X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=onegapignore.h;h=32818e3df6fce4bc5ab8a4ddda975572146a2a53;hb=fd98ee6efb944d38bbd61fc36ea9fea2557e3830;hp=785272e08c69a3e1491d5d1d2792bbc9ba3eda5d;hpb=f2d22832d127f781989c98457f42e94aea96075f;p=mothur.git

diff --git a/onegapignore.h b/onegapignore.h
index 785272e..32818e3 100644
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -25,6 +25,7 @@ public:
 		int minLength = 0;
 		int start = 0;
 		int end = 0;
+		bool overlap = false;
 		
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
@@ -35,6 +36,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
 //				cout << "start: " << start << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -42,6 +44,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				end = i;
 //				cout << "end: " << end << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -73,7 +76,10 @@ public:
 				openGapB = 0;
 			}
 		}
-
+		
+		//non-overlapping sequences
+		if (!overlap) { minLength = 0; }
+		
 		if(minLength == 0)	{	dist = 1.0000;							}
 		else				{	dist = (double)difference / minLength;	}
 	}