ms_spectral_lib_peak.hpp

/*
##############################################################################
# File: ms_spectral_lib_peak_list.hpp                                        #
# Mascot Parser toolkit                                                      #
# Encapsulates a single peak plus annotations for spectral library files     #
#                                                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 2015 Matrix Science Limited  All Rights Reserved.                #
#                                                                            #
##############################################################################
#    $Source: parser/inc/ms_spectral_lib_peak.hpp $
#    $Author: dcreasy@matrixscience.com $ 
#      $Date: 2019-01-09 17:36:22 +0000 $ 
#  $Revision: 8cb0d9cae7732a8c4def8cb60456be4a3be7a559 | MSPARSER_REL_2_8_1-0-gea32989045 $
##############################################################################
*/

#ifndef MS_SPECTRAL_LIB_PEAK
#define MS_SPECTRAL_LIB_PEAK


// Includes from the standard template library

#include <map>
#include <string>


namespace matrix_science {
  
    namespace ms_spectral_lib {
        enum FILE_FORMAT {
            FORMAT_UNKNOWN,   
            FORMAT_NIST_MSP,  
            FORMAT_SPECTRAST, 
            FORMAT_MGF,       
            FORMAT_XHUNTER    
        };
    };

    class MS_MASCOTRESFILE_API ms_spectral_lib_peak
    {
    public:
        ms_spectral_lib_peak(const std::string & text, 
                             ms_spectral_lib::FILE_FORMAT format,
                             matrix_science::ms_errs & errs);

        ms_spectral_lib_peak(const double mz, 
                             const double intensity, 
                             const std::string & annotation, 
                             ms_spectral_lib::FILE_FORMAT format);

        ms_spectral_lib_peak(const ms_spectral_lib_peak & src);

        void copyFrom(const ms_spectral_lib_peak* right);

#ifndef SWIG

        ms_spectral_lib_peak& operator=(const ms_spectral_lib_peak& right);
#endif

        double getMz() const;

        double getIntensity() const;

        std::string getAnnotation(ms_spectral_lib::FILE_FORMAT format = ms_spectral_lib::FORMAT_NIST_MSP) const;

        void setAnnotation(const std::string & annotation, ms_spectral_lib::FILE_FORMAT format);

        void clearAnnotation();

        double getDelta() const;

        bool isMatchedToCalculatedPeak() const;

        bool isSuspectAssignment() const;

        bool getConsensusData(int * numerator, int * denominator, double * medianDeviation) const;

        std::string asText(ms_spectral_lib::FILE_FORMAT format) const;

        bool isValid() const;

        static std::string getUnmatchedAnnotationStr(ms_spectral_lib::FILE_FORMAT format);


    private:
        bool            valid_;
        double          mz_;
        double          intensity_;
        std::string     mzText_;
        std::string     intensityText_;
        std::string     annotation_;
        ms_spectral_lib::FILE_FORMAT  currAnnotationFormat_;
        double          delta_;
        bool            consensusDataAvailable_;
        int             consensusNumerator_;
        int             consensusDenominator_;
        double          medianDeviationOfConsensusPeaks_;
    };

 // end of tools_group
} // namespace matrix_science

#endif // MS_SPECTRAL_LIB_PEAK

/*------------------------------- End of File -------------------------------*/