X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=87ec922ccd96cb68673774ddad84c9ba7fb7121f;hb=c6e8e8ccd10f21698226ae37196cd9680e6804a0;hp=41dbcc0f7f0c871d1a61b691ca9b18ef6803dad1;hpb=1750b2f1dcdb6e7de41d0ef7beda88dc3400afba;p=jalview.git

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 41dbcc0..87ec922 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -21,10 +21,10 @@
 package jalview.analysis;
 
 import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
 import jalview.datamodel.BinarySequence;
 import jalview.datamodel.BinarySequence.InvalidSequenceTypeException;
 import jalview.math.Matrix;
-import jalview.schemes.ResidueProperties;
 
 import java.io.PrintStream;
 
@@ -94,14 +94,14 @@ public class PCA implements Runnable
     String sm = s_m;
     if (sm != null)
     {
-      smtrx = ResidueProperties.getScoreMatrix(sm);
+      smtrx = (ScoreMatrix) ScoreModels.getInstance().forName(sm);
     }
     if (smtrx == null)
     {
       // either we were given a non-existent score matrix or a scoremodel that
       // isn't based on a pairwise symbol score matrix
-      smtrx = ResidueProperties.getScoreMatrix(sm = (nucleotides ? "DNA"
-              : "BLOSUM62"));
+      smtrx = (ScoreMatrix) ScoreModels.getInstance().forName(
+              sm = (nucleotides ? "DNA" : "BLOSUM62"));
     }
     details.append("PCA calculation using " + sm
             + " sequence similarity matrix\n========\n\n");