X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=eachgapignore.h;h=2e7fbd6bd228d3ed625cd1904ecd7d15075d9234;hp=f6824cf8d3e407dce231f3fc18194cb5f7b8bc0e;hb=615301e57c25e241356a9c2380648d117709458d;hpb=f2d22832d127f781989c98457f42e94aea96075f

diff --git a/eachgapignore.h b/eachgapignore.h
index f6824cf..2e7fbd6 100644
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -17,12 +17,15 @@
 class eachGapIgnoreTermGapDist : public Dist {
 	
 public:
+	eachGapIgnoreTermGapDist() {}
+	eachGapIgnoreTermGapDist(const eachGapIgnoreTermGapDist& ddb) {}
 	
 	void calcDist(Sequence A, Sequence B){		
 		int diff = 0;
 		int length = 0;
 		int start = 0;
 		int end = 0;
+		bool overlap = false;
 		
 		string seqA = A.getAligned();
 		string seqB = B.getAligned();
@@ -32,6 +35,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
 //				cout << "start: " << start << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -39,6 +43,7 @@ public:
 			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				end = i;
 //				cout << "end: " << end << endl;
+				overlap = true;
 				break;
 			}
 		}
@@ -55,6 +60,9 @@ public:
 			}
 		}
 		
+		//non-overlapping sequences
+		if (!overlap) { length = 0; }
+		
 		if(length == 0)	{	dist = 1.0000;								}
 		else			{	dist = ((double)diff  / (double)length);	}