class TaxEqualizer {
public:
- TaxEqualizer(string, int);
+ TaxEqualizer(string, int, string);
~TaxEqualizer() {};
string getEqualizedTaxFile() { return equalizedFile; }
private:
- string equalizedFile, testTax;
+ string equalizedFile, testTax, outputDir;
bool containsConfidence;
int cutoff, highestLevel;
map<string, int> seqLevels; //maps name to level of taxonomy
int getHighestLevel(ifstream&); //scans taxonomy file to find taxonomy with highest level
void extendTaxonomy(string, string&, int); //name, taxonomy, desired level
void truncateTaxonomy(string, string&, int); //name, taxonomy, desired level
- void removeConfidences(string&); //removes the confidence limits on the taxon
MothurOut* m;
};