containsConfidence = false;
ifstream inTax;
- openInputFile(tfile, inTax);
+ m->openInputFile(tfile, inTax);
highestLevel = getHighestLevel(inTax);
inTax.close();
ifstream in;
- openInputFile(tfile, in);
+ m->openInputFile(tfile, in);
ofstream out;
- equalizedFile = outputDir + getRootName(getSimpleName(tfile)) + "equalized.taxonomy";
- openOutputFile(equalizedFile, out);
+ equalizedFile = outputDir + m->getRootName(m->getSimpleName(tfile)) + "equalized.taxonomy";
+ m->openOutputFile(equalizedFile, out);
string name, tax;
if (m->control_pressed) { break; }
- in >> name >> tax; gobble(in);
+ in >> name >> tax; m->gobble(in);
if (containsConfidence) { removeConfidences(tax); }
in.close();
out.close();
- if (m->control_pressed) { remove(equalizedFile.c_str()); }
+ if (m->control_pressed) { m->mothurRemove(equalizedFile); }
}else { inTax.close(); }
}
string name, tax;
while (in) {
- in >> name >> tax; gobble(in);
+ in >> name >> tax; m->gobble(in);
//count levels in this taxonomy
int thisLevel = 0;