changes while testing

[mothur.git] / onegapdist.h

diff --git a/onegapdist.h b/onegapdist.h
index c466c5380e7abe662d3fad9efdb40f5e39aa650f..3e5b6c72f1d862ab88698360566a84e6a87953de 100644 (file)
--- a/onegapdist.h
+++ b/onegapdist.h
@@ -17,6 +17,9 @@
 class oneGapDist : public Dist {
        
 public:
+       
+       oneGapDist() {}
+       
        void calcDist(Sequence A, Sequence B){
                
                int difference = 0;
@@ -38,6 +41,9 @@ public:
 
                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++;
@@ -67,10 +73,6 @@ public:
                                        openGapB = 0;
                                }
                        }
-
-                       else if(seqA[i] == '.' && seqB[i] == '.'){
-                               break;
-                       }
                }
        
                if(minLength == 0)      {       dist = 1.0000;                                                  }