X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=onegapignore.h;h=32818e3df6fce4bc5ab8a4ddda975572146a2a53;hb=0bcfddf7bc721a334bdae42d86a580019303537d;hp=af284fcc6857a3c5a42545ca6c78c22cded9424d;hpb=e4ca037c5e637e3d34e64cb5e8ab11b03220188d;p=mothur.git

diff --git a/onegapignore.h b/onegapignore.h
index af284fc..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();
@@ -34,14 +35,16 @@ public:
 		for(int i=0;i<alignLength;i++){
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
-				cout << "start: " << start << endl;
+//				cout << "start: " << start << endl;
+				overlap = true;
 				break;
 			}
 		}
 		for(int i=alignLength-1;i>=0;i--){
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				end = i;
-				cout << "end: " << end << endl;
+//				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;	}
 	}