Applying adjustablenw_params.patch (JAL-4159)

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

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index fafee94..a499365 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -47,6 +47,10 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private float[][] alignmentScores;   // scores used by PaSiMap
 
+  private int GAP_OPEN_COST;
+
+  private int GAP_EXTEND_COST;
+
   AlignmentViewport av;
 
   Vector<SequenceI> sequences;
@@ -60,9 +64,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
    */
   public PairwiseAlignPanel(AlignmentViewport viewport)
   {
-    this(viewport, false);
+    this(viewport, false, 120, 20);    // default penalties used in AlignSeq
   }
-  public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps)
+  public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
   {
     super();
     this.av = viewport;
@@ -104,7 +108,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
       for (int j = 0; j < i; j++)
       {
         AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
-                seqStrings[j], type);
+                seqStrings[j], type, gapOpenCost, gapExtendCost);
 
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {