ms_searchparams.hpp

/*
##############################################################################
# file: ms_mascotresparams.hpp                                               #
# 'msparser' toolkit                                                         #
# Encapsulates the parameters & masses sections from the mascot results file #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2019 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Archive:: /MowseBranches/ms_mascotresfile_1.2/include/ms_mascotrespa $ #
#     $Author: villek@matrixscience.com $ #
#       $Date: 2024-09-23 15:59:15 +0100 $ #
#   $Revision: 80290236f1981378c76180c6677fb9983e5275d5 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/
 
#ifndef MS_MASCOTRESPARAMS_HPP
#define MS_MASCOTRESPARAMS_HPP
 
 
// Includes from the standard template library
#include <string>
 
namespace msparser_internal
{
    class ms_searchparamsbase;
    class ms_searchparams_dat;
    class ms_searchparams_msr;
}
namespace matrix_science {
 
 
    class MS_MASCOTRESFILE_API ms_searchparams
    {
        friend class ms_mascotresfilebase;
        public:
 
 
            enum MULTI_SITE_MODS {
                MSM_NOT_PERMITTED           = 0x0000, 
                MSM_EXCLUSIVE_PLUS_VARIABLE = 0x0001  
            };
 
            ms_searchparams(const ms_mascotresfilebase &resfile);
 
 
            ~ms_searchparams() {};
 
            std::string  getLICENSE();
#ifndef SWIGCSHARP
            std::string  getCOM();
#else
            std::wstring getCOM() {
                return getCOMWide();
            };      
#endif
            int          getSEG();
 
            double       getTOL();
 
            std::string  getTOLU();
 
            double       getITOL();
 
            std::string  getITOLU();
 
            int          getPFA();
 
            std::string  getDB(int idx = 1);
 
            int getNumberOfDatabases();
 
            std::string  getMODS();
 
            std::string  getMASS();
 
            MASS_TYPE    getMassType();
 
            std::string  getCLE();
 
            std::string  getFILENAME();
 
            std::string  getDATAURL();
 
            std::string  getQUE();
 
            std::string  getSEARCH();
 
#ifndef SWIGCSHARP
            std::string  getUSERNAME();
#else
            std::wstring getUSERNAME() {
                return getUSERNAMEWide();
            };
#endif
 
#ifndef SWIGCSHARP
            std::string  getUSEREMAIL();
#else
            std::wstring getUSEREMAIL() {
                return getUSEREMAILWide();
            };
#endif
 
            int getUSERID();
 
            std::string  getCHARGE();
 
            std::string  getINTERMEDIATE();
 
            int          getREPORT();
 
            bool         getOVERVIEW();
 
            std::string  getFORMAT();
 
            std::string  getFORMVER();
 
            std::string  getIT_MODS();
 
            std::string  getUSERField(int num);
 
            std::string getAllUSERParams() const;
 
            double       getPRECURSOR();
 
            std::string  getTAXONOMY();
 
            std::string  getREPTYPE();
 
            std::string  getACCESSION();
 
            int          getSUBCLUSTER();
 
            bool         getICAT();
 
            std::string  getINSTRUMENT();
 
            bool         getERRORTOLERANT();
 
            std::string  getRULES();
 
            double getMinInternalMass();
 
            double getMaxInternalMass();
 
        bool hasINTERNALS() const;
 
            double       getResidueMass(char residue);
 
            double       getCTermMass();
 
            double       getNTermMass();
 
            double       getHydrogenMass() const;
 
            double       getOxygenMass() const;
 
            double       getCarbonMass() const;
 
            double       getNitrogenMass() const;
 
            double       getElectronMass() const;
 
            // Returns the name of the specified variable modification selected by the user.
            std::string  getVarModsName(int num) const;
 
            double       getVarModsDelta(int num);
 
            double       getVarModsNeutralLoss(int num);
 
            std::vector<double> getVarModsNeutralLosses(int num) const;
 
            std::vector<double> getVarModsPepNeutralLoss(int num);
 
            std::vector<double> getVarModsReqPepNeutralLoss(int num);
 
            // Returns the name of the specified fixed modification.
            std::string  getFixedModsName(int num) const;
 
            double       getFixedModsDelta(int num);
 
            double       getFixedModsNeutralLoss(int num);
 
            std::string  getFixedModsResidues(int num) const;
 
            int          getNumberOfLibraryMods() const;
 
            std::string  getLibraryModName(int num) const;
 
            double       getLibraryModDelta(int num) const;
 
            std::string  getErrTolParentFilename();
 
            std::string  getQUANTITATION() const;
 
            std::string  getCROSSLINKING() const;
 
            int  getPEP_ISOTOPE_ERROR() const;
 
            int  getDECOY() const;
 
            double getTARGET_FDR_PERCENT() const;
 
            int  getPERCOLATE() const;
 
            std::vector<std::string>  getML_ADAPTER_PARAM() const;
 
            int  getLIBRARY_SEARCH() const;
 
            unsigned int getMULTI_SITE_MODS() const;
 
        protected:
            // Not safe to copy or assign this object.
#ifndef SWIG
            ms_searchparams(const ms_searchparams & rhs);
            ms_searchparams & operator=(const ms_searchparams & rhs);
#endif
        private:
 
            std::shared_ptr<msparser_internal::ms_searchparamsbase> impl_;
 
            std::wstring getCOMWide();
            std::wstring getUSERNAMEWide();
            std::wstring getUSEREMAILWide();
 
            bool isDefaultMass(const std::string symbol) const;
 
    }; // end of resfile_group
}   // matrix_science namespace
 
#endif // MS_MASCOTRESPARAMS_HPP
 
/*------------------------------- End of File -------------------------------*/