ms_quant_method.hpp

/*
##############################################################################
# file: ms_quant_method.hpp                                                  #
# 'msparser' toolkit                                                         #
# Encapsulates method-element from "quantitation.xml"-file                 #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2006 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
 * @(#)$Source: parser/inc/ms_quant_method.hpp $
 * @(#)$Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
 * @(#)$Date: 2018-07-30 16:23:53 +0100 $
##############################################################################
 */
 
#ifndef MS_QUANT_METHOD_HPP
#define MS_QUANT_METHOD_HPP
 
 
#include <string>
#include <vector>
 
// forward declarations
namespace msparser_internal {
    class ms_quant_xmlloader;
    class ms_quant_method_impl;
    class ms_quant_configfile_impl;
}
 
namespace matrix_science {
 
    class ms_quant_modgroup; // forward declaration
    class ms_quant_component; // forward declaration
    class ms_quant_quality; // forward declaration
    class ms_quant_integration; // forward delcaration
    class ms_quant_outliers; // forward declaration
    class ms_quant_normalisation; // forward declaration
    class ms_quant_protocol; // forward declaration
    class ms_quant_ratio; // forward declaration
    class ms_xml_schema; // forward declaration
    class ms_quant_localdef; // forward declaration
 
    class MS_MASCOTRESFILE_API ms_quant_method: public ms_xml_IValidatable
    {
        friend class msparser_internal::ms_quant_xmlloader;
        friend class msparser_internal::ms_quant_configfile_impl;
 
    public:
 
        enum METHOD_COMPATIBLE{
            COMPATIBLE,                             
            COMPATIBLE_DIFF_PROTOCOL,               
            COMPATIBLE_DIFF_NUM_COMPONENTS,         
            COMPATIBLE_MISSING_COMPONENT,           
            COMPATIBLE_DIFF_NUM_MOD_GROUPS,         
            COMPATIBLE_MISSING_MOD_GROUP,           
            COMPATIBLE_DIFF_NUM_LOCAL_MODS,         
            COMPATIBLE_DIFF_LOCAL_MOD,              
            COMPATIBLE_DIFF_NUM_MODS,               
            COMPATIBLE_MISSING_MOD,                 
            COMPATIBLE_MISSING_INTEGRATION,         
            COMPATIBLE_MISSING_INTEGRATION_PARAM,   
            COMPATIBLE_DIFF_INTEGRATION_PARAM,      
            COMPATIBLE_DIFF_NUM_ISOTOPES            
        };
 
        ms_quant_method();
 
        ms_quant_method(const ms_quant_method& src);
 
        virtual ~ms_quant_method();
 
        void defaultValues();
 
        void copyFrom(const ms_quant_method* right);
 
#ifndef SWIG
        ms_quant_method& operator=(const ms_quant_method& 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 getNumberOfModificationGroups() const;
 
        void clearModificationGroups();
 
        void appendModificationGroup(const ms_quant_modgroup *item);
 
        const ms_quant_modgroup * getModificationGroupByNumber(const int idx) const;
 
        const ms_quant_modgroup * getModificationGroupByName(const char *name) const;
 
        bool updateModificationGroupByNumber(const int idx, const ms_quant_modgroup* modgroup);
 
        bool updateModificationGroupByName(const char *name, const ms_quant_modgroup* modgroup);
 
        bool deleteModificationGroupByNumber(const int idx);
 
        bool deleteModificationGroupByName(const char *name);
 
        std::string getModificationGroupSchemaType() const;
 
        void getLocalModifications(std::vector<const ms_quant_localdef *> &localDefVector);
 
        int getNumberOfComponents() const;
 
        void clearComponents();
 
        void appendComponent(const ms_quant_component *item);
 
        const ms_quant_component * getComponentByNumber(const int idx) const;
 
        const ms_quant_component * getComponentByName(const char *name) const;
 
        bool updateComponentByNumber(const int idx, const ms_quant_component* comp);
 
        bool updateComponentByName(const char *name, const ms_quant_component* comp);
 
        bool deleteComponentByNumber(const int idx);
 
        bool deleteComponentByName(const char *name);
 
        std::string getComponentSchemaType() const;
 
 
        int getNumberOfReportRatios() const;
 
        void clearReportRatios();
 
        void appendReportRatio(const ms_quant_ratio *ratio);
 
        const ms_quant_ratio * getReportRatioByNumber(const int idx) const;
 
        const ms_quant_ratio * getReportRatioByName(const char *name) const;
 
        bool updateReportRatioByNumber(const int idx, const ms_quant_ratio* ratio);
 
        bool updateReportRatioByName(const char *name, const ms_quant_ratio* ratio);
 
        bool deleteReportRatioByNumber(const int idx);
 
        bool deleteReportRatioByName(const char *name);
 
        std::string getReportRatioSchemaType() const;
 
 
        int getNumberOfExclusions() const;
 
        void clearExclusions();
 
        void appendExclusion(const char* exclusion);
 
        std::string getExclusion(const int idx) const;
 
        bool updateExclusion(const int idx, const char* exclusion);
 
        bool deleteExclusion(const int idx);
 
        std::string getExclusionSchemaType() const;
 
 
        int getNumberOfSeqs() const;
 
        void clearSeqs();
 
        void appendSeq(const char* seq);
 
        std::string getSeq(const int idx) const;
 
        bool updateSeq(const int idx, const char* seq);
 
        bool deleteSeq(const int idx);
 
        std::string getSeqSchemaType() const;
 
 
        bool haveComp() const;
 
        std::string getComp() const;
 
        void setComp(const char* value);
 
        void dropComp();
 
        std::string getCompSchemaType() const;
 
 
        bool haveQuality() const;
 
        const ms_quant_quality* getQuality() const;
 
        void setQuality(const ms_quant_quality* quality);
 
        void dropQuality();
 
        std::string getQualitySchemaType() const;
 
 
        bool haveIntegration() const;
 
        const ms_quant_integration* getIntegration() const;
 
        void setIntegration(const ms_quant_integration* integration);
 
        void dropIntegration();
 
        std::string getIntegrationSchemaType() const;
 
 
        bool haveOutliers() const;
 
        const ms_quant_outliers* getOutliers() const;
 
        void setOutliers(const ms_quant_outliers* outliers);
 
        void dropOutliers();
 
        std::string getOutliersSchemaType() const;
 
 
        bool haveNormalisation() const;
 
        const ms_quant_normalisation* getNormalisation() const;
 
        void setNormalisation(const ms_quant_normalisation* normalisation);
 
        void dropNormalisation();
 
        std::string getNormalisationSchemaType() const;
 
 
        bool haveProtocol() const;
 
        const ms_quant_protocol* getProtocol() const;
 
        void setProtocol(const ms_quant_protocol* protocol);
 
        void dropProtocol();
 
        std::string getProtocolSchemaType() const;
 
 
        bool haveName() const;
 
        std::string getName() const;
 
        void setName(const char* value);
 
        void dropName();
 
        std::string getNameSchemaType() const;
 
 
        bool haveDescription() const;
 
        std::string getDescription() const;
 
        void setDescription(const char* value);
 
        void dropDescription();
 
        std::string getDescriptionSchemaType() const;
 
 
        bool haveConstrainSearch() const;
 
        bool isConstrainSearch() const;
 
        void setConstrainSearch(const bool value);
 
        void dropConstrainSearch();
 
        std::string getConstrainSearchSchemaType() const;
 
 
        bool haveProteinRatioType() const;
 
        std::string getProteinRatioType() const;
 
        void setProteinRatioType(const char* value);
 
        void dropProteinRatioType();
 
        std::string getProteinRatioTypeSchemaType() const;
 
 
        bool haveReportDetail() const;
 
        bool isReportDetail() const;
 
        void setReportDetail(const bool value);
 
        void dropReportDetail();
 
        std::string getReportDetailSchemaType() const;
 
 
        bool haveMinNumPeptides() const;
 
        int getMinNumPeptides() const;
 
        void setMinNumPeptides(const int value);
 
        void dropMinNumPeptides();
 
        std::string getMinNumPeptidesSchemaType() const;
 
 
        bool haveProtScoreType() const;
 
        std::string getProtScoreType() const;
 
        void setProtScoreType(const char* value);
 
        void dropProtScoreType();
 
        std::string getProtScoreTypeSchemaType() const;
 
 
        bool haveSigThresholdValue() const;
 
        std::string getSigThresholdValue() const;
 
        void setSigThresholdValue(const char* value);
 
        void dropSigThresholdValue();
 
        std::string getSigThresholdValueSchemaType() const;
 
 
        bool haveShowSubSets() const;
 
        std::string getShowSubSets() const;
 
        void setShowSubSets(const char* value);
 
        void dropShowSubSets();
 
        std::string getShowSubSetsSchemaType() const;
 
 
        bool haveRequireBoldRed() const;
 
        bool isRequireBoldRed() const;
 
        void setRequireBoldRed(const bool value);
 
        void dropRequireBoldRed();
 
        std::string getRequireBoldRedSchemaType() const;
#ifndef SWIG
        int isMethodCompatible(const ms_quant_method &other, std::string & reasonStrRef) const;
#else // SWIG Multiple return values
        int isMethodCompatible(const ms_quant_method &other, std::string & OUTPUT) const;
#endif
    private:
        msparser_internal::ms_quant_method_impl * m_pImpl;
    }; // class ms_quant_method
 // end of config_group
 
} // namespace matrix_science
 
#endif // MS_QUANT_METHOD_HPP
 
/*------------------------------- End of File -------------------------------*/