Fix bug with TreeConstructor indices to MSA

lafita · lafita · commit 04a9adbd78bb · 2015-11-09T16:30:20.000+01:00
diff --git a/biojava-phylo/src/main/java/demo/DemoTreeConstructor.java b/biojava-phylo/src/main/java/demo/DemoTreeConstructor.java
@@ -40,6 +40,7 @@ public static void main(String[] args) throws Exception {
 				new TreeConstructor<ProteinSequence, AminoAcidCompound>(
 				msa, TreeType.NJ, TreeConstructionAlgorithm.PID, 
 				new ProgressListenerStub());
+		
 		treeConstructor.process();
 		String newick = treeConstructor.getNewickString(true, true);
 
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
@@ -110,7 +110,7 @@ private double[][] calculateDistanceMatrix(MultipleSequenceAlignment<C, D> multi
         int numberOfSequences = multipleSequenceAlignment.getSize();
         String[] sequenceString = new String[numberOfSequences];
         for (int i = 0; i < multipleSequenceAlignment.getSize(); i++) {
-            sequenceString[i] = multipleSequenceAlignment.getAlignedSequence(i).getSequenceAsString();
+            sequenceString[i] = multipleSequenceAlignment.getAlignedSequence(i+1).getSequenceAsString();
 
         }
 
@@ -198,7 +198,7 @@ public void process() throws Exception {
             double[][] distances = calculateDistanceMatrix(multipleSequenceAlignment, treeConstructionAlgorithm);
             matrix = new BasicSymmetricalDistanceMatrix(multipleSequenceAlignment.getSize());
             for (int i = 0; i < matrix.getSize(); i++) {
-                matrix.setIdentifier(i, multipleSequenceAlignment.getAlignedSequence(i).getAccession().getID());
+                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++) {
