X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=eachgapignore.h;h=2e7fbd6bd228d3ed625cd1904ecd7d15075d9234;hp=edc1cab3e4a1bbaf006df491ce1cd79da69db046;hb=615301e57c25e241356a9c2380648d117709458d;hpb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875

diff --git a/eachgapignore.h b/eachgapignore.h
index edc1cab..2e7fbd6 100644
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -17,47 +17,52 @@
 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;
 		
-		for(int i=0;i<A.getLength();i++){
-			if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[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] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
 				start = i;
+//				cout << "start: " << start << endl;
+				overlap = true;
 				break;
 			}
 		}
-		for(int i=A.getLength()-1;i>=0;i--){
-			if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
-			}
-			else{
+		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<=end;i++){
-			if(A.getUnaligned()[i] == '-' && B.getUnaligned()[i] == '-'){}
-			else if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.'){
+			if(seqA[i] == '.' || seqB[i] == '.'){
 				break;	
 			}
-			else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
-				if(A.getUnaligned()[i] != B.getUnaligned()[i]){
+			else if(seqA[i] != '-' || seqB[i] != '-'){
+				if(seqA[i] != seqB[i]){
 					diff++;
 				}
 				length++;
 			}
-			else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
-				diff++;
-				length++;
-			}
 		}
 		
+		//non-overlapping sequences
+		if (!overlap) { length = 0; }
+		
 		if(length == 0)	{	dist = 1.0000;								}
 		else			{	dist = ((double)diff  / (double)length);	}