X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=e3a68cad9075df8244f8730108c8ad3c0cc8c7de;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=160d8538923936a2a90312ced7b8aed49a1d2e76;hpb=d06711617796df6df18ec872326a6b6b76d447c8;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 160d853..e3a68ca 100644
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -1,28 +1,40 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.api.analysis.ScoreModelI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.CigarArray;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.NewickFile;
+import jalview.schemes.ResidueProperties;
+
+import java.util.Enumeration;
+import java.util.List;
+import java.util.Vector;
 
 /**
  * DOCUMENT ME!
@@ -206,7 +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();
@@ -233,7 +245,7 @@ public class NJTree
       type = "AV";
     }
 
-    if (!(pwtype.equals("PID")))
+    if (sm == null && !(pwtype.equals("PID")))
     {
       if (ResidueProperties.getScoreMatrix(pwtype) == null)
       {
@@ -253,8 +265,7 @@ public class NJTree
 
     noseqs = i++;
 
-    distance = findDistances(this.seqData
-            .getSequenceStrings(Comparison.GapChars.charAt(0)));
+    distance = findDistances(sm);
     // System.err.println("Made distances");// dbg
     makeLeaves();
     // System.err.println("Made leaves");// dbg
@@ -275,8 +286,8 @@ public class NJTree
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
-    return fout.print(isHasBootstrap(),
-    isHasDistances(), isHasRootDistance()); // output all data available for tree
+    return fout.print(isHasBootstrap(), isHasDistances(),
+            isHasRootDistance()); // output all data available for tree
   }
 
   /**
@@ -312,7 +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);
@@ -346,24 +357,29 @@ public class NJTree
       }
     }
   }
+
   /**
-   * rename any nodes according to their associated sequence.
-   * This will modify the tree's metadata! (ie the original NewickFile or newly generated BinaryTree's label data) 
+   * rename any nodes according to their associated sequence. This will modify
+   * the tree's metadata! (ie the original NewickFile or newly generated
+   * BinaryTree's label data)
    */
-  public void renameAssociatedNodes() {
-    applyToNodes(new NodeTransformI() {
+  public void renameAssociatedNodes()
+  {
+    applyToNodes(new NodeTransformI()
+    {
 
       @Override
       public void transform(BinaryNode node)
       {
         Object el = node.element();
-        if (el!=null && el instanceof SequenceI)
+        if (el != null && el instanceof SequenceI)
         {
-          node.setName(((SequenceI)el).getName());
+          node.setName(((SequenceI) el).getName());
         }
       }
     });
   }
+
   /**
    * DOCUMENT ME!
    */
@@ -710,100 +726,26 @@ public class NJTree
   }
 
   /**
-   * DOCUMENT ME!
+   * Calculate a distance matrix given the sequence input data and score model
    * 
-   * @return DOCUMENT ME!
+   * @return similarity matrix used to compute tree
    */
-  public float[][] findDistances(String[] sequenceString)
+  public float[][] findDistances(ScoreModelI _pwmatrix)
   {
-    float[][] distance = new float[noseqs][noseqs];
 
-    if (pwtype.equals("PID"))
-    {
-      for (int i = 0; i < (noseqs - 1); i++)
-      {
-        for (int j = i; j < noseqs; j++)
-        {
-          if (j == i)
-          {
-            distance[i][i] = 0;
-          }
-          else
-          {
-            distance[i][j] = 100 - Comparison.PID(sequenceString[i],
-                    sequenceString[j]);
-
-            distance[j][i] = distance[i][j];
-          }
-        }
-      }
-    }
-    else
+    float[][] distance = new float[noseqs][noseqs];
+    if (_pwmatrix == null)
     {
-      // Pairwise substitution score (with no gap penalties)
-      ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
-      if (pwmatrix == null)
-      {
-        pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
-      }
-      int maxscore = 0;
-      int end = sequenceString[0].length();
-      for (int i = 0; i < (noseqs - 1); i++)
+      // Resolve substitution model
+      _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+      if (_pwmatrix == null)
       {
-        for (int j = i; j < noseqs; j++)
-        {
-          int score = 0;
-
-          for (int k = 0; k < end; k++)
-          {
-            try
-            {
-              score += pwmatrix.getPairwiseScore(
-                      sequenceString[i].charAt(k),
-                      sequenceString[j].charAt(k));
-            } catch (Exception ex)
-            {
-              System.err.println("err creating BLOSUM62 tree");
-              ex.printStackTrace();
-            }
-          }
-
-          distance[i][j] = (float) score;
-
-          if (score > maxscore)
-          {
-            maxscore = score;
-          }
-        }
+        _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
       }
-
-      for (int i = 0; i < (noseqs - 1); i++)
-      {
-        for (int j = i; j < noseqs; j++)
-        {
-          distance[i][j] = (float) maxscore - distance[i][j];
-          distance[j][i] = distance[i][j];
-        }
-      }
-
     }
+    distance = _pwmatrix.findDistances(seqData);
     return distance;
 
-    // else
-    /*
-     * else if (pwtype.equals("SW")) { float max = -1;
-     * 
-     * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
-     * { AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
-     * as.calcScoreMatrix(); as.traceAlignment(); as.printAlignment(System.out);
-     * distance[i][j] = (float) as.maxscore;
-     * 
-     * if (max < distance[i][j]) { max = distance[i][j]; } } }
-     * 
-     * for (int i = 0; i < (noseqs - 1); i++) { for (int j = i; j < noseqs; j++)
-     * { distance[i][j] = max - distance[i][j]; distance[j][i] = distance[i][j];
-     * } } }/
-     */
   }
 
   /**
@@ -925,12 +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());
     }
@@ -951,11 +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;
       }
     }
@@ -1157,9 +1099,8 @@ 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);
   }
 
   /**
@@ -1205,13 +1146,13 @@ 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--;
   }
@@ -1350,7 +1291,9 @@ public class NJTree
   {
     for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
             .transform((BinaryNode) nodes.nextElement()))
+    {
       ;
+    }
   }
 }