+ //set align file as new current fastafile
+ string currentFasta = "";
+ itTypes = outputTypes.find("fasta");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; }
+ }
+ currentFiles->setFastaFile(currentFasta);
+ cout << "current fasta = " << currentFiles->getFastaFile() << endl;