mothurOut("Reading in the " + fastaFileName + " template sequences...\t"); cout.flush();
while (!fastaFile.eof()) {
- Sequence temp(fastaFile);
+ Sequence temp(fastaFile); gobble(fastaFile);
- templateSequences.push_back(temp);
-
- //save longest base
- if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length(); }
-
- gobble(fastaFile);
+ if (temp.getName() != "") {
+ templateSequences.push_back(temp);
+ //save longest base
+ if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
+ }
}
numSeqs = templateSequences.size();