JAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix delegate of

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

diff --git a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java b/src/jalview/analysis/scoremodels/PairwiseDistanceModel.java
similarity index 59%
rename from src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
rename to src/jalview/analysis/scoremodels/PairwiseDistanceModel.java
index f980d8e..cb9ad07 100644 (file)
--- a/src/jalview/analysis/scoremodels/PairwiseSeqScoreModel.java
+++ b/src/jalview/analysis/scoremodels/PairwiseDistanceModel.java
@@ -20,22 +20,41 @@
  */
 package jalview.analysis.scoremodels;
 
-import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.DistanceModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.util.Comparison;
 
-public abstract class PairwiseSeqScoreModel implements ScoreModelI
+public class PairwiseDistanceModel implements DistanceModelI
 {
-  abstract public float getPairwiseScore(char c, char d);
+  PairwiseScoreModelI scoreModel;
 
+  /**
+   * Constructor given something to provide pairwise scores for residues
+   * 
+   * @param sm
+   */
+  public PairwiseDistanceModel(PairwiseScoreModelI sm)
+  {
+    scoreModel = sm;
+  }
+
+  /**
+   * Returns a matrix of [i][j] values representing distances between pairs of
+   * sequences
+   */
   @Override
   public float[][] findDistances(AlignmentView seqData)
   {
     String[] sequenceString = seqData
-            .getSequenceStrings(Comparison.GapChars.charAt(0));
+            .getSequenceStrings(Comparison.GAP_SPACE);
     int noseqs = sequenceString.length;
     float[][] distance = new float[noseqs][noseqs];
 
+    /*
+     * calculate similarity scores for the upper half of the matrix
+     * as [i, j] = the sum of pairwise scores of corresponding
+     * positions of sequence[i] and sequence[j]
+     */
     float maxscore = 0;
     int end = sequenceString[0].length();
     for (int i = 0; i < (noseqs - 1); i++)
@@ -48,7 +67,8 @@ public abstract class PairwiseSeqScoreModel implements ScoreModelI
         {
           try
           {
-            score += getPairwiseScore(sequenceString[i].charAt(k),
+            score += scoreModel.getPairwiseScore(
+                    sequenceString[i].charAt(k),
                     sequenceString[j].charAt(k));
           } catch (Exception ex)
           {
@@ -66,6 +86,12 @@ public abstract class PairwiseSeqScoreModel implements ScoreModelI
       }
     }
 
+    /*
+     * subtract similarity scores from the maximum value to
+     * convert to a distance measure; also populate the lower
+     * half of the result matrix with this value 
+     */
+    // FIXME this assumes the score matrix is symmetric - it may not be?
     for (int i = 0; i < (noseqs - 1); i++)
     {
       for (int j = i; j < noseqs; j++)
@@ -77,5 +103,26 @@ public abstract class PairwiseSeqScoreModel implements ScoreModelI
     return distance;
   }
 
-  abstract public float[][] getMatrix();
+  @Override
+  public String getName()
+  {
+    return scoreModel.getName();
+  }
+
+  @Override
+  public boolean isDNA()
+  {
+    return scoreModel.isDNA();
+  }
+
+  @Override
+  public boolean isProtein()
+  {
+    return scoreModel.isProtein();
+  }
+
+  public PairwiseScoreModelI getScoreModel()
+  {
+    return scoreModel;
+  }
 }