kmerClass.h

#ifndef KMERCLASS_H
#define KMERCLASS_H
 
#include <set>
#include <bitset>
#include <iostream>
#include <map>
#include "ftPropsClass.h"
 
namespace ft {
 
class KmerClass
{
public:
    KmerClass(std::string kmer);
    KmerClass();
 
    virtual ~KmerClass();
 
    const std::string& getKmer() const;
    const std::bitset<8>& getKFlags()const;
    const std::set<long long>& getKPositions()const;
    const std::set<ft::ReadID>& getReadIDs()const;
    uint getOCC()const {return _occ;};
    //uint getKmerMapSize()const;
 
    void setKFlags(std::set<ft::FlagType> kFlags);
    void setKPositions(const std::set<long long>& kPositions);
    void adjustPosForOffset(uint offset = 0);
    void setReadIDs(std::set<ft::ReadID> readIDs);
    void setOCC(uint occ) {_occ=occ;};
 
    void addKFlag(const ft::FlagType& kFlag);
    void addKPosition(const size_t& kPosition, const uint& offset = 0);
    void addReadID(const ft::ReadID& readID);
 
    void removeKFlag(ft::FlagType kFlag);
    void removeKPosition(size_t kPosition, uint offset = 0);
    void removeReadID(ft::ReadID readID);
 
    bool isKmerEqual(const KmerClass& test) const;
    bool hasKmer(const std::string& test) const;
    bool hasFlag(const ft::FlagType& flag);
    bool hasKPosition(const size_t& position) const;
    bool hasReadID(const ft::ReadID& readID) const;
 
    void convertPosToReadID(uint readLength, uint numOfReads, bool pairedReads, bool indexRevComp = false);
    bool matchingReadID(const ft::ReadID &a, const ft::ReadID &b) const;
    void adjustPositionsWithOffset(uint offset);
 
    bool operator< (const ft::KmerClass &k) const;
    bool operator== (const ft::KmerClass &k) const;
 
private:
    std::string _kmer;
    std::bitset<8> _kFlags;
    std::set<long long> _positions;
    std::set<ft::ReadID> _readIDs;
    uint _occ; //from sdsl::count(_index, _kmer)
    bool _isOffsetAdjusted;
 
};
}
 
#endif // KMERCLASS_H