Use HSDM substitution matrix instead of BLOSUM45 in MSA trees

lafita · lafita · commit 37eaaecb70a4 · 2016-02-04T17:51:06.000+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
@@ -78,8 +78,7 @@ public class MultipleAlignmentJmol extends AbstractAlignmentJmol {
 	private JCheckBox colorByBlocks;
 	private List<JCheckBox> selectedStructures;
 
-	private static final String LIGAND_DISPLAY_SCRIPT = 
-			"select ligand; wireframe 40; spacefill 120; color CPK;";
+	private static final String LIGAND_DISPLAY_SCRIPT = "select ligand; wireframe 40; spacefill 120; color CPK;";
 
 	private static final Logger logger = LoggerFactory
 			.getLogger(MultipleAlignmentJmol.class);
@@ -414,13 +413,12 @@ public void actionPerformed(ActionEvent ae) {
 				// Kimura, Structural and Fractional Dissimilarity Score
 				Phylogeny kimura = MultipleAlignmentTools
 						.getKimuraTree(multAln);
-				Phylogeny blosum = MultipleAlignmentTools
-						.getBLOSUM40Tree(multAln);
-				Phylogeny structural = MultipleAlignmentTools
-						.getStructuralTree(multAln);
+				Phylogeny hsdm = MultipleAlignmentTools.getHSDMTree(multAln);
+				// Phylogeny structural = MultipleAlignmentTools
+				// .getStructuralTree(multAln);
 
-				Archaeopteryx.createApplication(new Phylogeny[] { kimura,
-						blosum, structural });
+				Archaeopteryx
+						.createApplication(new Phylogeny[] { kimura, hsdm });
 			}
 		} catch (Exception e) {
 			logger.error("Could not complete display option.", e);
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
@@ -867,25 +867,25 @@ public static Phylogeny getKimuraTree(MultipleAlignment msta)
 
 	/**
 	 * Calculate a phylogenetic tree of the MultipleAlignment using
-	 * dissimilarity scores (DS), based in BLOSUM40 Substitution Matrix (ideal
-	 * for distantly related proteins, often the case in structural alignments)
-	 * and the Neighbor Joining algorithm from forester.
+	 * dissimilarity scores (DS), based in HSDM Substitution Matrix (ideal for
+	 * distantly related proteins, structure-derived) and the Neighbor Joining
+	 * algorithm from forester.
 	 * 
 	 * @param msta
 	 *            MultipleAlignment of protein structures
 	 * @return Phylogeny phylogenetic tree
 	 * @throws CompoundNotFoundException
 	 * @throws IOException
 	 */
-	public static Phylogeny getBLOSUM40Tree(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.getBlosum40());
+				.dissimilarityScore(msa, SubstitutionMatrixHelper.getAminoAcidSubstitutionMatrix("PRLA000102"));
 		Phylogeny tree = TreeConstructor.distanceTree(distmat,
 				TreeConstructorType.NJ);
-		tree.setName("BLOSUM40 Tree");
+		tree.setName("HSDM Tree");
 		return tree;
 	}
 
