X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=ignoregaps.h;h=894f92d9644182ece0a7d18e491384d2058f2d54;hp=8127b6205e42d18516561565e8a4eb29ccd56ab6;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=b01e4c8527e66f227eff16cf296eeadf060306b6

diff --git a/ignoregaps.h b/ignoregaps.h
index 8127b62..894f92d 100644
--- a/ignoregaps.h
+++ b/ignoregaps.h
@@ -20,41 +20,41 @@ class ignoreGaps : public Dist {
 	
 public:
 	
+	ignoreGaps() {}
+	
 	void calcDist(Sequence A, Sequence B){		
 		int diff = 0;
 		int length = 0;
 		int start = 0;
-		int end = 0;
+		bool overlap = false;
 		
-		for(int i=0;i<A.getLength();i++){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
+		string seqA = A.getAligned();
+		string seqB = B.getAligned();
+		int alignLength = seqA.length();
+		
+		for(int i=0;i<alignLength;i++){
+			if(seqA[i] != '.' && seqB[i] != '.'){
 				start = i;
-				break;
-			}
-		}
-		for(int i=A.getLength()-1;i>=0;i--){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
-			}
-			else{
-				end = i;
+				overlap = true;
 				break;
 			}
 		}
 		
-		for(int i=start; i<=end; i++){
-			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
+		for(int i=start; i<alignLength; i++){
+			if(seqA[i] == '.' || seqB[i] == '.'){
 				break;
 			}
-			else if((A.getAligned()[i] != '-' && B.getAligned()[i] != '-')){
-				if(A.getAligned()[i] != B.getAligned()[i]){
+			else if((seqA[i] != '-' && seqB[i] != '-')){
+				if(seqA[i] != seqB[i]){
 					diff++;
 				}
 				length++;
 			}
 		}
 		
+		//non-overlapping sequences
+		if (!overlap) { length = 0; }
+
 		if(length == 0)		{	dist = 1.0000;								}
 		else				{	dist = ((double)diff  / (double)length);	}