Reshape the TreeConstructor class

lafita · lafita · commit 6a1ebc846b3d · 2015-11-16T17:43:33.000+01:00
It contains static methods that communicate with forester for tree
construction. Only distance and NJ supported for now.
diff --git a/biojava-phylo/src/main/java/org/biojava/nbio/phylo/TreeConstructor.java b/biojava-phylo/src/main/java/org/biojava/nbio/phylo/TreeConstructor.java
@@ -18,187 +18,45 @@
  *      http://www.biojava.org/
  *
  */
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.biojava.nbio.phylo;
 
-import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
-import org.biojava.nbio.core.sequence.template.AbstractSequence;
-import org.biojava.nbio.core.sequence.template.Compound;
 import org.forester.evoinference.distance.NeighborJoining;
 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
-import org.forester.evoinference.matrix.distance.DistanceMatrix;
-import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.FileOutputStream;
-import java.io.PrintStream;
-import java.text.DecimalFormat;
-import java.util.ArrayList;
-import java.util.List;
-
 /**
- * TreeConstructor uses the forester tree library to build phylogenetic trees.
+ * The TreeConstructor uses the forester library to build different types of
+ * phylogenetic trees.
  *
  * @author Scooter Willis
  * @author Aleix Lafita
  * 
  */
-public class TreeConstructor<C extends AbstractSequence<D>, D extends Compound>
-		extends Thread {
+public class TreeConstructor {
 
 	private static final Logger logger = LoggerFactory
 			.getLogger(TreeConstructor.class);
 
-	private TreeType treeType;
-	private ScoreMatrixType scoreType;
-	private List<NJTreeProgressListener> progessListenerVector = new ArrayList<NJTreeProgressListener>();
-	private MultipleSequenceAlignment<C, D> multipleSequenceAlignment = new MultipleSequenceAlignment<C, D>();
-
-	public TreeConstructor(
-			MultipleSequenceAlignment<C, D> multipleSequenceAlignment,
-			TreeType _treeType,
-			ScoreMatrixType _scoreType,
-			NJTreeProgressListener _treeProgessListener) {
-
-		treeType = _treeType;
-		scoreType = _scoreType;
-		addProgessListener(_treeProgessListener);
-		this.multipleSequenceAlignment = multipleSequenceAlignment;
-
-	}
-
-	public TreeConstructor(BasicSymmetricalDistanceMatrix _matrix,
-			TreeType _treeType,
-			TreeConstructionAlgorithm _treeConstructionAlgorithm,
-			NJTreeProgressListener _treeProgessListener) {
-		matrix = _matrix;
-		copyDistanceMatrix = CheckTreeAccuracy.copyMatrix(matrix);
-		treeType = _treeType;
-		scoreType = _treeConstructionAlgorithm;
-		addProgessListener(_treeProgessListener);
-
-	}
-
-	public void outputPhylipDistances(String fileName) throws Exception {
-		DistanceMatrix distances = getDistanceMatrix();
-		if (distances == null) {
-			throw new Exception("distance matrix has not been calculated. "
-					+ "Requires process() method to be called first");
-		}
-		FileOutputStream fo = new FileOutputStream(fileName);
-		PrintStream dos = new PrintStream(fo);
-		DecimalFormat df = new DecimalFormat();
-		df.setMaximumFractionDigits(5);
-		df.setMinimumFractionDigits(5);
-		for (int row = 0; row < distances.getSize(); row++) {
-			dos.print(distances.getIdentifier(row));
-			for (int col = 0; col < distances.getSize(); col++) {
-				dos.print(" " + df.format(distances.getValue(col, row)));
-			}
-			dos.println();
-		}
-		dos.close();
-		fo.close();
-	}
-
-	public DistanceMatrix getDistanceMatrix() {
-		return copyDistanceMatrix;
-	}
-
-	public void cancel() {
-		// if (njtree != null) {
-		// njtree.cancel();
-		// }
-	}
-
-	boolean verbose = false;
-	Phylogeny p = null;
-	BasicSymmetricalDistanceMatrix matrix = null;
-	DistanceMatrix copyDistanceMatrix = null;
-
-	public void process() throws Exception {
-
-		if (matrix == null) {
-			double[][] distances = DistanceCalculator.calculateDistanceMatrix(
-					this, multipleSequenceAlignment, scoreType);
-			matrix = new BasicSymmetricalDistanceMatrix(
-					multipleSequenceAlignment.getSize());
-			for (int i = 0; i < matrix.getSize(); i++) {
-				matrix.setIdentifier(i, multipleSequenceAlignment
-						.getAlignedSequence(i + 1).getAccession().getID());
-			}
-			for (int col = 0; col < matrix.getSize(); col++) {
-				for (int row = 0; row < matrix.getSize(); row++) {
-					matrix.setValue(col, row, distances[col][row]);
-
-				}
-			}
-			copyDistanceMatrix = CheckTreeAccuracy.copyMatrix(matrix);
-		}
-
-		final List<Phylogeny> ps = new ArrayList<Phylogeny>();
-		final NeighborJoining nj = NeighborJoining.createInstance(verbose);
-
-		ps.add(nj.execute(matrix));
-		p = ps.get(0);
-
-	}
-
-	// public void getTreeAccuracy(){
-	// CheckTreeAccuracy checkTreeAccuracy = new CheckTreeAccuracy();
-	// checkTreeAccuracy.process(p,distanceMatrix );
-	// }
-	@Override
-	public void run() {
-		try {
-			process();
-		} catch (Exception e) {
-			logger.error("Exception: ", e);
-		}
-	}
-
-	public String getNewickString(boolean simpleNewick,
-			boolean writeDistanceToParent) throws Exception {
-		final PhylogenyWriter w = new PhylogenyWriter();
-		StringBuffer newickString = w.toNewHampshire(p, simpleNewick,
-				writeDistanceToParent);
-		return newickString.toString();
-	}
-
-	public void addProgessListener(NJTreeProgressListener treeProgessListener) {
-		if (treeProgessListener != null) {
-			progessListenerVector.add(treeProgessListener);
-		}
-	}
+	/** Prevent instantiation */
+	private TreeConstructor() {}
 
-	public void removeProgessListener(NJTreeProgressListener treeProgessListener) {
-		if (treeProgessListener != null) {
-			progessListenerVector.remove(treeProgessListener);
-		}
-	}
+	public static Phylogeny distanceTree(BasicSymmetricalDistanceMatrix distM,
+			TreeConstructorType constructor) {
 
-	public void broadcastComplete() {
-		for (NJTreeProgressListener treeProgressListener : progessListenerVector) {
-			treeProgressListener.complete(this);
+		Phylogeny p = null;
+		switch (constructor) {
+		case NJ:
+			NeighborJoining nj = NeighborJoining.createInstance();
+			p = nj.execute(distM);
+			p.setType(TreeType.DISTANCE.name);
+			break;
+		default:
+			logger.warn("Only NJ Tree Constructor Supported!");
+			break;
 		}
+		logger.info("Tree Completed");
+		return p;
 	}
-
-	public void updateProgress(String state, int percentage) {
-		for (NJTreeProgressListener treeProgressListener : progessListenerVector) {
-			treeProgressListener.progress(this, state, percentage);
-		}
-	}
-
-	public void updateProgress(String state, int currentCount, int totalCount) {
-		for (NJTreeProgressListener treeProgressListener : progessListenerVector) {
-			treeProgressListener
-					.progress(this, state, currentCount, totalCount);
-		}
-	}
-
 }
