ms_umod_configfile.hpp

/*
##############################################################################
# file: ms_umod_configfile.hpp                                               #
# 'msparser' toolkit                                                         #
# Represents unimod.xml file                                                 #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2003 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
# $Archive:: /Mowse/ms_mascotresfile/include/ms_umod_configfile.hpp                 $ #
# $Author: francoisr@matrixscience.com $ #
# $Date: 2019-03-08 13:54:54 +0000 $ #
# $Revision: 7979cc541377e595bc9460c7439a78c7ed72e3d9 | MSPARSER_REL_2_8_1-0-gea32989045 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/

#ifndef MS_UMOD_CONFIGFILE_HPP
#define MS_UMOD_CONFIGFILE_HPP


#include <string>
#include <vector>


namespace matrix_science {

    class ms_umod_element; // forward declaration
    class ms_umod_modification; // forward declaration
    class ms_umod_aminoacid; // forward declaration
    class ms_umod_modbrick; // forward declaration
    class ms_session;



    class MS_MASCOTRESFILE_API ms_umod_configfile: public ms_errors
    {
    public:

            enum MODFILE_FLAGS 
            { 
                MODFILE_FLAGS_EMPTY   = 0x00000000, 
                MODFILE_FLAGS_REGULAR = 0x00000001, 
                MODFILE_FLAGS_HIDDEN  = 0x00000002, 
                MODFILE_FLAGS_AASUBST = 0x00000004, 
                MODFILE_FLAGS_ALL     = 0x7FFFFFFF  
            };

        ms_umod_configfile();

        ms_umod_configfile(const char* fileName, const char* schemaFileName, 
            const ms_connection_settings * cs = 0, bool useSchema = true);

        ms_umod_configfile(const ms_umod_configfile& right);

        virtual ~ms_umod_configfile();

#ifndef SWIG

        ms_umod_configfile& operator=(const ms_umod_configfile& right);
#endif

        void copyFrom(const ms_umod_configfile* right);

        virtual void defaultValues();

        void updateMasses();


        std::string getFileName() const;

        void setFileName(const char* filename);


        void setSchemaFileName(const char* name);

        std::string getSchemaFileName() const;

        static std::string getDefaultSchemaFileName();

        void setConnectionSettings(const ms_connection_settings & cs);

        ms_connection_settings getConnectionSettings() const;


        void read_file();

        void save_file();

        void applyVisibility( const ms_session *session);

        void applyVisibility(const std::vector<int> & groupIds);

        void read_buffer(const char* buffer);

        std::string save_buffer(bool validateAgainstSchema = true);


        std::string validateDocument() const;


        int getNumberOfElements() const;

        void clearElements();

        void appendElement(const ms_umod_element *elem);

        const ms_umod_element * getElementByNumber(const int idx) const;

        const ms_umod_element * getElementByName(const char *name) const;

        bool updateElementByNumber(const int idx, const ms_umod_element* element);

        bool updateElementByName(const char *name, const ms_umod_element* element);

        bool deleteElementByNumber(const int idx);

        bool deleteElementByName(const char *name);


        std::vector< std::string > getModFileList(const unsigned int flags = MODFILE_FLAGS_ALL) const;

        int findModFileName(const char * modFileName) const;

        int findModification(const char* modName) const;


        int getNumberOfModifications() const;

        void clearModifications();

        void appendModification(const ms_umod_modification *mod);

        const ms_umod_modification * getModificationByNumber(const int idx) const;

        const ms_umod_modification * getModificationByName(const char *name) const;

        bool updateModificationByNumber(const int idx, const ms_umod_modification *mod);

        bool updateModificationByName(const char *name, const ms_umod_modification *mod);

        bool deleteModificationByNumber(const int idx);

        bool deleteModificationByName(const char *name);


        int getNumberOfAminoAcids() const;

        void clearAminoAcids();

        void appendAminoAcid(const ms_umod_aminoacid *aa);

        const ms_umod_aminoacid * getAminoAcidByNumber(const int idx) const;

        const ms_umod_aminoacid * getAminoAcidByName(const char *name) const;

        bool updateAminoAcidByNumber(const int idx, const ms_umod_aminoacid *aa);

        bool updateAminoAcidByName(const char *name, const ms_umod_aminoacid *aa);

        bool deleteAminoAcidByNumber(const int idx);

        bool deleteAminoAcidByName(const char *name);


        int getNumberOfModBricks() const;

        void clearModBricks();

        void appendModBrick(const ms_umod_modbrick *brick);

        const ms_umod_modbrick * getModBrickByNumber(const int idx) const;

        const ms_umod_modbrick * getModBrickByName(const char *name) const;

        bool updateModBrickByNumber(const int idx, const ms_umod_modbrick *brick);

        bool updateModBrickByName(const char *name, const ms_umod_modbrick *brick);

        bool deleteModBrickByNumber(const int idx);

        bool deleteModBrickByName(const char *name);

        std::string getMajorVersion() const;

        std::string getMinorVersion() const;

        void setMajorVersion(const std::string & version);

        void setMinorVersion(const std::string & version);
    private:

        void applyVisibilityHelper();

        std::string             m_fileName;
        std::string             m_schemaFileName;
        ms_connection_settings  m_cs;

        typedef std::vector< ms_umod_element* > element_vector;
        element_vector          m_elements;

        typedef std::vector< ms_umod_modification* > modification_vector;
        modification_vector     m_modifications;
        typedef std::map<std::string, size_t> modification_index_map;
        modification_index_map  m_modifications_nameToIndex;

        typedef std::vector< ms_umod_aminoacid* > aminoacid_vector;
        aminoacid_vector        m_aminoacids;

        typedef std::vector< ms_umod_modbrick* > modbrick_vector;
        modbrick_vector         m_modbricks;

        std::string m_majorVersion;
        std::string m_minorVersion;

        std::string m_encodingName;
        bool m_useSchema;
    }; // class ms_umod_configfile
 // end of config_group

} // namespace matrix_science

#endif // MS_UMOD_CONFIGFILE_HPP
/*------------------------------- End of File -------------------------------*/