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//
// dataset.h
// Mothur
//
// Created by Sarah Westcott on 3/24/16.
// Copyright (c) 2016 Schloss Lab. All rights reserved.
//
#ifndef __Mothur__dataset__
#define __Mothur__dataset__
#include "sequence.hpp"
#include "counttable.h"
#include "groupmap.h"
#include "sharedrabundvector.hpp"
#include "fastqdataset.h"
#include "utils.hpp"
class TestDataSet {
public:
TestDataSet();
vector<Sequence> getSeqs() { fillSeqs(); return seqs; }
map<string, string> getNameMap() { fillNames(); return nameMap; }
GroupMap* getGroupMap() { fillGroup(); return gMap; }
CountTable* getCountTable() { createCountTable(); return ct; }
vector<SharedRAbundVector*> getLookup() { fillLookup(); return lookup; }
vector<string> getSubsetFNGFiles(); //Fasta, name, group returned - containing 100 seqs
string getSubsetFNGDistFile();
string getSubsetFNGPhylipDistFile();
vector<string> getOptiRefFiles(); //fasta, count, column, phylip, list, betweendist
vector<string> getOligosFiles(); //single, paired, indexes, comboNamesTest
string getSharedFile(); //shared
string getRelabundFile(); //relabund
string getCountTableFile(); //count
private:
MothurOut* m;
Utils util;
TestFastqDataSet fastqData;
vector<Sequence> seqs;
map<string, string> nameMap;
CountTable* ct;
GroupMap* gMap;
vector<SharedRAbundVector*> lookup;
string testDir;
void fillNames();
void fillSeqs();
void fillGroup();
void createCountTable();
void fillLookup();
};
#endif /* defined(__Mothur__dataset__) */
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