changes while testing

[mothur.git] / gotohoverlap.cpp

diff --git a/gotohoverlap.cpp b/gotohoverlap.cpp
index f6fef1d6baeac3e950c5afbfa94ce4859496eb44..ea27df07068a5e2060d3a1be4220a9b2de57822c 100644 (file)
--- a/gotohoverlap.cpp
+++ b/gotohoverlap.cpp
@@ -25,8 +25,8 @@
 
 /**************************************************************************************************/
 
-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
@@ -43,7 +43,7 @@ GotohOverlap::GotohOverlap(float gO, float gE, float m, float mm, int r) :
                
        }
        catch(exception& e) {
-               errorOut(e, "GotohOverlap", "GotohOverlap");
+               m->errorOut(e, "GotohOverlap", "GotohOverlap");
                exit(1);
        }
 }
@@ -94,7 +94,7 @@ void GotohOverlap::align(string A, string B){
                
        }
        catch(exception& e) {
-               errorOut(e, "GotohOverlap", "align");
+               m->errorOut(e, "GotohOverlap", "align");
                exit(1);
        }
 }