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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 float[][] alignmentScores; // scores used by PaSiMap
+ private int GAP_OPEN_COST;
+
+ private int GAP_EXTEND_COST;
+
AlignmentViewport av;
Vector<SequenceI> sequences;
AlignmentViewport av;
Vector<SequenceI> sequences;
@@
-60,9
+64,9
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
*/
public PairwiseAlignPanel(AlignmentViewport viewport)
{
*/
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;
{
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],
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)
{
if (as.s1str.length() == 0 || as.s2str.length() == 0)
{