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#ifndef SPLITMATRIX_H
#define SPLITMATRIX_H
/*
* splitmatrix.h
* Mothur
*
* Created by westcott on 5/19/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "mothurout.h"
#include "utils.hpp"
#include "counttable.h"
/******************************************************/
class SplitMatrix {
public:
SplitMatrix(string, string, string, string, float, float, int, bool, string, bool); //fastafile, namefile, countfile, taxFile, taxcutoff, cutoff, processors, classic, outputDir, usingVsearchToCLuster
~SplitMatrix() = default;
vector< map<string, string> > getDistanceFiles(); //returns map of distance files -> namefile sorted by distance file size
string getSingletonNames() { return singleton; } //returns namesfile or countfile containing singletons
//long long getNumSingleton() { return numSingleton; } //returns namesfile containing singletons
private:
MothurOut* m;
Utils util;
string distFile, namefile, singleton, taxFile, fastafile, outputDir, countfile;
vector< map< string, string> > dists;
float cutoff, distCutoff;
bool classic, usingVsearchToCLuster;
int processors;
void splitClassify();
int createDistanceFilesFromTax(vector<vector<string> >&, vector<string>);
int createFastaFilesFromTax(vector<vector<string> >&, vector<string>);
};
/******************************************************/
#endif
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