it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
//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 = "";
- outputDir += hasPath(inFastaName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
}
oldNameMapFName = validParameter.validFile(parameters, "name", true);
if (abort == true) { return 0; }
//prepare filenames and open files
- string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names";
- string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName);
+ string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
+ string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
FastaMap fastamap;