X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=eachgapdist.h;h=1aca10c4bd208f6cf6c0dbfd9f97fdde97afe576;hp=f4f00c16d4b41632f2c435d921ddc5bb3554edad;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875

diff --git a/eachgapdist.h b/eachgapdist.h
index f4f00c1..1aca10c 100644
--- a/eachgapdist.h
+++ b/eachgapdist.h
@@ -9,6 +9,7 @@
  *
  */
 
+
 #include "dist.h"
 
 /**************************************************************************************************/
@@ -16,41 +17,44 @@
 class eachGapDist : public Dist {
 	
 public:
+	
+	eachGapDist() {}
+	
 	void calcDist(Sequence A, Sequence B){		
 		int diff = 0;
 		int length = 0;
 		int start = 0;
 		
-		for(int i=0; i<A.getLength(); i++){
-			if(A.getUnaligned()[i] != '.' || B.getUnaligned()[i] != '.'){
+		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=start;i<A.getLength();i++){
-			if((A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-') && (A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.')){}
-			else if(A.getUnaligned()[i] == '.' && B.getUnaligned()[i] == '.'){
+
+		for(int i=start;i<alignLength;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] == '-') || (seqA[i] == '-' && seqB[i] == '.') || (seqA[i] == '.' && seqB[i] == '-')){;}
+			else{
+				if(seqA[i] != seqB[i]){
 					diff++;
 				}
 				length++;
 			}
-			else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
-				diff++;
-				length++;
-			}
 		}
 		
 		if(length == 0)	{	dist = 1.0000;								}
 		else			{	dist = ((double)diff  / (double)length);	}
-		
 	}
 };
 
 /**************************************************************************************************/
 
-#endif
\ No newline at end of file
+#endif