abort = true;
}
}else if (taxonomyFileName == "not open") { abort = true; }
+ else { m->setTaxonomyFile(taxonomyFileName); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { namefile = ""; }
- else { readNamesFile(); }
+ else { readNamesFile(); m->setNameFile(namefile); }
//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"){