X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=onegapignore.h;h=dba3f38292ced957330631ece5572901ee3438ae;hb=d3aed959ca3b68890eeb7b815e24210bcfeb256c;hp=785272e08c69a3e1491d5d1d2792bbc9ba3eda5d;hpb=f2d22832d127f781989c98457f42e94aea96075f;p=mothur.git

diff --git a/onegapignore.h b/onegapignore.h
index 785272e..dba3f38 100644
--- a/onegapignore.h
+++ b/onegapignore.h
@@ -17,6 +17,10 @@
 class oneGapIgnoreTermGapDist : public Dist {
 	
 public:
+	
+	oneGapIgnoreTermGapDist() {}
+	oneGapIgnoreTermGapDist(const oneGapIgnoreTermGapDist& ddb) {}
+	
 	void calcDist(Sequence A, Sequence B){
 		
 		int difference = 0;
@@ -25,6 +29,7 @@ public:
 		int minLength = 0;
 		int start = 0;
 		int end = 0;
+		bool overlap = false;
 		
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
@@ -35,6 +40,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
 //				cout << "start: " << start << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -42,6 +48,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				end = i;
 //				cout << "end: " << end << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -73,7 +80,10 @@ public:
 				openGapB = 0;
 			}
 		}
-
+		
+		//non-overlapping sequences
+		if (!overlap) { minLength = 0; }
+		
 		if(minLength == 0)	{	dist = 1.0000;							}
 		else				{	dist = (double)difference / minLength;	}
 	}