}else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
}else { m->setFastaFile(fastafile); }
namefile = validParameter.validFile(parameters, "name", true);
}
string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
}
string temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "100"; }
//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); }
vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
int numDots = 0;
vector<int> counts; counts.resize(5, 0); //A,T,G,C,Gap
int numDots = 0;
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
//as long as you are not at the end of the file or done wih the lines you want
while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {