kmergenerator.h

#ifndef __KMER_GENERATOR_H__
#define __KMER_GENERATOR_H__
 
#include <set>
#include <string>
#include <map>
#include "ikmergenerator.h"
#include "queryClass.h"
#include "ftPropsClass.h"
 
namespace ft {
 
class KmerGenerator
{
 
public:
    KmerGenerator(const uint& _kmerSize ,
                    const bool& _refOnly ,
                    const SearchType& _searchType ,
                    const uint& _overlap = 0,
                    const uint& _stride = 1,
                    const uint& _maxKmers = 1000000000,
                    const bool& _verbose = false);
 
    virtual ~KmerGenerator();
 
    virtual std::set<std::string> genSlidingSearchStrings(const std::string& queryString);
 
    virtual std::set<std::string> genCenteredSearchStrings(const std::string& queryString);
 
    virtual std::set<std::string> genSearchKmers(const ft::QueryClass& queryObj);
 
    uint getKmerSize() const;
    bool getRefOnly() const;
    SearchType getSearchType() const;
    uint getOverlap() const;
    uint getStride() const;
    uint getMaxKmers() const;
 
private:
    std::map<std::string, uint> _counter;
 
    uint _kmerSize;
    bool _refOnly;
    SearchType _searchType;
    uint _overlap;
    uint _stride;
    uint _maxKmers;
    bool _verbose;
 
};
}
 
#endif // kmerGenerator class