X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ignoregaps.h;h=894f92d9644182ece0a7d18e491384d2058f2d54;hp=e81ab92e2aaaced862fad7ae0e2f14cdf1d9f386;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186

diff --git a/ignoregaps.h b/ignoregaps.h
index e81ab92..894f92d 100644
--- a/ignoregaps.h
+++ b/ignoregaps.h
@@ -20,10 +20,13 @@ class ignoreGaps : public Dist {
 	
 public:
 	
+	ignoreGaps() {}
+	
 	void calcDist(Sequence A, Sequence B){		
 		int diff = 0;
 		int length = 0;
 		int start = 0;
+		bool overlap = false;
 		
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
@@ -32,6 +35,7 @@ public:
 		for(int i=0;i<alignLength;i++){
 			if(seqA[i] != '.' && seqB[i] != '.'){
 				start = i;
+				overlap = true;
 				break;
 			}
 		}
@@ -47,6 +51,9 @@ public:
 				length++;
 			}
 		}
+		
+		//non-overlapping sequences
+		if (!overlap) { length = 0; }
 
 		if(length == 0)		{	dist = 1.0000;								}
 		else				{	dist = ((double)diff  / (double)length);	}