Add CookBook demo for creating a phylogenetic tree from MSA

lafita · lafita · commit 38b2c377d3da · 2015-11-09T16:21:30.000+01:00
diff --git a/biojava-phylo/src/main/java/demo/DemoTreeConstructor.java b/biojava-phylo/src/main/java/demo/DemoTreeConstructor.java
@@ -0,0 +1,48 @@
+package demo;
+
+import org.biojava.nbio.core.sequence.MultipleSequenceAlignment;
+import org.biojava.nbio.core.sequence.ProteinSequence;
+import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
+import org.biojava.nbio.phylo.TreeConstructionAlgorithm;
+import org.biojava.nbio.phylo.ProgressListenerStub;
+import org.biojava.nbio.phylo.TreeConstructor;
+import org.biojava.nbio.phylo.TreeType;
+
+/**
+ * This demo contains the CookBook examples to create a phylogenetic tree from a
+ * given multiple sequence alignment (MSA).
+ * 
+ * @author Aleix Lafita
+ *
+ */
+public class DemoTreeConstructor {
+
+	public static void main(String[] args) throws Exception {
+
+		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = new 
+				MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound>();
+
+		ProteinSequence pSeq1 = new ProteinSequence(
+				"RER-RDGGGNSRKYDDRRSPRDGE---IDYDERTVSHYQRQFQDERISDGM"
+				+ "LNTLKQSLKGLDCQPIHLKDSKANRSIMIDEIHTGTADSVTFEQKLPDGEMKL");
+		ProteinSequence pSeq2 = new ProteinSequence(
+				"RDRHRD---DRHRYDEDRDHRRDQRNVSDYDSEELRKFEEDYKSDRLGQYV"
+				+ "FSDLNSAVKGLVVQPIHL-NKEVNRTVIIDSICKESAEKVRFEFGKGEDAREI");
+		ProteinSequence pSeq3 = new ProteinSequence(
+				"RPTH---GGLSLNIDVSTTMILEPGPVIEF-----LKANQSVETPRQIDWI"
+				+ "-----KAAKML--KHMRVKATHRNMEFKIIGLSSKPCNQQLFSMKIKDGEREV");
+
+		msa.addAlignedSequence(pSeq1);
+		msa.addAlignedSequence(pSeq2);
+		msa.addAlignedSequence(pSeq3);
+
+		TreeConstructor<ProteinSequence, AminoAcidCompound> treeConstructor = 
+				new TreeConstructor<ProteinSequence, AminoAcidCompound>(
+				msa, TreeType.NJ, TreeConstructionAlgorithm.PID, 
+				new ProgressListenerStub());
+		treeConstructor.process();
+		String newick = treeConstructor.getNewickString(true, true);
+
+		System.out.println(newick);
+	}
+}
diff --git a/biojava-phylo/src/main/java/org/biojava/nbio/phylo/ProgressListenerStub.java b/biojava-phylo/src/main/java/org/biojava/nbio/phylo/ProgressListenerStub.java
@@ -38,6 +38,7 @@ public class ProgressListenerStub implements NJTreeProgressListener {
 	private static final Logger logger = LoggerFactory.getLogger(ProgressListenerStub.class);
 
 	String priorState = "";
+	
     @Override
 	public void progress(Object njtree,String state, int percentageComplete) {
         if(!priorState.equals(state)){
