Fix PaSiMap taking scoreModels input and allow AlignSeq/PairwiseAlignPanel to take...

[jalview.git] / src / jalview / gui / PairwiseAlignPanel.java

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 6800b0c..65f1c6d 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
@@ -115,6 +116,10 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
   
   public void calculate()
   {
+    calculate(null);
+  }
+  public void calculate (ScoreMatrix sm)
+  {
 
     StringBuilder sb = new StringBuilder(1024);
 
@@ -176,6 +181,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       {
         AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
                 seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
+        if (sm != null)
+         as.setScoreMatrix(sm);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {