/**************************************************************************************************/
-GotohOverlap::GotohOverlap(float gO, float gE, float m, float mm, int r) :
- gapOpen(gO), gapExtend(gE), match(m), mismatch(mm), Alignment(r) {
+GotohOverlap::GotohOverlap(float gO, float gE, float f, float mm, int r) :
+ gapOpen(gO), gapExtend(gE), match(f), mismatch(mm), Alignment(r) {
try {
for(int i=1;i<nCols;i++){ // we initialize the dynamic programming matrix by setting the pointers in
}
catch(exception& e) {
- errorOut(e, "GotohOverlap", "GotohOverlap");
+ m->errorOut(e, "GotohOverlap", "GotohOverlap");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "GotohOverlap", "align");
+ m->errorOut(e, "GotohOverlap", "align");
exit(1);
}
}