ms_masses.hpp

/*
##############################################################################
# file: ms_masses.hpp                                                        #
# 'msparser' toolkit                                                         #
# Encapsulates "masses"-file that defines atom and residue masses            #
# about several consecutive erros                                            #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2003 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Archive:: /Mowse/ms_mascotresfile/include/ms_masses.hpp              $ #
#     $Author: villek@matrixscience.com $ #
#       $Date: 2018-07-30 16:23:53 +0100 $ #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/

#ifndef MS_MASSES_HPP
#define MS_MASSES_HPP


#include <string>


namespace matrix_science {

    class ms_umod_configfile; // forward declaration
    class ms_quant_component; // forward declaration



    class MS_MASCOTRESFILE_API ms_masses: public ms_errors
    {
    public:
        ms_masses();

        ms_masses(const ms_masses& src);

        ms_masses(const ms_umod_configfile& src, bool addMissingResidueMasses=true);

        ms_masses(const ms_umod_configfile& src, const ms_quant_component& quantComp);

        ms_masses(const char* filename, const matrix_science::ms_connection_settings * cs = 0);

        ~ms_masses();

        void defaultValues(bool useDefaultResidueMasses=true);

        void copyFrom(const ms_masses* right);

        void copyFrom(const ms_umod_configfile *right, bool addMissingResidueMasses=true);

        ms_modvector applyFixedMods(const ms_modvector *mods, ms_errs *err);

        void applyIsotopes(const ms_umod_configfile *umodFile, const ms_quant_component *quantComp);

        bool isSame(const ms_masses& other, const MASS_TYPE massType) const;

#ifndef SWIG

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

        std::string getFileName() const;

        void setFileName(const char* name);

        void setConnectionSettings(const matrix_science::ms_connection_settings & cs);

        matrix_science::ms_connection_settings getConnectionSettings() const;

        void read_file();

        void save_file();

        double getResidueMass(const matrix_science::MASS_TYPE massType, const char residue) const;

        void setResidueMasses(const char residue, const double massMono, const double massAve);

        double getNtermDelta(const matrix_science::MASS_TYPE massType) const;

        double getNterminalMass(const matrix_science::MASS_TYPE massType) const;

        double getNtermNeutralLoss(const matrix_science::MASS_TYPE massType) const;

        void setNtermModification(const double monoDelta, 
                                  const double aveDelta, 
                                  const double monoNeutralLoss = 0.0,
                                  const double aveNeutralLoss = 0.0);

        double getCtermDelta(const matrix_science::MASS_TYPE massType) const;

        double getCterminalMass(const matrix_science::MASS_TYPE massType) const;

        double getCtermNeutralLoss(const matrix_science::MASS_TYPE massType) const;

        void setCtermModification(const double monoDelta, 
                                  const double aveDelta, 
                                  const double monoNeutralLoss = 0.0,
                                  const double aveNeutralLoss = 0.0);

        double getFragResidueMass(const matrix_science::MASS_TYPE massType, const char residue) const;

        bool isResidueModified(const char residue) const;

        void setResidueModification(const double monoDelta, 
                                    const double aveDelta, 
                                    const double monoNeutralLoss,
                                    const double aveNeutralLoss,
                                    const char *residues);

        double getHydrogenMass(const matrix_science::MASS_TYPE massType) const;

        void setHydrogenMass(const double massMono, const double massAve);

        double getCarbonMass(const matrix_science::MASS_TYPE massType) const;

        void setCarbonMass(const double massMono, const double massAve);

        double getNitrogenMass(const matrix_science::MASS_TYPE  massType) const;

        void setNitrogenMass(const double massMono, const double massAve);

        double getOxygenMass(const matrix_science::MASS_TYPE  massType) const;

        void setOxygenMass(const double massMono, const double massAve);

        double getElectronMass() const;

        void setElectronMass(const double mass);

        void setStorage(double* res_mono, 
                        double* res_ave, 
                        double* hydrogen, 
                        double* carbon, 
                        double* nitrogen, 
                        double* oxygen, 
                        double* electron);

        void defaultMasses(double* res_mono, 
                           double* res_ave, 
                           double* hydrogen, 
                           double* carbon, 
                           double* nitrogen, 
                           double* oxygen, 
                           double* electron,
                           bool useDefaultResidueMasses = true);

    private:

        bool getTwoMasses(char * line, 
                          char *lineForError, 
                          double *pMono, 
                          double *pAve, 
                          const double dMin, 
                          const double dMax);

        void setCustomProperty();

    private:
        // final destinations - they are assigned either 
        // 1) supplied array pointers 
        // 2) the internal storages
        double* res_mono;
        double* res_ave;

        // mass combined with neutral loss for residue-specific mods
        bool res_mod[26];
        double* frag_res_mono;
        double* frag_res_ave;

        // masses of terminal groups for terminus mods
        double ntermDelta[2];
        double ctermDelta[2];

        // neutral losses on terminal groups for terminus mods
        double neutralLossNterm[2];
        double neutralLossCterm[2];

        double* hydrogen;
        double* carbon;
        double* nitrogen;
        double* oxygen;

        double* electron;

        // internal storages in case they are not supplied with a proper constructor
        double _res_mono[26];
        double _res_ave[26];
        double _frag_res_mono[26];
        double _frag_res_ave[26];

        double _hydrogen[2];
        double _carbon[2];
        double _nitrogen[2];
        double _oxygen[2];

        double _electron;

        std::string _fn;
        ms_customproperty _custprop;
        ms_connection_settings cs_;
    }; // class ms_masses // end of config_group
}

#endif // MS_MASSES_HPP