ms_ms1quant_match.hpp

/*
##############################################################################
# file: ms_ms1quant_match.hpp
# 'msparser' toolkit
# An extracted ion chromatogram
##############################################################################
# COPYRIGHT NOTICE
# Copyright 1998-2014 Matrix Science Limited  All Rights Reserved.
#
##############################################################################
 * @(#)$Source: parser/inc/ms_ms1quant_match.hpp $
 * @(#)$Revision: 13df8a1acb577c00eb17a154317b079d156f9538 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $
 * @(#)$Date: 2022-01-05 16:48:40 +0000 $
##############################################################################
 */
 
#ifndef MS_MS1QUANT_MATCH_HPP
#define MS_MS1QUANT_MATCH_HPP
 
 
// Includes from the standard template library
#include <string>
 
namespace matrix_science
{
    //=========================================================================
    class ms_ms1quant_match_body;
    class ms_protein;
    class ms_peptide;
    class ms_quant_component;
 
 
    class MS_MASCOTRESFILE_API ms_ms1quant_match :
        public ms_handle
    {
        public:
 
            enum chargeType
            {
                CHARGETYPE_ORIGINAL,       
                CHARGETYPE_ALL             
            };
 
            static std::string getXmlCode(chargeType code);
 
            static chargeType getCodeFromXml(std::string text);
 
            ms_ms1quant_match();
 
            ms_ms1quant_match(const ms_ms1quant_match_body & body);
 
#ifndef SWIG
            ms_ms1quant_match_body * body();
            const ms_ms1quant_match_body * body() const;
 
            bool addProteinHit(const int hit, const int member);
            void setKey(const int id);
            void applyThresholds();
#endif
 
            matrix_science::ms_peptide_quant_key getKey() const;
 
            bool hasIdentifiedComponent() const;
 
            bool allComponentsIdentified() const;
 
            std::string getPeptideString() const;
 
            std::string getVarMods() const;
 
            int getFirstXicScanId() const;
 
            void setFirstXicScanId(int value) ;
 
            int getLastXicScanId() const;
 
            void setLastXicScanId(int value) ;
 
            double getDisplayIntensity() const;
 
            void setDisplayIntensity(double value);
 
            int getChargeState() const;
 
            chargeType getChargeType() const;
 
            std::string getLabelFreeVarMods() const;
 
            std::string getReadableLabelFreeVarMods() const;
 
            std::string getConciseLabelFreeVarMods() const;
 
            int getDataSourceId() const;
 
            const ms_matrix & getCorrectionMatrix() const;
 
#if !defined(SWIGJAVA) && !defined(SWIGCSHARP)
            ms_matrix & getCorrectionMatrix();
#endif
            const ms_matrix & getPerfectObservedMatrix() const;
 
#if !defined(SWIGJAVA) && !defined(SWIGCSHARP)
            ms_matrix & getPerfectObservedMatrix();
#endif
            const ms_matrix & getPredictionMatrix() const;
 
#if !defined(SWIGJAVA) && !defined(SWIGCSHARP)
            ms_matrix & getPredictionMatrix();
#endif
            int getNumHits() const;
            const ms_protein * getHit(int index1) const;
 
            int getNumComponents() const;
            ms_ms1quant_match_component getComponent(int index) const;
 
            bool hasComponent(std::string componentName) const;
            ms_ms1quant_match_component getComponent(std::string componentName) const;
 
            ms_ms1quant_match_component * addCreatedComponent(
                    const matrix_science::ms_peptide & peptide,
                    const matrix_science::ms_quant_component & component,
                    const int file_index = matrix_science::ms_quant_file_index::file_index_value_not_set);
 
            ms_ms1quant_match_component * addCreatedComponent(const std::string & componentName);
 
            ms_ms1quant_match_component * addCreatedComponent(
                const matrix_science::ms_ms1quant_match_component & component);
 
            ms_ms1quant_match_component * addComponent(const matrix_science::ms_ms1quant_match_component & component);
 
            bool removeComponent(const std::string & componentName);
 
            ms_ms1quant_match_component * addIdentifiedComponent(
                    const matrix_science::ms_peptide & peptide,
                    const matrix_science::ms_quant_component & component,
                    const int file_index = matrix_science::ms_quant_file_index::file_index_value_not_set);
 
            int getNumPeptideRatios() const;
            ms_ms1quant_match_ratio getPeptideRatio(int index) const;
 
            bool hasPeptideRatio(const std::string & ratioName) const;
            ms_ms1quant_match_ratio getPeptideRatio(const std::string & ratioName) const;
            void setPeptideRatio(const std::string & ratioName, const ms_ms1quant_match_ratio & ratio);
 
            ms_ms1quant_charge_state getChargeStateData() const;
            void setChargeStateData(const ms_ms1quant_charge_state & csData);
 
            bool isHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber) const;
            bool isHitRatioUsedForAverage(const std::string & ratioName, int hitId, int memberNumber) const;
            bool isHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber) const;
 
            void setHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber);
 
            void clearHitRatioExcluded(const std::string & ratioName, int hitId, int memberNumber);
 
            void setHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber);
 
            void clearHitRatioOutlier(const std::string & ratioName, int hitId, int memberNumber);
    };
 
 // end of quantitation_group
    //=========================================================================
 
} // namespace matrix_science
 
#endif // MS_MS1QUANT_MATCH_HPP
 
/*------------------------------- End of File -------------------------------*/