X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2Fscoremodels%2FPairwiseSeqScoreModel.java;h=f980d8ecd365bf6e642691687c6670aa4a2ff11b;hb=4724cafdcdcc4f3acc77c09261afe56f518a1e87;hp=c518b21cb3e2a48a91ba932bc9057aa64bb41c83;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java b/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
index c518b21..f980d8e 100644
--- a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
+++ b/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * 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.
  * 
@@ -22,13 +22,13 @@ package jalview.analysis.scoremodels;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.datamodel.AlignmentView;
-import jalview.schemes.ScoreMatrix;
 import jalview.util.Comparison;
 
 public abstract class PairwiseSeqScoreModel implements ScoreModelI
 {
-  abstract public int getPairwiseScore(char c, char d);
+  abstract public float getPairwiseScore(char c, char d);
 
+  @Override
   public float[][] findDistances(AlignmentView seqData)
   {
     String[] sequenceString = seqData
@@ -36,13 +36,13 @@ public abstract class PairwiseSeqScoreModel implements ScoreModelI
     int noseqs = sequenceString.length;
     float[][] distance = new float[noseqs][noseqs];
 
-    int maxscore = 0;
+    float 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;
+        float score = 0;
 
         for (int k = 0; k < end; k++)
         {
@@ -57,7 +57,7 @@ public abstract class PairwiseSeqScoreModel implements ScoreModelI
           }
         }
 
-        distance[i][j] = (float) score;
+        distance[i][j] = score;
 
         if (score > maxscore)
         {
@@ -70,12 +70,12 @@ public abstract class PairwiseSeqScoreModel implements ScoreModelI
     {
       for (int j = i; j < noseqs; j++)
       {
-        distance[i][j] = (float) maxscore - distance[i][j];
+        distance[i][j] = maxscore - distance[i][j];
         distance[j][i] = distance[i][j];
       }
     }
     return distance;
   }
 
-  abstract public int[][] getMatrix();
+  abstract public float[][] getMatrix();
 }