+ 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); }