*/
#include "mothur.h"
+#include "mothurout.h"
//reads in taxonomy file and makes all the taxonomies the same length
//by appending the last taxon to a given taxonomy as many times as needed to
class TaxEqualizer {
public:
- TaxEqualizer(string, int);
+ TaxEqualizer(string, int, string);
~TaxEqualizer() {};
- string getEqualizedTaxFile() { return equalizedFile; }
+ string getEqualizedTaxFile() { return equalizedFile; }
+ int getHighestLevel() { return highestLevel; }
private:
- string equalizedFile, testTax;
+ string equalizedFile, testTax, outputDir;
bool containsConfidence;
- int cutoff;
+ 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;
};