fixed bug in venn command

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
index e280ce0ea45e3c828205a5d8872a47cacf8fcc02..ee6cc5267931816a654c99f4e748d19bb2940901 100644 (file)
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -26,7 +26,7 @@ public:
                int end = 0;
                
                for(int i=0;i<A.getLength();i++){
-                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
+                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
                        }
                        else{
                                start = i;
@@ -34,7 +34,7 @@ public:
                        }
                }
                for(int i=A.getLength()-1;i>=0;i--){
-                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
+                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
                        }
                        else{
                                end = i;
@@ -44,8 +44,8 @@ public:
                
                
                for(int i=start;i<=end;i++){
-                       if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] == '-'){}
-                       else if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] != '-'){
+                       if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
+                       else if(A.getAligned()[i] == '-' && B.getAligned()[i] != '-'){
                                if(openGapA == 0){
                                        difference++;
                                        minLength++;
@@ -53,7 +53,7 @@ public:
                                        openGapB = 0;
                                }
                        }
-                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] == '-'){
+                       else if(A.getAligned()[i] != '-' && B.getAligned()[i] == '-'){
                                if(openGapB == 0){
                                        difference++;
                                        minLength++;
@@ -61,8 +61,8 @@ 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;