JAL-1807

[jalview.git] / src / jalview / analysis / NJTree.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index ec5b79b..16395c2 100644 (file)
--- 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.
  * 
@@ -31,13 +31,14 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.io.NewickFile;
 import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
 
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
 
 /**
- * DOCUMENT ME!
+ * NeighborJoining tree
  * 
  * @author $author$
  * @version $Revision$
@@ -116,7 +117,7 @@ public class NJTree
     }
     /*
      * sequenceString = new String[odata.length]; char gapChar =
-     * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i <
+     * Comparison.GapChars.charAt(0); for (int i = 0; i <
      * odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
      * sequenceString[i] = oseq_aligned.getSequence(); }
      */
@@ -179,8 +180,8 @@ public class NJTree
         if (one2many.contains(nam))
         {
           countOne2Many++;
-          // if (jalview.bin.Cache.log.isDebugEnabled())
-          // jalview.bin.Cache.log.debug("One 2 many relationship for
+          // if (Cache.log.isDebugEnabled())
+          // Cache.log.debug("One 2 many relationship for
           // "+nam.getName());
         }
         else
@@ -195,8 +196,8 @@ public class NJTree
         j.setPlaceholder(true);
       }
     }
-    // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
-    // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+    // if (Cache.log.isDebugEnabled() && countOne2Many>0) {
+    // Cache.log.debug("There were "+countOne2Many+" alignment
     // sequence ids (out of "+one2many.size()+" unique ids) linked to two or
     // more leaves.");
     // }
@@ -218,7 +219,7 @@ 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 +246,7 @@ public class NJTree
       type = "AV";
     }
 
-    if (!(pwtype.equals("PID")))
+    if (sm == null && !(pwtype.equals("PID")))
     {
       if (ResidueProperties.getScoreMatrix(pwtype) == null)
       {
@@ -265,7 +266,7 @@ public class NJTree
 
     noseqs = i++;
 
-    distance = findDistances();
+    distance = findDistances(sm);
     // System.err.println("Made distances");// dbg
     makeLeaves();
     // System.err.println("Made leaves");// dbg
@@ -284,7 +285,7 @@ public class NJTree
    */
   public String toString()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+    NewickFile fout = new NewickFile(getTopNode());
 
     return fout.print(isHasBootstrap(), isHasDistances(),
             isHasRootDistance()); // output all data available for tree
@@ -323,7 +324,7 @@ 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 +731,18 @@ 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 +868,12 @@ 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 +894,11 @@ 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;
       }
     }
@@ -1066,8 +1069,7 @@ public class NJTree
     String[] seqdatas = seqData.getSequenceStrings(gapChar);
     for (int i = 0; i < seqdatas.length; i++)
     {
-      sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
-              .getName()));
+      sb.append(new Format("%-" + 15 + "s").form(sequence[i].getName()));
       sb.append(" " + seqdatas[i] + "\n");
     }
     return sb.toString();
@@ -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()))
+    {
       ;
+    }
   }
 }