ms_spectral_lib_peak_list.hpp

/*
##############################################################################
# File: ms_spectral_lib_peak_list.hpp                                        #
# Mascot Parser toolkit                                                      #
# Encapsulates peak lists for spectral library files (e.g. msp, sptext)      #
#                                                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 2015 Matrix Science Limited  All Rights Reserved.                #
#                                                                            #
##############################################################################
#    $Source: parser/inc/ms_spectral_lib_peak_list.hpp $
#    $Author: villek@matrixscience.com $ 
#      $Date: 2018-07-30 16:23:53 +0100 $ 
#  $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $
##############################################################################
*/

#ifndef MS_SPECTRAL_LIB_PEAK_LIST
#define MS_SPECTRAL_LIB_PEAK_LIST


// Includes from the standard template library

#include <vector>
#include <map>
#include <string>


namespace matrix_science {
  

    class MS_MASCOTRESFILE_API ms_spectral_lib_peak_list : public ms_errors 
    {
    public:

        enum PEAK_ANNOTATION_LEVEL {
            ANNOT_LVL_NONE,             
            ANNOT_LVL_QUESTION_MARKS,   
            ANNOT_LVL_SOME_PEAKS,       
            ANNOT_LVL_CANNOT_ANNOTATE,  
        };
        ms_spectral_lib_peak_list();
        
        ~ms_spectral_lib_peak_list();
        
        ms_spectral_lib_peak_list(std::vector<std::string> input, ms_spectral_lib::FILE_FORMAT format);

        ms_spectral_lib_peak_list(const ms_spectral_lib_peak_list & src);

        void copyFrom(const ms_spectral_lib_peak_list* right);

#ifndef SWIG

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

        int getNumPeaks() const;

        const ms_spectral_lib_peak * getPeak(const int pkNum) const;
        
        void addPeaks(const std::vector<double> &vecMz, const std::vector<double> &vecIntensity);

        void annotatePeaks(const ms_fragmentvector *fragments, const double fragmentToleranceValue, const std::string fragmentToleranceUnit, double precursorMz);
        
#ifndef SWIG

        void annotatePeaks(const std::vector<ms_fragment> *fragments, const double fragmentToleranceValue, const std::string fragmentToleranceUnit, double precursorMz);
#endif

        void clearAnnotation();

        PEAK_ANNOTATION_LEVEL getPeakAnnotationLevel() const;

        std::vector<std::string> asText(ms_spectral_lib::FILE_FORMAT format) const;

        std::string getChecksum() const;

        void setAnnotationLevel(PEAK_ANNOTATION_LEVEL level);

    private:
        void setAnnotationLevel(const ms_spectral_lib_peak & pk);

        std::vector<ms_spectral_lib_peak> peakList_;
        bool isConsensusSpectrum_;
        PEAK_ANNOTATION_LEVEL annotationLevel_;
        std::string checksum_;
    };

 // end of tools_group
} // namespace matrix_science

#endif // MS_SPECTRAL_LIB_PEAK_LIST

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