fixed splash page citation

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index aa1f1c7eae3c0b1cb08105a070a172169ecf320e..b2c2b53d0b4078e6e296312662dcdfe0ffe5fbec 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -21,10 +21,10 @@ Sequence::Sequence(string newName, string sequence) {
 
        initialize();   
        name = newName;
-       if(sequence.find_first_of('-') != string::npos) {
-               setAligned(sequence);
-       }
+       
+       //setUnaligned removes any gap characters for us
        setUnaligned(sequence);
+       setAligned(sequence);
        
 }
 //********************************************************************************************************************
@@ -53,10 +53,9 @@ Sequence::Sequence(ifstream& fastaFile){
                }
        }
 
-       if(sequence.find_first_of('-') != string::npos){        //      if there are any gaps in the sequence, assume that it is
-               setAligned(sequence);                                                   //      an alignment file
-       }
-       setUnaligned(sequence);                                                         //      also set the unaligned sequence file
+       setAligned(sequence);   
+       //setUnaligned removes any gap characters for us                                                
+       setUnaligned(sequence);                                                         
 }
 
 //********************************************************************************************************************
@@ -292,6 +291,7 @@ void Sequence::reverseComplement(){
                else                                            {       temp += 'N';    }
        }
        unaligned = temp;
+       aligned = temp;
        
 }