#include "database.hpp"
#include "phylotree.h"
-
class Sequence;
-
/**************************************************************************************************/
class Classify {
protected:
map<string, string> taxonomy; //name maps to taxonomy
- //map<string, int> genusCount; //maps genus to count - in essence a list of how many seqs are in each taxonomy
map<string, int>::iterator itTax;
map<string, string>::iterator it;
Database* database;
string taxFile, templateFile, simpleTax;
vector<string> names;
- int threadID;
+ int threadID, numLevels, numTaxa;
bool flip, flipped, shortcuts;
int readTaxonomy(string);
vector<string> parseTax(string);
+ double getLogExpSum(vector<double>, int&);
MothurOut* m;
};