MzmlManager.h

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#ifndef __KOME_IO_MZML_MANAGER_H__
#define __KOME_IO_MZML_MANAGER_H__


namespace kome {
    namespace io {
        namespace mzml {

            class Accession;

            class MzmlManager {
            protected:
                MzmlManager();

                virtual ~MzmlManager();

            protected:
                std::map< kome::objects::Spectrum*, long long > m_specIdxMap;

                std::map< kome::objects::Chromatogram*, long long > m_chromIdxMap;

                const bool m_reverseFlg;

            protected:
                void init();

            public:
                bool exportDataSet( const char* path,
                                    kome::objects::DataSet& dataSet,
                                    kome::core::Progress& progress,
                                    kome::objects::SettingParameterValues* saveSettings     // @date 2012/08/21 <Add> FUJITA
                                    );

            protected:
                void exportDataSet( FILE* fp,
                                    kome::objects::DataSet& dataSet,
                                    kome::core::Progress& progress,
                                    kome::objects::SettingParameterValues* saveSettings     // @date 2012/08/21 <Add> FUJITA
                                    );
                
                static bool lessSpec( kome::objects::Spectrum* spec0, kome::objects::Spectrum* spec1 );
            protected:
                void writeHeader( FILE* fp );

                void writeFileDescription( FILE* fp, std::vector< kome::objects::Sample* >& samples );

                void writeFileContent( FILE* fp, std::vector< kome::objects::Sample* >& samples );

                void writeSourceFileList( FILE* fp, std::vector< kome::objects::Sample* >& samples );

                void writeReferenceableParamGroup( FILE* fp, const bool specFlg, const bool chromFlg );

                void writeSoftwareList( FILE* fp, std::vector< kome::objects::Sample* >& samples );

                void writeInstrumentList( FILE* fp, std::vector< kome::objects::Sample* >& samples );

                void writeProcessingList( FILE* fp );

                void writeRun(
                    FILE* fp,
                    std::vector< kome::objects::Sample* >& samples,
                    std::vector< kome::objects::Spectrum* >& spectra,
                    std::vector< kome::objects::Chromatogram* >& chroms,
                    kome::core::Progress* specPrgs,
                    kome::core::Progress* chromPrgs,
                    kome::objects::SettingParameterValues* saveSettings     // @date 2012/08/21 <Add> FUJITA
                );

                void writeSpectrum( 
                        FILE* fp,
                        kome::objects::Spectrum& spec,
                        kome::objects::SettingParameterValues* saveSettings     // @date 2012/08/21 <Add> FUJITA
                        );

                void writeChromatogram( 
                        FILE* fp,
                        kome::objects::Chromatogram& chrom,
                        kome::objects::SettingParameterValues* saveSettings     // @date 2012/08/21 <Add> FUJITA
                        );

                void writeIndexList(
                    FILE* fp,
                    std::vector< kome::objects::Spectrum* >& spectra,
                    std::vector< kome::objects::Chromatogram* >& chroms
                );

            protected:
                static double getSimilarityScore( const char* s0, const char* s1 );

                static double getMatchScore( const char* s0, int idx0, const char* s1, int idx1 );

            public:
                static MzmlManager& getInstance();
            };
        }
    }
}

#endif      // __KOME_IO_MZML_MANAGER_H__