fixed bug in venn command

[mothur.git] / onegapdist.h

diff --git a/onegapdist.h b/onegapdist.h
index ef290fe22b91f0ac1e1fbc9a29bc86e86eea8511..b6b257cb2f452027f19ff06e199f432076a2ef5b 100644 (file)
--- a/onegapdist.h
+++ b/onegapdist.h
@@ -26,7 +26,7 @@ public:
                int start = 0;
                
                for(int i=0;i<A.getLength();i++){
-                       if(A.getUnaligned()[i] == '.' && B.getUnaligned()[i] == '.'){
+                       if(A.getAligned()[i] == '.' && B.getAligned()[i] == '.'){
                        }
                        else{
                                start = i;
@@ -34,8 +34,8 @@ public:
                        }
                }
                for(int i=start;i<A.getLength();i++){
-                       if((A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-') && (A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.')){}
-                       else if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '.'){
+                       if((A.getAligned()[i] == '-' || B.getAligned()[i] == '-') && (A.getAligned()[i] == '.' || B.getAligned()[i] == '.')){}
+                       else if(A.getAligned()[i] == '-' && B.getAligned()[i] != '-' && B.getAligned()[i] != '.'){
                                if(openGapA == 0){
                                        difference++;
                                        minLength++;
@@ -43,7 +43,7 @@ public:
                                        openGapB = 0;
                                }
                        }
-                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] == '-' && A.getUnaligned()[i] != '.'){
+                       else if(A.getAligned()[i] != '-' && B.getAligned()[i] == '-' && A.getAligned()[i] != '.'){
                                if(openGapB == 0){
                                        difference++;
                                        minLength++;
@@ -51,8 +51,8 @@ public:
                                        openGapB = 1;
                                }
                        }
-                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
-                               if(A.getUnaligned()[i] != B.getUnaligned()[i]){
+                       else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
+                               if(A.getAligned()[i] != B.getAligned()[i]){
                                        difference++;
                                        minLength++;
                                        openGapA = 0;
@@ -64,7 +64,7 @@ public:
                                        openGapB = 0;
                                }
                        }
-                       else if(A.getUnaligned()[i] == '.' && B.getUnaligned()[i] == '.'){
+                       else if(A.getAligned()[i] == '.' && B.getAligned()[i] == '.'){
                                break;
                        }
                }