sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / eachgapdist.h

diff --git a/eachgapdist.h b/eachgapdist.h
index f4f00c16d4b41632f2c435d921ddc5bb3554edad..1aca10c4bd208f6cf6c0dbfd9f97fdde97afe576 100644 (file)
--- a/eachgapdist.h
+++ b/eachgapdist.h
@@ -9,6 +9,7 @@
  *
  */
 
+
 #include "dist.h"
 
 /**************************************************************************************************/
@@ -16,41 +17,44 @@
 class eachGapDist : public Dist {
        
 public:
+       
+       eachGapDist() {}
+       
        void calcDist(Sequence A, Sequence B){          
                int diff = 0;
                int length = 0;
                int start = 0;
                
-               for(int i=0; i<A.getLength(); i++){
-                       if(A.getUnaligned()[i] != '.' || B.getUnaligned()[i] != '.'){
+               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=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] == '.'){
+
+               for(int i=start;i<alignLength;i++){
+                       if(seqA[i] == '.' && seqB[i] == '.'){
                                break;  
                        }
-                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
-                               if(A.getUnaligned()[i] != B.getUnaligned()[i]){
+                       else if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-')){;}
+                       else{
+                               if(seqA[i] != seqB[i]){
                                        diff++;
                                }
                                length++;
                        }
-                       else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
-                               diff++;
-                               length++;
-                       }
                }
                
                if(length == 0) {       dist = 1.0000;                                                          }
                else                    {       dist = ((double)diff  / (double)length);        }
-               
        }
 };
 
 /**************************************************************************************************/
 
-#endif
\ No newline at end of file
+#endif