exit(1);
}
}
+//**********************************************************************************************************************
+string ClusterFragmentsCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "fasta") { outputFileName = "fragclust.fasta"; }
+ else if (type == "name") { outputFileName = "fragclust.names"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterFragmentsCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
ClusterFragmentsCommand::ClusterFragmentsCommand(){
try {
string fileroot = outputDir + m->getRootName(m->getSimpleName(fastafile));
- string newFastaFile = fileroot + "fragclust.fasta";
- string newNamesFile = fileroot + "fragclust.names";
+ string newFastaFile = fileroot + getOutputFileNameTag("fasta");
+ string newNamesFile = fileroot + getOutputFileNameTag("name");
if (m->control_pressed) { return 0; }