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); }
+ if (containsConfidence) { m->removeConfidences(tax); }
//is this a taxonomy that needs to be extended?
if (seqLevels[name] < highestLevel) {
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;
//save sequences level
seqLevels[name] = thisLevel;
-
+
//is this the longest taxonomy?
if (thisLevel > level) {
level = thisLevel;
testTax = tax; //testTax is used to figure out if this file has confidences we need to strip out
- }
+ }
}
int pos = testTax.find_first_of('(');
//if there are '(' then there are confidences we need to take out
if (pos != -1) { containsConfidence = true; }
-
+
return level;
}
}
}
/**************************************************************************************************/
-void TaxEqualizer::removeConfidences(string& tax) {
- try {
-
- string taxon;
- string newTax = "";
-
- while (tax.find_first_of(';') != -1) {
- //get taxon
- taxon = tax.substr(0,tax.find_first_of(';'));
- taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
- taxon += ";";
-
- tax = tax.substr(tax.find_first_of(';')+1, tax.length());
- newTax += taxon;
- }
-
- tax = newTax;
- }
- catch(exception& e) {
- m->errorOut(e, "TaxEqualizer", "removeConfidences");
- exit(1);
- }
-}
-
-/**************************************************************************************************/