X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=eachgapignore.h;h=2e7fbd6bd228d3ed625cd1904ecd7d15075d9234;hp=8e027b7d72e33cb27599268f6c779c369ea8bdd6;hb=615301e57c25e241356a9c2380648d117709458d;hpb=e4ca037c5e637e3d34e64cb5e8ab11b03220188d

diff --git a/eachgapignore.h b/eachgapignore.h
index 8e027b7..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();
@@ -31,14 +34,16 @@ 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;
 			}
 		}
@@ -55,6 +60,9 @@ public:
 			}
 		}
 		
+		//non-overlapping sequences
+		if (!overlap) { length = 0; }
+		
 		if(length == 0)	{	dist = 1.0000;								}
 		else			{	dist = ((double)diff  / (double)length);	}