ms_umod_specificity.hpp

/*
##############################################################################
# file: ms_umod_specificity.hpp                                              #
# 'msparser' toolkit                                                         #
# Represents 'specificity' object from unimod.xml file                       #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2006 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
 * @(#)$Source: parser/inc/ms_umod_specificity.hpp $
 * @(#)$Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $
 * @(#)$Date: 2018-07-30 16:23:53 +0100 $
##############################################################################
 */

#ifndef MS_UMOD_SPECIFICITY_HPP
#define MS_UMOD_SPECIFICITY_HPP


#include <string>
#include <vector>

// forward declarations
namespace msparser_internal {
    class ms_umod_xmlloader;
}

namespace matrix_science {

    class ms_umod_neutralloss; // forward declaration
    class ms_quant_specificity; // forward declaration
    class ms_umod_configfile;  // forward declaration
    class ms_xml_schema; // forward declaration


    class MS_MASCOTRESFILE_API ms_umod_specificity
    {
        friend class msparser_internal::ms_umod_xmlloader;
        friend class ms_umod_modification;
        friend class ms_umod_configfile;

    public:
        ms_umod_specificity();

        ms_umod_specificity(const ms_umod_specificity& src);

        ms_umod_specificity(const ms_quant_specificity& src, const ms_umod_configfile& umodFile);

        virtual ~ms_umod_specificity();

        void defaultValues();

        void copyFrom(const ms_umod_specificity* right);

        void copyFrom(const ms_quant_specificity* right, const ms_umod_configfile& umodFile);

#ifndef SWIG

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

        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;


        int getNumberOfNeutralLosses() const;

        void clearNeutralLosses();

        void appendNeutralLoss(const ms_umod_neutralloss *nl);

        const ms_umod_neutralloss* getNeutralLoss(const int idx) const;

        bool updateNeutralLoss(const int idx, const ms_umod_neutralloss *nl);

        bool deleteNeutralLoss(const int idx);

        std::string getNeutralLossSchemaType() const;


        int getNumberOfPepNeutralLosses() const;

        void clearPepNeutralLosses();

        void appendPepNeutralLoss(const ms_umod_neutralloss *pnl);

        const ms_umod_neutralloss* getPepNeutralLoss(const int idx) const;

        bool updatePepNeutralLoss(const int idx, const ms_umod_neutralloss *pnl);

        bool deletePepNeutralLoss(const int idx);

        std::string getPepNeutralLossSchemaType() const;


        bool haveMiscNotes() const;

        std::string getMiscNotes() const;

        void setMiscNotes(const char* value);

        void dropMiscNotes();

        std::string getMiscNotesSchemaType() const;


        bool haveHidden() const;

        bool isHidden() const;

        void setHidden(const bool value);

        void dropHidden();

        std::string getHiddenSchemaType() const;


        bool haveSite() const;

        std::string getSite() const;

        void setSite(const char* value);

        void dropSite();

        std::string getSiteSchemaType() const;


        bool havePosition() const;

        std::string getPosition() const;

        void setPosition(const char* value);

        void dropPosition();

        std::string getPositionSchemaType() const;


        bool haveClassification() const;

        std::string getClassification() const;

        void setClassification(const char* value);

        void dropClassification();

        std::string getClassificationSchemaType() const;


        bool haveSpecGroup() const;

        int getSpecGroup() const;

        void setSpecGroup(const int value);

        void dropSpecGroup();

        std::string getSpecGroupSchemaType() const;

        bool inShortList() const;

        // ! Sets whether this specificity is in the short list on the Mascot search form.
        void showInShortList(bool b);

        bool inLongList() const;

        // ! Sets whether this specificity is in the full list on the Mascot search form.
        void showInLongList(bool b);

        // ! Indicates if this specificity is included in error tolerant searches.
        bool inErrorTolerant() const;

        // ! Sets if this specificity is included in error tolerant searches.
        void useInErrorTolerant(bool b);

        bool isSameAs(const ms_umod_specificity& right) const;

    private:

        typedef std::vector< ms_umod_neutralloss* > nl_vector;
        nl_vector _neutrallosses;

        typedef std::vector< ms_umod_neutralloss* > pnl_vector;
        pnl_vector _pepneutrallosses;

        std::string _miscNotes;
        bool _miscNotes_set;

        bool _hidden;
        bool _hidden_set;

        std::string _site;
        bool _site_set;

        std::string _position;
        bool _position_set;

        std::string _classification;
        bool _classification_set;

        int _specGroup;
        bool _specGroup_set;

        // Not persistent in unimod xml files
        bool _show_in_long_list;
        bool _use_in_error_tolerant;

    }; // class ms_umod_specificity
 // end of config_group

} // namespace matrix_science

#endif // MS_UMOD_SPECIFICITY_HPP

/*------------------------------- End of File -------------------------------*/