initialize();
name = newName;
- if(sequence.find_first_of('-') != string::npos) {
- setAligned(sequence);
- }
+
+ //setUnaligned removes any gap characters for us
setUnaligned(sequence);
+ setAligned(sequence);
}
//********************************************************************************************************************
initialize();
fastaFile >> name;
name = name.substr(1);
- char c;
-
- while ((c = fastaFile.get()) != EOF) { if (c == 10){ break; } } // get rest of line if there's any crap there
+ while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
char letter;
string sequence;
}
}
- 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);
}
//********************************************************************************************************************
void Sequence::setUnaligned(string sequence){
- if(sequence.find_first_of('-') != string::npos) {
+ if(sequence.find_first_of('.') != string::npos || sequence.find_first_of('-') != string::npos) {
string temp = "";
for(int j=0;j<sequence.length();j++) {
if(isalpha(sequence[j])) { temp += sequence[j]; }
else { temp += 'N'; }
}
unaligned = temp;
+ aligned = temp;
}