pat's minor edits to distance calculations

[mothur.git] / eachgapignore.h

diff --git a/eachgapignore.h b/eachgapignore.h
index 9763a6d1af138dc7ebeffe66a94cf0b3c4eb5a9c..8e027b7d72e33cb27599268f6c779c369ea8bdd6 100644 (file)
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -22,19 +22,28 @@ public:
                int diff = 0;
                int length = 0;
                int start = 0;
+               int end = 0;
                
                string seqA = A.getAligned();
                string seqB = B.getAligned();
                int alignLength = seqA.length();
                
-               for(int i=0; i<alignLength; i++){
-                       if(seqA[i] != '.' && seqB[i] != '.'){
+               for(int i=0;i<alignLength;i++){
+                       if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                start = i;
+                               cout << "start: " << start << endl;
+                               break;
+                       }
+               }
+               for(int i=alignLength-1;i>=0;i--){
+                       if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
+                               end = i;
+                               cout << "end: " << end << endl;
                                break;
                        }
                }
                
-               for(int i=start;i<alignLength;i++){
+               for(int i=start;i<=end;i++){
                        if(seqA[i] == '.' || seqB[i] == '.'){
                                break;  
                        }