Use homologous structure derived matrix HSDM for msa tree building

lafita · lafita · commit e80f5a486d25 · 2016-03-03T11:48:35.000+01:00
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MultipleAlignmentJmol.java
@@ -415,7 +415,7 @@ public void actionPerformed(ActionEvent ae) {
 				Phylogeny kimura = MultipleAlignmentTools
 						.getKimuraTree(multAln);
 				Phylogeny sdm = MultipleAlignmentTools
-						.getSDMTree(multAln);
+						.getHSDMTree(multAln);
 				// Phylogeny structural = MultipleAlignmentTools
 				//		.getStructuralTree(multAln);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/multiple/util/MultipleAlignmentTools.java
@@ -877,15 +877,15 @@ public static Phylogeny getKimuraTree(MultipleAlignment msta)
 	 * @throws CompoundNotFoundException
 	 * @throws IOException
 	 */
-	public static Phylogeny getSDMTree(MultipleAlignment msta)
+	public static Phylogeny getHSDMTree(MultipleAlignment msta)
 			throws CompoundNotFoundException, IOException {
 		MultipleSequenceAlignment<ProteinSequence, AminoAcidCompound> msa = MultipleAlignmentTools
 				.toProteinMSA(msta);
 		BasicSymmetricalDistanceMatrix distmat = (BasicSymmetricalDistanceMatrix) DistanceMatrixCalculator
-				.dissimilarityScore(msa, SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix("PRLA000101"));
+				.dissimilarityScore(msa, SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix("PRLA000102"));
 		Phylogeny tree = TreeConstructor.distanceTree(distmat,
 				TreeConstructorType.NJ);
-		tree.setName("SDM Tree");
+		tree.setName("HSDM Tree");
 		return tree;
 	}
 
