRoot = "/Users/rvosa/Documents/workspace/nexml/trunk/nexml";
+			nexmlRoot = "/Users/rvosa/Dropbox/documents/projects/current/nexml/src/nexml/trunk/nexml";
 		}		
 		Document document = DocumentFactory.parse(new File(nexmlRoot+"/examples/trees.xml"));
 		//System.out.println(document.getXmlString());
@@ -49,7 +49,7 @@ public void parseFloatTree() throws Throwable {
 	public void parseIntTree() throws Throwable {
 		String nexmlRoot = System.getenv("NEXML_ROOT");
 		if ( nexmlRoot == null ) {
-			nexmlRoot = "/Users/rvosa/Documents/workspace/nexml/trunk/nexml";
+			nexmlRoot = "/Users/rvosa/Dropbox/documents/projects/current/nexml/src/nexml/trunk/nexml";
 		}	
 		Document document = DocumentFactory.parse(new File(nexmlRoot+
 						"/examples/02_dogfish_no_taxrefs.xml"));