X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=eachgapignore.h;h=824a8b87b936c75dbfe21fdaf6a1b9a54c1440b0;hb=1d5962b46d9e72a2b855b4176d1c47df9a163fac;hp=f6824cf8d3e407dce231f3fc18194cb5f7b8bc0e;hpb=f2d22832d127f781989c98457f42e94aea96075f;p=mothur.git

diff --git a/eachgapignore.h b/eachgapignore.h
index f6824cf..824a8b8 100644
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -23,6 +23,7 @@ public:
 		int length = 0;
 		int start = 0;
 		int end = 0;
+		bool overlap = false;
 		
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
@@ -32,6 +33,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
 //				cout << "start: " << start << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -39,6 +41,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				end = i;
 //				cout << "end: " << end << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -55,6 +58,9 @@ public:
 			}
 		}
 		
+		//non-overlapping sequences
+		if (!overlap) { length = 0; }
+		
 		if(length == 0)	{	dist = 1.0000;								}
 		else			{	dist = ((double)diff  / (double)length);	}