*/
#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; }
private:
- string equalizedFile, testTax;
+ string equalizedFile, testTax, outputDir;
bool containsConfidence;
int cutoff, highestLevel;
map<string, int> seqLevels; //maps name to level of taxonomy
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;
};