ms_xic.hpp

/*
##############################################################################
# file: ms_xic.hpp
# 'msparser' toolkit
# An extracted ion chromatogram
##############################################################################
# COPYRIGHT NOTICE
# Copyright 1998-2014 Matrix Science Limited  All Rights Reserved.
#
##############################################################################
 * @(#)$Source: parser/inc/ms_xic.hpp $
 * @(#)$Revision: f7c430569a82a92eac8833564053b59680ac20a8 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
 * @(#)$Date: 2021-01-11 13:23:17 +0000 $
##############################################################################
 */
 
#ifndef MS_XIC_HPP
#define MS_XIC_HPP
 
 
// Includes from the standard template library
#include <string>
 
namespace matrix_science
{
    //=========================================================================
    class ms_xic_body;
    class ms_cache_file;
 
 
    class MS_MASCOTRESFILE_API ms_xic_point
    {
        public:
            ms_xic_point();
            ms_xic_point(double rt, int scanId, double intensity);
 
            double getRt() const;
            int    getScanId() const;
            double getIntensity() const;
 
            void setRt(double rt);
            void setScanId(int scanId);
            void setIntensity(double intensity);
 
        private:
            double rt_;
            int scanId_;
            double intensity_;
    };
 
 
    class MS_MASCOTRESFILE_API ms_xic :   
        public ms_handle
    {
        public:
 
            enum peakState
            {
                PEAK_STATE_UNKNOWN = 0, 
                PEAK_STATE_OK = 1,      
                PEAK_STATE_DISCARD =3,  
            };
 
            static std::string getXmlCode(peakState code);
 
            static peakState getCodeFromXml(std::string text);
 
            ms_xic();
 
            explicit ms_xic(const ms_xic_body & body);
 
            explicit ms_xic(ms_xic_body * body);
 
            void defaultValues();
 
            void copyFrom(const ms_xic * src);
 
#ifndef SWIG
            ms_xic_body * body();
 
            const ms_xic_body * body() const;
            void setCacheFile(matrix_science::ms_cache_file * cacheFile);
#endif
 
            peakState getPeakState() const;
 
            bool hasIndexes() const;
 
            int getPeakStartIndex() const;
 
            int getPeakEndIndex() const;
 
            int getRegionStartIndex() const;
 
            int getRegionEndIndex() const;
 
            int getStartIndex() const;
 
            int getEndIndex() const;
 
            int getPeakStartScanId() const;
 
            int getPeakEndScanId() const;
 
            int getRegionStartScanId() const;
 
            int getRegionEndScanId() const;
 
            int getStartScanId() const;
 
            int getEndScanId() const;
 
            bool getUseTimeShift() const;
 
            double getElutionTimeShift() const;
 
            double getRtPeakStart() const;
 
            double getRtPeakEnd() const;
 
            double getRtRegionStart() const;
 
            double getRtRegionEnd() const;
 
            int getNumPoints() const;
#ifndef SWIG
            void getPoint(int index, double & rt, int & scanId, double & intensity) const;
#else // SWIG Multiple return values
            void getPoint(int index, double & OUTPUT, int & OUTPUT, double & OUTPUT) const;
#endif
            void setPeakStartIndex(int value);
 
            void setPeakEndIndex(int value);
 
            void setRegionStartIndex(int value);
 
            void setRegionEndIndex(int value);
 
            void setStartIndex(int value);
 
            void setEndIndex(int value);
 
            void setPeakStartScanId(int value);
 
            void setPeakEndScanId(int scanId);
 
            void setRegionStartScanId(int scanId);
 
            void setRegionEndScanId(int scanId);
 
            void setStartScanId(int scanId);
 
            void setEndScanId(int scanId);
 
            void setRtPeakStart(double value);
 
            void setRtPeakEnd(double value);
 
            void setRtRegionStart(double value);
 
            void setRtRegionEnd(double value);
 
            void setUseTimeShift(bool value);
 
            void setElutionTimeShift(double value);
 
            void setPeakState(peakState value);
 
        protected:
            std::deque<ms_xic_point> & getPoints();
 
            const std::deque<ms_xic_point> & getPoints() const;
 
    };
 // end of quantitation_group
    //=========================================================================
 
} // namespace matrix_science
 
#endif // MS_XIC_HPP
 
/*------------------------------- End of File -------------------------------*/