pat's minor edits to distance calculations

[mothur.git] / onegapignore.h

diff --git a/onegapignore.h b/onegapignore.h
index 6421741c0d4c153794ab40efc9318af6d64349a4..af284fcc6857a3c5a42545ca6c78c22cded9424d 100644 (file)
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -9,6 +9,7 @@
  *
  */
 
+
 #include "dist.h"
 
 /**************************************************************************************************/
@@ -28,17 +29,19 @@ public:
                string seqA = A.getAligned();
                string seqB = B.getAligned();
                int alignLength = seqA.length();
-               
+
                // this assumes that sequences start and end with '.'s instead of'-'s.
                for(int i=0;i<alignLength;i++){
-                       if(seqA[i] != '.' && seqB[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] != '.'){
+                       if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
                                end = i;
+                               cout << "end: " << end << endl;
                                break;
                        }
                }