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: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $
# @(#)$Date: 2018-07-30 16:23:53 +0100 $ 
# @(#)$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  
        };

        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);

        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_;
    }; // 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 -------------------------------*/