added distance command and filterseqs

[mothur.git] / eachgapdist.h

diff --git a/eachgapdist.h b/eachgapdist.h
index 767c4bf819aa25f2bee0c4f40a99374a30bb35e5..f4f00c16d4b41632f2c435d921ddc5bb3554edad 100644 (file)
--- a/eachgapdist.h
+++ b/eachgapdist.h
@@ -22,24 +22,24 @@ public:
                int start = 0;
                
                for(int i=0; i<A.getLength(); i++){
-                       if(A.getAligned()[i] != '.' || B.getAligned()[i] != '.'){
+                       if(A.getUnaligned()[i] != '.' || B.getUnaligned()[i] != '.'){
                                start = i;
                                break;
                        }
                }
                
                for(int i=start;i<A.getLength();i++){
-                       if((A.getAligned()[i] == '-' || B.getAligned()[i] == '-') && (A.getAligned()[i] == '.' || B.getAligned()[i] == '.')){}
-                       else if(A.getAligned()[i] == '.' && B.getAligned()[i] == '.'){
+                       if((A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-') && (A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.')){}
+                       else if(A.getUnaligned()[i] == '.' && B.getUnaligned()[i] == '.'){
                                break;  
                        }
-                       else if(A.getAligned()[i] != '-' && B.getAligned()[i] != '-'){
-                               if(A.getAligned()[i] != B.getAligned()[i]){
+                       else if(A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-'){
+                               if(A.getUnaligned()[i] != B.getUnaligned()[i]){
                                        diff++;
                                }
                                length++;
                        }
-                       else if(A.getAligned()[i] != '-' || B.getAligned()[i] != '-'){
+                       else if(A.getUnaligned()[i] != '-' || B.getUnaligned()[i] != '-'){
                                diff++;
                                length++;
                        }