changing command name classify.shared to classifyrf.shared

[mothur.git] / onegapdist.h

diff --git a/onegapdist.h b/onegapdist.h
index ef290fe22b91f0ac1e1fbc9a29bc86e86eea8511..3e5b6c72f1d862ab88698360566a84e6a87953de 100644 (file)
--- a/onegapdist.h
+++ b/onegapdist.h
@@ -17,25 +17,34 @@
 class oneGapDist : public Dist {
        
 public:
+       
+       oneGapDist() {}
+       
        void calcDist(Sequence A, Sequence B){
                
                int difference = 0;
+               int minLength = 0;
                int openGapA = 0;
                int openGapB = 0;
-               int minLength = 0;
                int start = 0;
                
-               for(int i=0;i<A.getLength();i++){
-                       if(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=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] != '-' && B.getUnaligned()[i] != '.'){
+
+               for(int i=start;i<alignLength;i++){
+                       if((seqA[i] == '-' && seqB[i] == '-') || (seqA[i] == '.' && seqB[i] == '-') || (seqA[i] == '-' && seqB[i] == '.')){     ;       }
+                       else if(seqA[i] == '.' && seqB[i] == '.'){
+                               break;
+                       }
+                       else if(seqB[i] != '-' && (seqA[i] == '-' || seqA[i] == '.')){
                                if(openGapA == 0){
                                        difference++;
                                        minLength++;
@@ -43,7 +52,7 @@ public:
                                        openGapB = 0;
                                }
                        }
-                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] == '-' && A.getUnaligned()[i] != '.'){
+                       else if(seqA[i] != '-' && (seqB[i] == '-' || seqB[i] == '.')){
                                if(openGapB == 0){
                                        difference++;
                                        minLength++;
@@ -51,8 +60,8 @@ public:
                                        openGapB = 1;
                                }
                        }
-                       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]){
                                        difference++;
                                        minLength++;
                                        openGapA = 0;
@@ -64,10 +73,8 @@ public:
                                        openGapB = 0;
                                }
                        }
-                       else if(A.getUnaligned()[i] == '.' && B.getUnaligned()[i] == '.'){
-                               break;
-                       }
                }
+       
                if(minLength == 0)      {       dist = 1.0000;                                                  }
                else                            {       dist = (double)difference / minLength;  }
        }
@@ -76,4 +83,4 @@ public:
 
 /**************************************************************************************************/
 
-#endif
\ No newline at end of file
+#endif