writerbridge.h

#ifndef __WRITER_BRIDGE_H__
#define __WRITER_BRIDGE_H__
 
#include <experimental/filesystem>
#include "utils.h"
#include "iutils.h"
#include "iwriterbridge.h"
#include "ftMapClass.h"
 
namespace ft {
 
class WriterBridge : public IWriterBridge {
public:
    WriterBridge();
 
    virtual ~WriterBridge();
 
    void saveOutput(const ft::FTMap& ftMap);
 
    void setOutputOptions(const ft::FTMap& ftMap);
    std::string joinString(const std::set<std::string>& setOfStr, std::string delimeter);
    std::string createHeader();
    std::string formatOutputMap();
    std::string getFlagKmers(const ft::QueryClass& query, const ft::FlagType flag);
    void addQueryToOutput( const ft::QueryClass& query, const std::string prefix);
    void overrideUtils(std::shared_ptr<IUtils> utils);
 
    bool getRefData();
    bool getAltData();
    bool getCroData();
    bool getOCKFlag();
    bool getNUKFlag();
    bool getMatchesOnlyFlag();
    std::map<std::string, std::string> getOutputMap();
 
private:
    std::map<std::string, std::string> _outputMap;
    bool _refData;
    bool _altData;
    bool _croData;
    bool _OCK;
    bool _NUK;
    bool _MatchesOnly;
 
 
    Utils _ownedUtils;
    IUtils* _utils;
};
}
 
#endif // end of __WRITER_BRIDGE_H__