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_2_8_1-0-gea32989045 $
 * @(#)$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 -------------------------------*/