JAL-1632 add score model params to PCAModel and PCA constructors

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

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 1797296..43f2161 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -22,6 +22,7 @@ package jalview.analysis;
 
 import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.api.analysis.SimilarityScoreModelI;
 import jalview.datamodel.AlignmentView;
 import jalview.math.MatrixI;
@@ -46,12 +47,15 @@ public class PCA implements Runnable
   private AlignmentView seqs;
 
   private ScoreModelI scoreModel;
+  
+  private SimilarityParamsI similarityParams;
 
-  public PCA(AlignmentView s, ScoreModelI sm)
+  public PCA(AlignmentView s, ScoreModelI sm, SimilarityParamsI options)
   {
     this.seqs = s;
-
-    scoreModel = sm;
+    this.similarityParams = options;
+    this.scoreModel = sm;
+    
     details.append("PCA calculation using " + sm.getName()
             + " sequence similarity matrix\n========\n\n");
   }
@@ -230,11 +234,13 @@ public class PCA implements Runnable
     MatrixI result = null;
     if (scoreModel instanceof SimilarityScoreModelI)
     {
-      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av);
+      result = ((SimilarityScoreModelI) scoreModel).findSimilarities(av,
+              similarityParams);
     }
     else if (scoreModel instanceof DistanceScoreModelI)
     {
-      result = ((DistanceScoreModelI) scoreModel).findDistances(av);
+      result = ((DistanceScoreModelI) scoreModel).findDistances(av,
+              similarityParams);
       result.reverseRange(false);
     }
     else