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_3_0_0-2024-09-24-0-g93ebaeb4f4 $
 * @(#)$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 -------------------------------*/