inFastaName = m->getFastaFile();
if (inFastaName != "") { m->mothurOut("Using " + inFastaName + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
+ }else { m->setFastaFile(inFastaName); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
oldNameMapFName = validParameter.validFile(parameters, "name", true);
if (oldNameMapFName == "not open") { abort = true; }
else if (oldNameMapFName == "not found"){ oldNameMapFName = ""; }
+ else { m->setNameFile(oldNameMapFName); }
}
}