X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=3470dbc2624f1b1fdb42d50db364046c3c52f1e9;hb=3b5fd72d019a6cd71f611b4110651ff6b62ce5bf;hp=ec5b79bfd23ff697e69de9a638f04c89aaeac345;hpb=7a2f4e9ee4119f0369743e7996bcebbb6ab46f9e;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index ec5b79b..3470dbc 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -218,7 +218,7 @@ public class NJTree
    *          DOCUMENT ME!
    */
   public NJTree(SequenceI[] sequence, AlignmentView seqData, String type,
-          String pwtype, int start, int end)
+          String pwtype, ScoreModelI sm, int start, int end)
   {
     this.sequence = sequence;
     this.node = new Vector();
@@ -245,7 +245,7 @@ public class NJTree
       type = "AV";
     }
 
-    if (!(pwtype.equals("PID")))
+    if (sm == null && !(pwtype.equals("PID")))
     {
       if (ResidueProperties.getScoreMatrix(pwtype) == null)
       {
@@ -265,7 +265,7 @@ public class NJTree
 
     noseqs = i++;
 
-    distance = findDistances();
+    distance = findDistances(sm);
     // System.err.println("Made distances");// dbg
     makeLeaves();
     // System.err.println("Made leaves");// dbg
@@ -323,7 +323,7 @@ public class NJTree
 
           for (int j = 0; j < seqs.length; j++)
           {
-            seqs[j] = (SequenceI) list.get(j);
+            seqs[j] = list.get(j);
           }
 
           seqmatcher = new SequenceIdMatcher(seqs);
@@ -730,16 +730,18 @@ public class NJTree
    * 
    * @return similarity matrix used to compute tree
    */
-  public float[][] findDistances()
+  public float[][] findDistances(ScoreModelI _pwmatrix)
   {
 
     float[][] distance = new float[noseqs][noseqs];
-
-    // Pairwise substitution score (with no gap penalties)
-    ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
     if (_pwmatrix == null)
     {
-      _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+      // Resolve substitution model
+      _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+      if (_pwmatrix == null)
+      {
+        _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+      }
     }
     distance = _pwmatrix.findDistances(seqData);
     return distance;
@@ -865,12 +867,12 @@ public class NJTree
     {
       System.out
               .println("Leaf = " + ((SequenceI) node.element()).getName());
-      System.out.println("Dist " + ((SequenceNode) node).dist);
+      System.out.println("Dist " + node.dist);
       System.out.println("Boot " + node.getBootstrap());
     }
     else
     {
-      System.out.println("Dist " + ((SequenceNode) node).dist);
+      System.out.println("Dist " + node.dist);
       printNode((SequenceNode) node.left());
       printNode((SequenceNode) node.right());
     }
@@ -891,11 +893,11 @@ public class NJTree
 
     if ((node.left() == null) && (node.right() == null))
     {
-      float dist = ((SequenceNode) node).dist;
+      float dist = node.dist;
 
       if (dist > maxDistValue)
       {
-        maxdist = (SequenceNode) node;
+        maxdist = node;
         maxDistValue = dist;
       }
     }
@@ -1097,9 +1099,9 @@ public class NJTree
               + ((SequenceI) node.element()).getName());
     }
 
-    System.out.println(" dist = " + ((SequenceNode) node).dist + " "
-            + ((SequenceNode) node).count + " "
-            + ((SequenceNode) node).height);
+    System.out.println(" dist = " + node.dist + " "
+            + node.count + " "
+            + node.height);
   }
 
   /**
@@ -1145,13 +1147,13 @@ public class NJTree
       SequenceNode l = (SequenceNode) node.left();
       SequenceNode r = (SequenceNode) node.right();
 
-      ((SequenceNode) node).count = l.count + r.count;
-      ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+      node.count = l.count + r.count;
+      node.ycount = (l.ycount + r.ycount) / 2;
     }
     else
     {
-      ((SequenceNode) node).count = 1;
-      ((SequenceNode) node).ycount = ycount++;
+      node.count = 1;
+      node.ycount = ycount++;
     }
     _lycount--;
   }
@@ -1290,7 +1292,9 @@ public class NJTree
   {
     for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
             .transform((BinaryNode) nodes.nextElement()))
+    {
       ;
+    }
   }
 }