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#ifndef Mothur_sequencecountparser_h
#define Mothur_sequencecountparser_h
//
// sequencecountparser.h
// Mothur
//
// Created by Sarah Westcott on 8/7/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "mothur.h"
#include "mothurout.h"
#include "sequence.hpp"
#include "counttable.h"
#include "utils.hpp"
/* This class reads a fasta and count file and parses the data by group. The countfile must contain group information.
Note: THIS CODE IS NOT THREAD SAFE. ONLY CALL WHEN A SINGLE THREAD IS RUNNING
*/
class SequenceCountParser {
public:
SequenceCountParser(string, string, vector<string>); //count, fasta, groups - file mismatches will set m->setControl_pressed(true)
~SequenceCountParser();
//general operations
int getNumGroups();
vector<string> getNamesOfGroups();
vector<string> getFiles(string); //returns fasta and count file a specific group.
map<string, vector<string> > getFiles() { return groupToFiles; } //returns all files groupName - > vector of groups files (fasta, count);
private:
MothurOut* m;
Utils util;
map<string, vector<string> > groupToFiles;
vector<string> namesOfGroups; //namesOfGroups in same order as groupToSeqs
};
#endif
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