MzmlHandler.h

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#ifndef __KOME_IO_MZML_HANDLER_H__
#define __KOME_IO_MZML_HANDLER_H__


#include "MzmlSample.h"

#include <map>


namespace kome {
    namespace io {
        namespace mzml {

            class Accession;
            class MzmlSpectrum;
            class MzmlChromatogram;

            class MzmlHandler : public kome::xml::XmlHandler {
            public:
                MzmlHandler( MzmlSample& file );

                virtual ~MzmlHandler();

            protected:
                MzmlSample& m_file;

            protected:
                Accession* m_machineAcc;

                Accession* m_arrAcc;

                Accession* m_specAcc;

                Accession* m_softwareAcc;

                long long m_pos;

            protected:
                typedef enum {
                    TYPE_OTHER,
                    TYPE_MZ,
                    TYPE_RT,
                    TYPE_INT
                } ArrayType;

                MzmlSpectrum* m_currSpec;

                MzmlChromatogram* m_currChrom;

                ArrayType m_currType;

                MzmlSample::ArrayInfo m_arrayInfo;

            protected:
                int m_scanNum;

                struct SpecInfo {
                    int stage;
                    int centroid;
                    kome::objects::Spectrum::Polarity polarity;
                    double mzLowerLimit;
                    double mzUpperLimit;
                    double tic;
                    double bpm;
                    double bpi;
                    double rt;
                    double prec;
                    std::string collisionEnergy;
                    std::vector< std::pair< std::string, std::string > > props;
                };

                std::map< std::string, SpecInfo > m_specMap;

                SpecInfo* m_currSpecInfo;

            protected:
                std::string m_currSoftwareName;

                std::string m_currSoftwareVersion;

            protected:
                bool m_inIonTag;

                bool m_inPrecursor;

                bool m_inProduct;

            protected:
                std::map< std::string, MzmlSpectrum* > m_specIdMap;

                std::map< int, MzmlSpectrum* > m_specScanMap;

                std::map< std::string, MzmlChromatogram* > m_chromIdMap;

                int m_offsetScan;

                std::string m_offsetId;

            protected:
                SpecInfo* getSpecInfo( const char* name );

                void setSpecInfo( kome::objects::Spectrum* spec, SpecInfo* info );
            
            protected:
                virtual void onStartDocument();

                virtual void onEndDocument();

                virtual void onStartElement( const char* name, kome::core::Properties& attrs );

                virtual void onEndElement( const char* name, const char* text );
            };
        }
    }
}


#endif      // __KOME_IO_MZML_HANDLER_H__