ms_spectral_lib_entry.hpp

/*
##############################################################################
# File: ms_spectral_lib_entry.hpp                                            #
# Mascot Parser toolkit                                                      #
# Encapsulates a single entry from a spectral library file                   #
#                                                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 2015 Matrix Science Limited  All Rights Reserved.                #
#                                                                            #
##############################################################################
#    $Source: parser/inc/ms_spectral_lib_entry.hpp $
#    $Author: francoisr@matrixscience.com $ 
#      $Date: 2021-05-27 10:03:04 +0100 $ 
#  $Revision: a47aab4c911db687b9c37e6e2e3e9b23174da535 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
##############################################################################
*/
 
#ifndef MS_SPECTRAL_LIB_ENTRY
#define MS_SPECTRAL_LIB_ENTRY
 
 
// Includes from the standard template library
 
#include <map>
#include <string>
 
 
namespace matrix_science {
  
 
    class MS_MASCOTRESFILE_API ms_spectral_lib_entry : public ms_errors
    {
    public:
 
        enum WHAT_TO_ANNOTATE {
            ANNOTATE_NONE,                     
            ANNOTATE_REPLACE_ALL,              
            ANNOTATE_REPLACE_QUESTION_MARKS,   
            ANNOTATE_REPLACE_IF_ALL_EMPTY      
        };
 
        ms_spectral_lib_entry();
 
        ms_spectral_lib_entry(const ms_spectral_lib_entry & src);
 
        ms_spectral_lib_entry(const std::string & entry, const std::string & fileName, const ms_spectral_lib::FILE_FORMAT format);
 
        ms_spectral_lib_entry(const std::vector<std::string> & entry, const std::string & fileName, const ms_spectral_lib::FILE_FORMAT format);
 
        virtual ~ms_spectral_lib_entry();
 
        void copyFrom(const ms_spectral_lib_entry* right);
 
#ifndef SWIG
        ms_spectral_lib_entry& operator=(const ms_spectral_lib_entry& right);
#endif
 
        const std::string get() const;
 
        std::string getLine(const char * key) const;
 
        std::string getName() const;
 
        double getPrecursorMZ() const;
 
        int getCharge() const;
 
        std::string getSequence() const;
 
        std::string getComment() const;
 
         std::string getCommentField(const char * fieldName) const;
 
        int getMods(std::vector<std::string> & names, 
                    std::vector<int>         & positions) const;
 
        int getMods(std::vector<std::string> & names, 
                    std::vector<int>         & positions,
                    bool                     & anyModfileStyleName,
                    std::string              & modsWithoutSpecificities) const;
 
        int getNumPeaks() const;
 
        double getMW() const;
 
        std::vector<std::string> getPeakList(bool convertToNISTformat = false) const;
 
        matrix_science::ms_spectral_lib_peak_list getPeakListObject() const;
 
        std::string getPeakListChecksum() const;
 
        std::string getFileName() const;
 
        bool annotatePeaks(const WHAT_TO_ANNOTATE whatToAnnotate, const double fragmentToleranceValue, const std::string fragmentToleranceUnit, const ms_umod_configfile * unimod = 0);
 
        void clearAnnotation();
 
    private:
        bool parseLines(const std::vector<std::string> & lines);
        bool parseMSPLines(const std::vector<std::string> & lines, ms_spectral_lib::FILE_FORMAT format);
        bool parseXHunterLines(const std::vector<std::string> & lines);
 
        typedef std::map<std::string, std::string> values_t;
        values_t values_;
        std::vector<std::string> originalLines_;
        ms_spectral_lib_peak_list peakList_;
        ms_spectral_lib::FILE_FORMAT format_;
        std::string fileName_;
    }; // class ms_spectral_lib_entry
 // end of tools_group
} // namespace matrix_science
 
#endif // MS_SPECTRAL_LIB_ENTRY
 
/*------------------------------- End of File -------------------------------*/