Added parsing of input matrix cells. Values seem to have been ignored previously.

Author: balhoff

src/org/nexml/model/impl/CategoricalMatrixImpl.java

@@ -63,7 +63,7 @@ protected CategoricalMatrixImpl(Document document, Element element, OTUsImpl otu
 
 		for ( Element row : getChildrenByTagName( getMatrixElement(), "row") ) {
 			OTU otu = otus.getThingById(row.getAttribute("otu"));
-			MatrixRowImpl<CharacterState> matrixRow = new MatrixRowImpl<CharacterState>(getDocument(),row);
+			MatrixRowImpl<CharacterState> matrixRow = new MatrixRowImpl<CharacterState>(getDocument(),row, this, false);
 			matrixRow.setOTU(otu);
 			mMatrixRows.put(otu, matrixRow);
 		}

src/org/nexml/model/impl/ContinuousMatrixImpl.java

@@ -63,7 +63,7 @@ private void processMatrix(Element matrix,OTUsImpl otus,Map<String,Character> ch
 		setMatrixElement(matrix);
 		for ( Element rowElement : getChildrenByTagName(matrix, "row") ) {
 			OTU otu = otus.getThingById(rowElement.getAttribute("otu"));
-			MatrixRow<Double> matrixRow = new MatrixRowImpl<Double>(getDocument(),rowElement);
+			MatrixRow<Double> matrixRow = new MatrixRowImpl<Double>(getDocument(),rowElement, this, true);
 			matrixRow.setOTU(otu);
 			mMatrixRows.put(otu, matrixRow);
 		}		

src/org/nexml/model/impl/MatrixImpl.java

@@ -62,14 +62,7 @@ protected MatrixImpl(Document document,String type) {
      * @author rvosa
      */
 	protected MatrixImpl(Document document,Element element) {
-		super(document,element);
-		for (Element rowElement : getChildrenByTagName(element, "row")) {
-			String otuId = rowElement.getAttribute("otu");
-			OTU otu = ((OTUsImpl)getOTUs()).getThingById(otuId);
-			MatrixRow<T> row = new MatrixRowImpl<T>(document, rowElement);
-			row.setOTU(otu);
-			mMatrixRows.put(otu, row);
-		}		
+		super(document,element);	
 	}
 
 	/*

src/org/nexml/model/impl/MatrixRowImpl.java

@@ -6,6 +6,7 @@
 import java.util.Map;
 
 import org.nexml.model.Character;
+import org.nexml.model.CharacterState;
 import org.nexml.model.MatrixCell;
 import org.nexml.model.MatrixRow;
 import org.w3c.dom.Document;
@@ -55,15 +56,27 @@ protected MatrixRowImpl(Document document,MatrixImpl<T> matrix) {
      * the <otus/> element)
      * @author rvosa
      */
-	protected MatrixRowImpl(Document document, Element element) {
+	protected MatrixRowImpl(Document document, Element element, MatrixImpl<T> matrix, boolean continuous) {
 		super(document, element);
+		mMatrix = matrix;
 		List<Element> seqElements = getChildrenByTagName(element, "seq");
 		if ( ! seqElements.isEmpty() ) {
 			mSeqElement = seqElements.get(0);
 		}
 		List<Element> cellElements = getChildrenByTagName(element, "cell");
 		for ( Element cellElement : cellElements ) {
+			Character character = findCharacter(cellElement.getAttribute("char"));
+			Object value;
+			if (continuous) {
+				value = Double.parseDouble(cellElement.getAttribute("state"));
+				
+			} else {
+				value = findState(cellElement.getAttribute("state"), character);
+			}
+			mStateForCharacter.put(character, (T)value);
 			MatrixCellImpl<T> cell = new MatrixCellImpl<T>(getDocument(),cellElement);
+			cell.setValue((T)value);
+			mCellForCharacter.put(character, cell);
 			mMatrixCell.add(cell);
 		}
 	}	
@@ -195,5 +208,23 @@ public String getSeq() {
 	private MatrixImpl<T> getMatrix() {
 		return mMatrix;
 	}
+	
+	private Character findCharacter(String id) {
+		for (Character character : getMatrix().getCharacters()) {
+			if (character.getId().equals(id)) {
+				return character;
+			}
+		}
+		return null;
+	}
+	
+	private CharacterState findState(String id, Character character) {
+		for (CharacterState state : character.getCharacterStateSet().getCharacterStates()) {
+			if (state.getId().equals(id)) {
+				return state;
+			}
+		}
+		return null;
+	}
 
 }

src/org/nexml/model/impl/MolecularMatrixImpl.java

@@ -65,7 +65,7 @@ protected MolecularMatrixImpl(Document document, Element element, OTUsImpl otus,
 
 		for ( Element row : getChildrenByTagName( getMatrixElement(), "row") ) {
 			OTU otu = otus.getThingById(row.getAttribute("otu"));
-			MatrixRowImpl<CharacterState> matrixRow = new MatrixRowImpl<CharacterState>(getDocument(),row);
+			MatrixRowImpl<CharacterState> matrixRow = new MatrixRowImpl<CharacterState>(getDocument(),row, this, false);
 			matrixRow.setOTU(otu);
 			mMatrixRows.put(otu, matrixRow);
 		}

test/org/nexml/model/TestFileParse.java

@@ -5,6 +5,7 @@
 
 import java.io.File;
 import java.io.IOException;
+
 import javax.xml.parsers.ParserConfigurationException;
 
 import junit.framework.Assert;
@@ -39,5 +40,18 @@ public void parseCharacters() {
 		}
 		System.out.println(doc.getXmlString());
 	}
+	
+	@Test
+	public void parsePhenoscapeMatrix() throws SAXException, IOException, ParserConfigurationException {
+		final File file = new File("test_files/Buckup_1998.xml");
+		final Document doc = DocumentFactory.parse(file);
+		for (Matrix<?> matrix : doc.getMatrices()) {
+			for (Character character : matrix.getCharacters()) {
+				for (OTU otu : matrix.getOTUs()) {
+					System.out.println(matrix.getRowObject(otu).getCell(character).getValue());
+				}
+			}
+		}
+	}
 
 }