JAL-1632 JAL-2416 load score matrices from file, as float[][]

[jalview.git] / src / jalview / analysis / scoremodels / PairwiseSeqScoreModel.java

diff --git a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java b/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
index 2ff2518..f980d8e 100644 (file)
--- a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
+++ b/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
@@ -26,8 +26,9 @@ 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
@@ -35,13 +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++)
         {
@@ -56,7 +57,7 @@ public abstract class PairwiseSeqScoreModel implements ScoreModelI
           }
         }
 
-        distance[i][j] = (float) score;
+        distance[i][j] = score;
 
         if (score > maxscore)
         {
@@ -69,12 +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();
 }