added distance command and filterseqs

[mothur.git] / eachgapignore.h

diff --git a/eachgapignore.h b/eachgapignore.h
index 9b9d1673249d454bf1a7ce19f41d9b568568ccb6..edc1cab3e4a1bbaf006df491ce1cd79da69db046 100644 (file)
--- a/eachgapignore.h
+++ b/eachgapignore.h
@@ -25,7 +25,7 @@ public:
                int end = 0;
                
                for(int i=0;i<A.getLength();i++){
-                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
+                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
                        }
                        else{
                                start = i;
@@ -33,7 +33,7 @@ public:
                        }
                }
                for(int i=A.getLength()-1;i>=0;i--){
-                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
+                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
                        }
                        else{
                                end = i;
@@ -42,17 +42,17 @@ public:
                }
                
                for(int i=start;i<=end;i++){
-                       if(A.getAligned()[i] == '-' && B.getAligned()[i] == '-'){}
-                       else if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
+                       if(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++;
                        }