fmindex.h

#ifndef __FM_INDEX_H__
#define __FM_INDEX_H__
#include <time.h>
#include <future>
#include <chrono>
#include <fstream>
#include <vector>
#include <iostream>
#include "ifmindex.h"
#include <sdsl/suffix_arrays.hpp>
#include <mutex>
#include "indexPropsClass.h"
 
namespace algo {
 
class FmIndex : public IFmIndex {
 
public:
 
    FmIndex();
    FmIndex(bool verbose);
 
    virtual ~FmIndex();
 
    std::pair<fs::path, fs::path> createFMIndex(const algo::IndexProps& _props, const fs::path& preprocessedFasta);
 
    void loadIndexFromFile(const fs::path& indexname);
 
    ft::KmerClass search(const std::string& kmer,
                         u_int maxOcc = 200
                         );
 
 
    void parallelFmIndex(algo::IndexProps& _props);
 
 
    int indexCount();
 
private:
 
    FmIndex(const FmIndex& other);
    const FmIndex& operator=(const FmIndex& other);
 
    bool _verbose = 0;
 
    csa_wt<wt_huff<rrr_vector<256>>, 512, 1024> _index;
    long long *_indexPosition;
 
    std::mutex _mtx;
 
    size_t _kmerMapSize;
};
}
 
#endif // end of __FM_INDEX_H__