fastafile = validParameter.validFile(parameters, "fasta", false);
if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the chimera.bellerophon command."); m->mothurOutEndLine(); abort = true; }
else {
- splitAtDash(fastafile, fastaFileNames);
+ m->splitAtDash(fastafile, fastaFileNames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
if (inputDir != "") {
- string path = hasPath(fastaFileNames[i]);
+ string path = m->hasPath(fastaFileNames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
}
int ableToOpen;
ifstream in;
- ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+ ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
//if you can't open it, try default location
if (ableToOpen == 1) {
if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ableToOpen = openInputFile(tryPath, in, "noerror");
+ ableToOpen = m->openInputFile(tryPath, in, "noerror");
fastaFileNames[i] = tryPath;
}
}
//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(fastafile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
string temp;
temp = validParameter.validFile(parameters, "filter", false); if (temp == "not found") { temp = "F"; }
- filter = isTrue(temp);
+ filter = m->isTrue(temp);
temp = validParameter.validFile(parameters, "correction", false); if (temp == "not found") { temp = "T"; }
- correction = isTrue(temp);
+ correction = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found") { temp = "1"; }
convert(temp, processors);
chimera = new Bellerophon(fastaFileNames[i], filter, correction, window, increment, processors, outputDir);
- string outputFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "bellerophon.chimeras";
- string accnosFileName = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.chimeras";
+ string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "bellerophon.accnos";
chimera->getChimeras();
#else
ofstream out;
- openOutputFile(outputFileName, out);
+ m->openOutputFile(outputFileName, out);
ofstream out2;
- openOutputFile(accnosFileName, out2);
+ m->openOutputFile(accnosFileName, out2);
numSeqs = chimera->print(out, out2);
out.close();