JAL-2403 unit tests for PCA.computeSimilarity, signature simplified

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

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 11c73c1..d8863f7 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -43,7 +43,7 @@ public class PCA implements Runnable
 
   StringBuilder details = new StringBuilder(1024);
 
-  private AlignmentView seqs;
+  final private AlignmentView seqs;
 
   private ScoreModelI scoreModel;
   
@@ -172,7 +172,7 @@ public class PCA implements Runnable
     // long now = System.currentTimeMillis();
     try
     {
-      eigenvector = computeSimilarity(seqs);
+      eigenvector = computeSimilarity();
 
       details.append(" --- OrigT * Orig ---- \n");
       eigenvector.print(ps, "%8.2f");
@@ -223,20 +223,20 @@ public class PCA implements Runnable
    * @param av
    * @return
    */
-  MatrixI computeSimilarity(AlignmentView av)
+  MatrixI computeSimilarity()
   {
     MatrixI result = null;
     if (scoreModel instanceof SimilarityScoreModelI)
     {
-      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
+      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(seqs,
               similarityParams);
       if (scoreModel instanceof PIDModel)
       {
         /*
-         * scale % identities to width of alignment for backwards
+         * scale score to width of alignment for backwards
          * compatibility with Jalview 2.10.1 SeqSpace PCA calculation 
          */
-        result.multiply(av.getWidth() / 100d);
+        result.multiply(seqs.getWidth() / 100d);
       }
     }
     else if (scoreModel instanceof DistanceScoreModelI)
@@ -245,7 +245,7 @@ public class PCA implements Runnable
        * find distances and convert to similarity scores
        * reverseRange(false) preserves but reverses the min-max range
        */
-      result = ((DistanceScoreModelI) scoreModel).findDistances(av,
+      result = ((DistanceScoreModelI) scoreModel).findDistances(seqs,
               similarityParams);
       result.reverseRange(false);
     }