This contains Pat's bug fixes and updates. It represents mothur v.1.3.0

[mothur.git] / eachgapignore.h

diff --git a/eachgapignore.h b/eachgapignore.h
index 9b9d1673249d454bf1a7ce19f41d9b568568ccb6..9763a6d1af138dc7ebeffe66a94cf0b3c4eb5a9c 100644 (file)
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -22,40 +22,28 @@ public:
                int diff = 0;
                int length = 0;
                int start = 0;
-               int end = 0;
                
-               for(int i=0;i<A.getLength();i++){
-                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-                       }
-                       else{
+               string seqA = A.getAligned();
+               string seqB = B.getAligned();
+               int alignLength = seqA.length();
+               
+               for(int i=0; i<alignLength; i++){
+                       if(seqA[i] != '.' && seqB[i] != '.'){
                                start = i;
                                break;
                        }
                }
-               for(int i=A.getLength()-1;i>=0;i--){
-                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-                       }
-                       else{
-                               end = i;
-                               break;
-                       }
-               }
                
-               for(int i=start;i<=end;i++){
-                       if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
-                       else if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
+               for(int i=start;i<alignLength;i++){
+                       if(seqA[i] == '.' || seqB[i] == '.'){
                                break;  
                        }
-                       else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
-                               if(A.getAligned()[i] != B.getAligned()[i]){
+                       else if(seqA[i] != '-' || seqB[i] != '-'){
+                               if(seqA[i] != seqB[i]){
                                        diff++;
                                }
                                length++;
                        }
-                       else if(A.getAligned()[i] != '-' || B.getAligned()[i] != '-'){
-                               diff++;
-                               length++;
-                       }
                }
                
                if(length == 0) {       dist = 1.0000;                                                          }