ms_fragmentationrules.hpp

/*
##############################################################################
# file: ms_fragmentationrules.hpp                                            #
# 'msparser' toolkit                                                         #
# Encapsulates a fragmentation_rules file (mascot configuration files)       #
#                                                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2006 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
# @(#)$Source: parser/inc/ms_fragmentationrules.hpp $
# @(#)$Revision: 02a06a729c26ca3a83c94c5de5852f4f3f38c3cf | MSPARSER_REL_3_1_0-2025-07-27-0-gea47708fac $
# @(#)$Date: 2024-12-08 15:34:14 +0000 $ 
# @(#)$Author: villek@matrixscience.com $ 
##############################################################################
*/
 
#ifndef MS_FRAGMENTATIONRULES_HPP
#define MS_FRAGMENTATIONRULES_HPP
 
 
// Includes from the standard template library
#include <vector>
#include <string>
 
 
namespace matrix_science {
    class ms_filesource;
 
 
    class MS_MASCOTRESFILE_API ms_fragmentationrules : public ms_customproperty
    {
        friend class ms_fragrulesfile;
    public:
 
 
        enum  FRAG_SERIES_TYPE
        {
            FRAG_IMMONIUM        = 4,  
            FRAG_A_SERIES        = 5,  
            FRAG_A_MINUS_NH3     = 6,  
            FRAG_A_MINUS_H2O     = 7,  
            FRAG_B_SERIES        = 8,  
            FRAG_B_MINUS_NH3     = 9,  
            FRAG_B_MINUS_H2O     = 10, 
            FRAG_C_SERIES        = 11, 
            FRAG_X_SERIES        = 12, 
            FRAG_Y_SERIES        = 13, 
            FRAG_Y_MINUS_NH3     = 14, 
            FRAG_Y_MINUS_H2O     = 15, 
            FRAG_Z_SERIES        = 16, 
            FRAG_INTERNAL_YB     = 17, 
            FRAG_INTERNAL_YA     = 18, 
            FRAG_Z_PLUS_1        = 21, 
            FRAG_D_SERIES        = 22, 
            FRAG_V_SERIES        = 23, 
            FRAG_W_SERIES        = 24, 
            FRAG_Z_PLUS_2        = 25  
        };
 
        enum ACQUISITION_MODE {
            ACQUISITION_MODE_DDA = 0, 
            ACQUISITION_MODE_DIA = 1  
        };
 
        ms_fragmentationrules();
 
        ms_fragmentationrules(const ms_fragmentationrules& src);
 
        ~ms_fragmentationrules();
 
        void defaultValues();
 
        void copyFrom(const ms_fragmentationrules* right);
 
#ifndef SWIG
        ms_fragmentationrules& operator=(const ms_fragmentationrules& right);
#endif
        std::string getTitle() const;
 
        void setTitle(const char * title);
 
        static int getFirstSeries();
 
        static int getFirstSerie();
 
        static int getLastSeries();
 
        static int getLastSerie();
 
        bool isSinglyCharged() const;
 
        void setSinglyCharged(const bool value);
 
        bool isCharged2Plus() const;
 
        void setCharged2Plus(const bool value);
 
        bool isCharged3Plus() const;
 
        void setCharged3Plus(const bool value);
 
        bool isSeriesUsed(const int series) const;
 
        void clearSeries();
 
        void setSeriesUsed(const int series, const bool val);
 
        bool isValid() const;
 
        bool verifyRule(ms_errs* err_, const bool tryToFix);
 
        static std::string getSeriesDescription(const int series);
 
        double getMinInternalMass() const;
 
        void setMinInternalMass(const double mass);
 
        double getMaxInternalMass() const;
 
        void setMaxInternalMass(const double mass);
 
    ACQUISITION_MODE getAcquisitionMode() const;
 
        void setAcquisitionMode(const ACQUISITION_MODE m);
 
    int getOption_PERCOLATE() const;
 
        void setOption_PERCOLATE(const int v);
 
    std::string getOption_ML_ADAPTER_PARAM() const;
 
        void setOption_ML_ADAPTER_PARAM(const std::string &v);
 
 
        static std::string getSeriesName(const int series);
 
        static bool isBackboneSeries(const int series);
 
        static bool isNeutralLossSeries(const int series);
 
        bool anyNLseriesUsed(const int series) const;
 
        static int getTotalSeriesOutput();
 
#ifdef SUPPRESS_MS_CUSTOMPROPERTY_INHERITANCE
#include "suppress_ms_customproperty.hpp"
#endif
 
    private:
        std::string title_;
        bool* which_series_;
        double minInternalMass_;
        double maxInternalMass_;
        ACQUISITION_MODE acquisitionMode_;
        int option_PERCOLATE_;
        std::string option_ML_ADAPTER_PARAM_;
    }; // class ms_fragmentationrules
 
 
    class MS_MASCOTRESFILE_API ms_fragrulesfile: public ms_errors
    {
    public:
        ms_fragrulesfile();
        
        ms_fragrulesfile(const char* filename, const matrix_science::ms_connection_settings * cs = 0);
 
        ms_fragrulesfile(const ms_fragrulesfile& src);
 
        ~ms_fragrulesfile();
 
        void defaultValues();
 
        void copyFrom(const ms_fragrulesfile* right);
 
#ifndef SWIG
        ms_fragrulesfile& operator=(const ms_fragrulesfile& right);
#endif        
        void setFileName(const char* filename);
 
        std::string getFileName() const;
 
        void setConnectionSettings(const matrix_science::ms_connection_settings & cs);
 
        matrix_science::ms_connection_settings getConnectionSettings() const;
 
        void read_file();
 
        void read_buffer(const char * buffer);
 
        void save_file();
 
        int  getNumberOfInstruments() const;
 
        void clearInstruments();
 
        void appendInstrument(const ms_fragmentationrules* item);
 
        std::string getInstrumentName(const int instrumentNum) const;
 
        const ms_fragmentationrules* getInstrumentByName(const char * name) const;
 
        const ms_fragmentationrules* getInstrumentByNumber(const int instrumentNum) const;
 
        bool updateInstrumentByNumber(const int num, const ms_fragmentationrules item);
 
        bool updateInstrumentByName(const char* name, const ms_fragmentationrules item);
 
        bool deleteInstrumentByNumber(const int num);
 
        bool deleteInstrumentByName(const char* name);
 
    private:
        void read_filesource(ms_filesource & fsource);
 
        std::string filename_;
        std::vector< ms_fragmentationrules* > rules_;
        std::vector< std::string > comments_;
        ms_connection_settings cs_;
    }; // ms_fragrulesfile // end of config_group
}   // matrix_science namespace
 
#endif // MS_FRAGMENTATIONRULES_HPP
 
/*------------------------------- End of File -------------------------------*/