ifstream in;
openInputFile(file, in);
vector<Sequence*> container;
+ int count = 0;
+ int length = 0;
+ unaligned = false;
//read in seqs and store in vector
while(!in.eof()){
Sequence* current = new Sequence(in); gobble(in);
+ if (count == 0) { length = current->getAligned().length(); count++; } //gets first seqs length
+ else if (length != current->getAligned().length()) { //seqs are unaligned
+ unaligned = true;
+ }
+
if (current->getName() != "") { container.push_back(current); }
}