X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=onegapdist.h;h=cb63ae678fa691b0a08b3935432eec9a5e874bd8;hb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;hp=c466c5380e7abe662d3fad9efdb40f5e39aa650f;hpb=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186;p=mothur.git

diff --git a/onegapdist.h b/onegapdist.h
index c466c53..cb63ae6 100644
--- a/onegapdist.h
+++ b/onegapdist.h
@@ -38,6 +38,9 @@ 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 +70,6 @@ public:
 					openGapB = 0;
 				}
 			}
-
-			else if(seqA[i] == '.' && seqB[i] == '.'){
-				break;
-			}
 		}
 	
 		if(minLength == 0)	{	dist = 1.0000;							}