ms_umod_modification.hpp

/*
##############################################################################
# file: ms_umod_modification.hpp                                             #
# 'msparser' toolkit                                                         #
# Represents modification object in unimod.xml file                          #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2006 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
 * @(#)$Source: parser/inc/ms_umod_modification.hpp $
 * @(#)$Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
 * @(#)$Date: 2018-07-30 16:23:53 +0100 $
##############################################################################
 */
 
#ifndef MS_UMOD_MODIFICATION_HPP
#define MS_UMOD_MODIFICATION_HPP
 
 
#include <string>
#include <vector>
 
// forward declarations
namespace msparser_internal {
    class ms_umod_xmlloader;
}
 
namespace matrix_science {
 
    class ms_umod_composition; // forward declaration
    class ms_umod_specificity;  // forward declaration
    class ms_umod_xref; // forward declaration
    class ms_quant_localdef; // forward declaration
    class ms_quant_unmodified;  // forward declaration
    class ms_umod_configfile; // forward declaration
    class ms_quant_component; // forward declaration
    class ms_xml_schema; // forward declaration
 
    class MS_MASCOTRESFILE_API ms_umod_modification: public ms_xml_IValidatable
    {
        friend class msparser_internal::ms_umod_xmlloader;
        friend class ms_umod_configfile;
 
    public:
        ms_umod_modification();
 
        ms_umod_modification(const ms_umod_modification& src);
 
        ms_umod_modification(const ms_quant_localdef& src, const ms_umod_configfile& umodFile);
 
        ms_umod_modification(const ms_quant_unmodified& src);
 
        void updateMasses(const ms_umod_configfile& umodFile, const ms_quant_component& quantComp);
 
        virtual ~ms_umod_modification();
 
        void defaultValues();
 
        void copyFrom(const ms_umod_modification* right);
 
        void copyFrom(const ms_quant_localdef* right, const ms_umod_configfile& umodFile);
 
        void copyFrom(const ms_quant_unmodified* right);
 
#ifndef SWIG
        ms_umod_modification& operator=(const ms_umod_modification& right);
#endif
 
        bool isSameAs(const ms_umod_modification& right_mod) const;
 
        virtual std::string getSchemaType() const;
 
        virtual std::string validateShallow(const ms_xml_schema *pSchemaFileObj) const;
 
        virtual std::string validateDeep(const ms_xml_schema *pSchemaFileObj) const;
 
 
        std::vector< std::string > getModFileList(const unsigned int flags = ms_umod_configfile::MODFILE_FLAGS_ALL) const;
 
        int findSpecGroup(const char* modFileName) const;
 
        int getNumberOfSpecificities() const;
 
        void clearSpecificities();
 
        void appendSpecificity(const ms_umod_specificity *specificity);
 
        const ms_umod_specificity * getSpecificity(const int idx) const;
 
        const ms_umod_specificity * getSpecificityBySite(const char *site) const;
 
        const ms_umod_specificity * getSpecificityBySiteAndPosition(const char *site, const char *position) const;
 
        bool updateSpecificity(const int idx, const ms_umod_specificity *specificity);
 
        bool deleteSpecificity(const int idx);
 
        std::string getSpecificitySchemaType() const;
 
 
        bool haveDelta() const;
 
        const ms_umod_composition* getDelta() const;
 
        void setDelta(const ms_umod_composition* delta);
 
        void dropDelta();
 
        std::string getDeltaSchemaType() const;
 
 
        int getNumberOfIgnores() const;
 
        void clearIgnores();
 
        void appendIgnore(const ms_umod_composition *ignore);
 
        const ms_umod_composition * getIgnore(const int idx) const;
 
        bool updateIgnore(const int idx, const ms_umod_composition *ignore);
 
        bool deleteIgnore(const int idx);
 
        std::string getIgnoreSchemaType() const;
 
 
        int getNumberOfAltNames() const;
 
        void clearAltNames();
 
        void appendAltName(const char *alt_name);
 
        std::string getAltName(const int idx) const;
 
        bool updateAltName(const int idx, const char *alt_name);
 
        bool deleteAltName(const int idx);
 
        std::string getAltNameSchemaType() const;
 
 
        int getNumberOfXrefs() const;
 
        void clearXrefs();
 
        void appendXref(const ms_umod_xref *xref);
 
        const ms_umod_xref* getXref(const int idx) const;
 
        bool updateXref(const int idx, const ms_umod_xref *xref);
 
        bool deleteXref(const int idx);
 
        std::string getXrefSchemaType() const;
 
 
        bool haveMiscNotes() const;
 
        std::string getMiscNotes() const;
 
        void setMiscNotes(const char* value);
 
        void dropMiscNotes();
 
        std::string getMiscNotesSchemaType() const;
 
 
        bool haveTitle() const;
 
        std::string getTitle() const;
 
        void setTitle(const char* value);
 
        void dropTitle();
 
        std::string getTitleSchemaType() const;
 
 
        bool haveFullName() const;
 
        std::string getFullName() const;
 
        void setFullName(const char* value);
 
        void dropFullName();
 
        std::string getFullNameSchemaType() const;
 
 
        bool haveApproved() const;
 
        bool isApproved() const;
 
        void setApproved(const bool value);
 
        void dropApproved();
 
        std::string getApprovedSchemaType() const;
 
 
        bool haveUsernameOfPoster() const;
 
        std::string getUsernameOfPoster() const;
 
        void setUsernameOfPoster(const char* value);
 
        void dropUsernameOfPoster();
 
        std::string getUsernameOfPosterSchemaType() const;
 
 
        bool haveGroupOfPoster() const;
 
        std::string getGroupOfPoster() const;
 
        void setGroupOfPoster(const char* value);
 
        void dropGroupOfPoster();
 
        std::string getGroupOfPosterSchemaType() const;
 
 
        bool haveDateTimePosted() const;
 
        std::string getDateTimePosted() const;
 
        void setDateTimePosted(const char* value);
 
        void dropDateTimePosted();
 
        std::string getDateTimePostedSchemaType() const;
 
 
        bool haveDateTimeModified() const;
 
        std::string getDateTimeModified() const;
 
        void setDateTimeModified(const char* value);
 
        void dropDateTimeModified();
 
        std::string getDateTimeModifiedSchemaType() const;
 
        bool haveRecordID() const;
 
        std::string getRecordID() const;
 
        void setRecordID(const char* value);
 
        void dropRecordID();
 
        std::string getRecordIDSchemaType() const;
 
        bool isPrivate() const;
 
        void setPrivate(bool b);
 
        bool isPrivacyEnabled() const;
 
        void setPrivacyEnabled(bool b);
 
    private:
 
        typedef std::vector< ms_umod_specificity * > specificity_vector;
        specificity_vector _specificities;
 
        ms_umod_composition* _delta;
        bool _delta_set;
 
        typedef std::vector< ms_umod_composition* > ignore_vector;
        ignore_vector _ignores;
 
        typedef std::vector< std::string > altNames_vector;
        altNames_vector _altnames;
 
        typedef std::vector< ms_umod_xref* > xref_vector;
        xref_vector _xrefs;
 
        std::string _miscNotes;
        bool _miscNotes_set;
 
        std::string _title;
        bool _title_set;
 
        std::string _fullName;
        bool _fullName_set;
 
        bool _approved;
        bool _approved_set;
 
        std::string _usernameOfPoster;
        bool _usernameOfPoster_set;
 
        std::string _groupOfPoster;
        bool _groupOfPoster_set;
 
        std::string _dateTimePosted;
        bool _dateTimePosted_set;
 
        std::string _dateTimeModified;
        bool _dateTimeModified_set;
 
        std::string _recordID;
        bool _recordID_set;
 
        bool _isPrivate;
        bool _isPrivacyEnabled;
 
    }; // class ms_umod_modification
 // end of config_group
 
} // namespace matrix_science
 
#endif // MS_UMOD_MODIFICATION_HPP
 
/*------------------------------- End of File -------------------------------*/