changed random forest output filename

[mothur.git] / ignoregaps.h

diff --git a/ignoregaps.h b/ignoregaps.h
index aa106c9b1bbc6bcc1cde4be9dd02fb5876b3ef85..894f92d9644182ece0a7d18e491384d2058f2d54 100644 (file)
--- a/ignoregaps.h
+++ b/ignoregaps.h
@@ -20,41 +20,41 @@ class ignoreGaps : public Dist {
        
 public:
        
+       ignoreGaps() {}
+       
        void calcDist(Sequence A, Sequence B){          
                int diff = 0;
                int length = 0;
                int start = 0;
-               int end = 0;
+               bool overlap = false;
                
-               for(int i=0;i<A.getLength();i++){
-                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[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.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
-                       }
-                       else{
-                               end = i;
+                               overlap = true;
                                break;
                        }
                }
                
-               for(int i=start; i<=end; i++){
-                       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] != '-')){
+                               if(seqA[i] != seqB[i]){
                                        diff++;
                                }
                                length++;
                        }
                }
                
+               //non-overlapping sequences
+               if (!overlap) { length = 0; }
+
                if(length == 0)         {       dist = 1.0000;                                                          }
                else                            {       dist = ((double)diff  / (double)length);        }