ms_enzyme.hpp

/*
##############################################################################
# file: ms_enzyme.hpp                                                        #
# 'msparser' toolkit                                                         #
# Encapsulates "enzymes"-file that describes available enzymes               #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2005 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Archive:: /Mowse/ms_mascotresfile/include/ms_enzyme.hpp              $ #
#     $Author: villek@matrixscience.com $ #
#       $Date: 2018-07-30 16:23:53 +0100 $ #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/
 
#ifndef MS_ENZYME_HPP
#define MS_ENZYME_HPP
 
 
#include <string>
#include <vector>
 
 
namespace matrix_science {
 
    class MS_MASCOTRESFILE_API ms_enzyme : public ms_customproperty
    {
        friend class ms_enzymefile;
 
    public:
 
        enum cuttertype
        {
            UNDEFINED_CUTTER = 0x0000, 
            NTERM_CUTTER     = 0x0001, 
            CTERM_CUTTER     = 0x0002  
        };
 
        ms_enzyme();
 
        ms_enzyme(const ms_enzyme& src);
 
        ~ms_enzyme();
 
        void defaultValues();
 
        void copyFrom(const ms_enzyme* right);
 
#ifndef SWIG
        ms_enzyme& operator=(const ms_enzyme& right);
#endif
        bool isValid() const;
 
        bool verifyEnzyme(ms_errs* errObj) const;
 
        std::string getTitle() const;
 
        void setTitle(const char* str);
 
        bool isSemiSpecific() const;
 
        void setSemiSpecific(const bool value);
 
        bool isIndependent() const;
 
        void setIndependent(const bool bit);
 
        int getNumberOfCutters() const;
 
        void clearAllCutters();
 
        void addCutter(const cuttertype type, const char* cleaveAtStr, const char* restrictStr);
        
        ms_enzyme::cuttertype getCutterType(const int cutterNum) const;
 
        std::string getCleave(const int cutterNum) const;
 
        std::string getRestrict(const int cutterNum) const;
 
        bool canCleave(const int  cutterNum, 
                       const char leftResidue, 
                       const char rightResidue) const;
 
#ifdef SUPPRESS_MS_CUSTOMPROPERTY_INHERITANCE
#include "suppress_ms_customproperty.hpp"
#endif
 
    private:
        void setNTerm(std::string& cleaveStr, std::string& restrictStr);
        void setCTerm(std::string& cleaveStr, std::string& restrictStr);
        std::string::size_type prepareNextNTerm();
        std::string::size_type prepareNextCTerm();
        void setIndependentInternal(const bool bit);
        void setSemiSpecificInternal(const bool bit);
        void makeCustomPropIndexed();
 
    private:
        std::string     title_;
        bool            semiSpecific_;
 
        bool            independent_;
        
        typedef std::vector< bool* > residue_flags_vector;
 
        residue_flags_vector cleavageNTerm;
        residue_flags_vector cleavageCTerm;
        residue_flags_vector restrictNTerm;
        residue_flags_vector restrictCTerm;
    };// class ms_enzyme
 
    class ms_filesource;
 
 
    class MS_MASCOTRESFILE_API ms_enzymefile : public ms_errors
    {
    public:
        ms_enzymefile();
 
        ms_enzymefile(const ms_enzymefile& src);
 
        ms_enzymefile(const char* filename, const matrix_science::ms_connection_settings * cs = 0);
 
        ~ms_enzymefile();
 
        void defaultValues();
 
        void copyFrom(const ms_enzymefile* right);
 
#ifndef SWIG
        ms_enzymefile& operator=(const ms_enzymefile& 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 getNumberOfEnzymes() const;
 
        void clearEnzymes();
 
        void appendEnzyme(const ms_enzyme* item);
 
        const ms_enzyme* getEnzymeByNumber(const int num) const;
 
        const ms_enzyme* getEnzymeByName(const char* name) const;
 
        bool isNoneFound() const;
 
        bool updateEnzymeByNumber(const int num, const ms_enzyme enzyme);
 
        bool updateEnzymeByName(const char* name, const ms_enzyme enzyme);
 
        bool deleteEnzymeByNumber(const int num);
 
        bool deleteEnzymeByName(const char* name);
 
 
    private:
 
        void read_internal(ms_filesource *pFSource);
 
        std::string filename_;
        std::vector<ms_enzyme*> entries_;
        std::vector< std::string > comments_;
        bool noneFound_;
        ms_connection_settings cs_;
 
    }; // class ms_enzymefile // end of config_group
} // matrix_science
 
#endif // MS_ENZYME_HPP
 
/*------------------------------- End of File -------------------------------*/