initialize();
name = newName;
- if(sequence.find_first_of('-') != string::npos) {
- setAligned(sequence);
- }
+
+ //setUnaligned removes any gap characters for us
setUnaligned(sequence);
+ setAligned(sequence);
}
//********************************************************************************************************************
}
}
- if((sequence.find_first_of('-') != string::npos) || (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);
}
//********************************************************************************************************************