X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=733e7f99e333f60532e73d9ccf32f33971159c7c;hb=066a11f5ce0580b9d7bf0f855432c341aa279bd4;hp=89c635397fdbfc9c369769ae7bbe660251430380;hpb=608bc7b65ff89fc814d05275fcaa87bdfa4cd9be;p=jalview.git

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index 89c6353..733e7f9 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -70,6 +70,10 @@ public class PCA implements Runnable
    */
   public PCA(String[] s, boolean nucleotides)
   {
+    this(s, nucleotides, null);
+  }
+  public PCA(String[] s, boolean nucleotides, String s_m)
+  {
 
     BinarySequence[] bs = new BinarySequence[s.length];
     int ii = 0;
@@ -83,9 +87,17 @@ public class PCA implements Runnable
 
     BinarySequence[] bs2 = new BinarySequence[s.length];
     ii = 0;
-
-    String sm = nucleotides ? "DNA" : "BLOSUM62";
-    ScoreMatrix smtrx = ResidueProperties.getScoreMatrix(sm);
+    ScoreMatrix smtrx = null;
+    String sm=s_m;
+    if (sm!=null)
+    {
+      smtrx = ResidueProperties.getScoreMatrix(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"));
+    }
     details.append("PCA calculation using " + sm
             + " sequence similarity matrix\n========\n\n");
     while ((ii < s.length) && (s[ii] != null))