ftMapClass.h

#ifndef __TYPE_DEFS_H__
#define __TYPE_DEFS_H__
 
#include <set>
#include <iostream>
#include <map>
#include <future>
#include <vector>
#include "kmerClass.h"
#include "queryClass.h"
#include "qkMapClass.h"
#include "ftPropsClass.h"
#include "kmergenerator.h"
#include "utils.h"
#include <unordered_map>
 
namespace ft {
 
class FTMap
{
public:
    FTMap(const FTProp& _ftProps);
    virtual ~FTMap();
 
    void addInputQueries(const std::set<Query> &inputQueries);
    void genQKMap();
 
 
    const std::vector<std::map<std::string, ft::KmerClass>>& getResults();
    const FTProp& getFTProps() const;
    const std::unordered_map<std::string, ft::KmerClass>& getKmerSet() const;
 
    bool checkForKmer(const std::string& testKmer) const;
    void addKmer(const std::string &kmer);
    const ft::KmerClass& getKmer(const std::string& kmer) const;
 
    bool checkForQIDT(const ft::QIdT& testQueryObject) const;
    void addQuery(int queryID, ft::QueryType queryType, const std::string& queryString);
    const ft::QueryClass& getQuery(const ft::QIdT& qIDT) const;
    void addReadIDsToQuery(ft::QIdT qIDT, std::set<ft::ReadID>& readIds);
 
    void addIndexResults(const std::map<std::string, ft::KmerClass> & indexResults);
    void addKmerResults(const ft::KmerClass& kmerResult);
    void processResults();
    void processIndexResults(const std::map<std::string, ft::KmerClass>& indexResults);
    void processQueryResults(const ft::QIdT& qIDT);
    void addKmersToQueryResults(ft::QueryClass& query, std::set<std::string>& kmers,  std::set<ft::ReadID>& readIds);
    int calculateQueryCount(const std::set<ft::ReadID>& readIds);
    void removeMultiHits();
    void removeMultiHitsAsPairs();
 
    void showResources() const;
private:
    FTProp  _ftProps;
    std::unordered_map<std::string, ft::KmerClass> _kmerSet;
    std::map<ft::QIdT, ft::QueryClass> _querySet;
    QKMap _qkMap;
    QKMap _qkRCMap;
    std::vector<std::map<std::string, ft::KmerClass>> _searchResults;
 
 
    void createKmer(const std::string& kmer);
    ft::KmerClass* findKmer(const std::string& kmer);
 
    bool operator()(const ft::QIdT& a, const ft::QIdT& b) const;
};
 
}
 
#endif // TYPE_DEFINITION