+ this.GAP_OPEN_COST = gapOpenCost;
+ this.GAP_EXTEND_COST = gapExtendCost;
+ this.endGaps = endGaps;
+ this.total = MiscMath.combinations(av.getAlignment().getHeight(), 2);
+
+ if (run)
+ calculate();
+System.out.println("Creating pap");
+ }
+
+ public void calculate()
+ {
+
+ SequenceGroup selectionGroup = av.getSelectionGroup();
+ StringBuilder sb = new StringBuilder(1024);