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#ifndef CLASSIFY_H
#define CLASSIFY_H
/*
* classify.h
* Mothur
*
* Created by westcott on 11/3/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
/* This class is a parent to bayesian, knn. */
#include "mothur.h"
#include "searchdatabase.hpp"
#include "phylotree.h"
class Sequence;
/**************************************************************************************************/
class Classify {
public:
Classify();
virtual ~Classify(){};
virtual string getTaxonomy(Sequence*, string&, bool&) = 0;
int getMaxLevel() { return maxLevel; }
virtual void setDistName(string s) {} //for knn, so if distance method is selected with knn you can create the smallest distance file in the right place.
protected:
map<string, string> taxonomy; //name maps to taxonomy
map<string, int>::iterator itTax;
map<string, string>::iterator it;
SearchDatabase* database;
PhyloTree* phyloTree;
string taxFile, templateFile;
vector<string> names;
int threadID, numLevels, numTaxa, maxLevel;
bool flip, shortcuts;
MothurOut* m;
int readTaxonomy(string);
vector<string> parseTax(string);
double getLogExpSum(vector<double>, int&);
bool checkReleaseDate(vector<ifstream*>&, string);
virtual void generateDatabaseAndNames(string, string, string, int, float, float, float, float, string);
};
/**************************************************************************************************/
#endif
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