X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=ignoregaps.h;fp=ignoregaps.h;h=8127b6205e42d18516561565e8a4eb29ccd56ab6;hb=b01e4c8527e66f227eff16cf296eeadf060306b6;hp=aa106c9b1bbc6bcc1cde4be9dd02fb5876b3ef85;hpb=ec453945974b5c72af0bea042e3517312566d592;p=mothur.git

diff --git a/ignoregaps.h b/ignoregaps.h
index aa106c9..8127b62 100644
--- a/ignoregaps.h
+++ b/ignoregaps.h
@@ -27,7 +27,7 @@ public:
 		int end = 0;
 		
 		for(int i=0;i<A.getLength();i++){
-			if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
+			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
 			}
 			else{
 				start = i;
@@ -35,7 +35,7 @@ public:
 			}
 		}
 		for(int i=A.getLength()-1;i>=0;i--){
-			if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
+			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
 			}
 			else{
 				end = i;
@@ -44,11 +44,11 @@ public:
 		}
 		
 		for(int i=start; i<=end; i++){
-			if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.'){
+			if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
 				break;
 			}
-			else if((A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-')){
-				if(A.getUnaligned()[i] != B.getUnaligned()[i]){
+			else if((A.getAligned()[i] != '-' && B.getAligned()[i] != '-')){
+				if(A.getAligned()[i] != B.getAligned()[i]){
 					diff++;
 				}
 				length++;