X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=eachgapignore.h;h=2e7fbd6bd228d3ed625cd1904ecd7d15075d9234;hp=9763a6d1af138dc7ebeffe66a94cf0b3c4eb5a9c;hb=615301e57c25e241356a9c2380648d117709458d;hpb=cdcf99b7760701e6869ca8e4e6e91c8e8c4ae186

diff --git a/eachgapignore.h b/eachgapignore.h
index 9763a6d..2e7fbd6 100644
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -17,24 +17,38 @@
 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();
 		int alignLength = seqA.length();
 		
-		for(int i=0; i<alignLength; i++){
-			if(seqA[i] != '.' && seqB[i] != '.'){
+		for(int i=0;i<alignLength;i++){
+			if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
+//				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;
+				overlap = true;
 				break;
 			}
 		}
 		
-		for(int i=start;i<alignLength;i++){
+		for(int i=start;i<=end;i++){
 			if(seqA[i] == '.' || seqB[i] == '.'){
 				break;	
 			}
@@ -46,6 +60,9 @@ public:
 			}
 		}
 		
+		//non-overlapping sequences
+		if (!overlap) { length = 0; }
+		
 		if(length == 0)	{	dist = 1.0000;								}
 		else			{	dist = ((double)diff  / (double)length);	}