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; }
}
//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(fasta); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fasta); //if user entered a file with a path then preserve it
}
}
if (abort == true) { return 0; }
ifstream inFASTA;
- openInputFile(fasta, inFASTA);
+ m->openInputFile(fasta, inFASTA);
ofstream outFASTA;
- string reverseFile = outputDir + getRootName(getSimpleName(fasta)) + "rc" + getExtension(fasta);
- openOutputFile(reverseFile, outFASTA);
+ string reverseFile = outputDir + m->getRootName(m->getSimpleName(fasta)) + "rc" + m->getExtension(fasta);
+ m->openOutputFile(reverseFile, outFASTA);
while(!inFASTA.eof()){
if (m->control_pressed) { inFASTA.close(); outFASTA.close(); remove(reverseFile.c_str()); return 0; }
- Sequence currSeq(inFASTA); gobble(inFASTA);
+ Sequence currSeq(inFASTA); m->gobble(inFASTA);
if (currSeq.getName() != "") {
currSeq.reverseComplement();
currSeq.printSequence(outFASTA);