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: 2024-08-19 15:33:52 +0100 $ #
#   $Revision: d48a6aa34bb34c80a33469ce907f789f718e62a6 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $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();
 
#ifndef SWIG
        void saveToString(std::string & modfileAsStr);
#else // SWIG Multiple return values
        void saveToString(std::string & OUTPUT);
#endif
 
        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