JAL-1473 refactor score matrices and tree score calculations to interface/api and...

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 944354f..41d599e 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -20,6 +20,7 @@ package jalview.analysis;
 
 import java.util.*;
 
+import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
@@ -254,8 +255,7 @@ public class NJTree
 
     noseqs = i++;
 
-    distance = findDistances(this.seqData
-            .getSequenceStrings(Comparison.GapChars.charAt(0)));
+    distance = findDistances();
     // System.err.println("Made distances");// dbg
     makeLeaves();
     // System.err.println("Made leaves");// dbg
@@ -716,100 +716,25 @@ 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()
   {
+    
     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
-    {
       // Pairwise substitution score (with no gap penalties)
-      ScoreMatrix pwmatrix = ResidueProperties.getScoreMatrix(pwtype);
-      if (pwmatrix == null)
+      ScoreModelI _pwmatrix = ResidueProperties.getScoreModel(pwtype);
+      if (_pwmatrix == null)
       {
-        pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
+        _pwmatrix = ResidueProperties.getScoreMatrix("BLOSUM62");
       }
-      int maxscore = 0;
-      int end = sequenceString[0].length();
-      for (int i = 0; i < (noseqs - 1); i++)
-      {
-        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;
-          }
-        }
-      }
-
-      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];
-     * } } }/
-     */
+
   }
 
   /**