Merge branch 'develop' into features/JAL-2393customMatrices

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

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 9babaee..b6766c6 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -20,9 +20,10 @@
  */
 package jalview.analysis;
 
+import jalview.analysis.scoremodels.PairwiseDistanceModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.math.MatrixI;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
 
 import java.io.PrintStream;
 
@@ -80,14 +81,15 @@ public class PCA implements Runnable
     String sm = s_m;
     if (sm != null)
     {
-      scoreMatrix = ResidueProperties.getScoreMatrix(sm);
+      scoreMatrix = (ScoreMatrix) ((PairwiseDistanceModel) ScoreModels
+              .getInstance()
+              .forName(sm)).getScoreModel();
     }
     if (scoreMatrix == null)
     {
       // either we were given a non-existent score matrix or a scoremodel that
       // isn't based on a pairwise symbol score matrix
-      scoreMatrix = ResidueProperties
-              .getScoreMatrix(sm = (nucleotides ? "DNA" : "BLOSUM62"));
+      scoreMatrix = ScoreModels.getInstance().getDefaultModel(!nucleotides);
     }
     details.append("PCA calculation using " + sm
             + " sequence similarity matrix\n========\n\n");