}else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
}else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
//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"){ outputDir = m->hasPath(fastafile); }
//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"){ outputDir = m->hasPath(fastafile); }