ms_protein_quant_ratio.hpp

/*
##############################################################################
# file: ms_protein_quant_ratio.hpp                                           #
# 'msparser' toolkit                                                         #
# Protein ratio for relative quantitation, estimated from peptide ratios     #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2013 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Author: villek@matrixscience.com $ #
#       $Date: 2018-07-30 16:23:53 +0100 $ #
#   $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/

#ifndef MS_PROTEIN_QUANT_RATIO_HPP
#define MS_PROTEIN_QUANT_RATIO_HPP


// Includes from the standard template library
#include <string>
#include <map>

namespace matrix_science {
    class ms_peptide_quant_key;
    class ms_peptide_quant_key_vector;



    class MS_MASCOTRESFILE_API ms_protein_quant_ratio
    {
        friend class ms_quantitation;
        friend class ms_ms1quantitation;
        friend class ms_ms2quantitation;
        friend class ms_customquantitation;

        public:
            ms_protein_quant_ratio(const std::string &accession, int dbIdx, const std::string &ratioName);

            ms_protein_quant_ratio(const std::string &accession, int dbIdx, const std::string &ratioName, double value, double stdev, double stderror, double hypothesisPvalue, double normalityPvalue, unsigned int sampleSize);

            ms_protein_quant_ratio(const ms_protein_quant_ratio& src);

            ~ms_protein_quant_ratio();

#ifndef SWIG

            ms_protein_quant_ratio& operator=(const ms_protein_quant_ratio& right);

            bool operator==(const ms_protein_quant_ratio& right) const;

            bool operator!=(const ms_protein_quant_ratio& right) const;
#endif

            void copyFrom(const ms_protein_quant_ratio* src);

            bool isMissing() const;

            std::string getAccession() const;

            int getDB() const;

            std::string getRatioName() const;

            double getValue() const;

            unsigned int getSampleSize() const;

            double getStandardDeviation() const;
            
            double getStandardDeviation(std::string &whyUnavailable) const;

            double getStandardError() const;

            double getStandardError(std::string &whyUnavailable) const;

            ms_peptide_quant_key_vector getActiveKeys() const;

            ms_peptide_quant_key_vector getSkippedKeys() const;

            ms_peptide_quant_key_vector getOutlierKeys() const;

            ms_peptide_quant_key_vector getExcludedKeys() const;

            double getHypothesisPvalue() const;

            double getHypothesisPvalue(std::string &whyUnavailable) const;

            bool isSignificant(double threshold = 0.05) const;

            double getNormalityPvalue() const;

            double getNormalityPvalue(std::string &whyUnavailable) const;

            bool isLogNormal(double threshold = 0.05) const;

            static ms_protein_quant_ratio fromSerialisedString(const std::string &serialisedStr);

            std::string serialise() const;

            static std::string serialisationFormatVersion();
            
        private:
            enum PEPQUANTKEY_STATE {
                PEPQUANTKEY_SKIPPED  = 0x0001,
                PEPQUANTKEY_OUTLIER  = 0x0002,
                PEPQUANTKEY_EXCLUDED = 0x0004
            };

            enum REASON_WHY_UNAVAILABLE {
                REASON_NOT_UNAVAILABLE = 0,
                REASON_MISSING_RATIO = 1,
                REASON_TYPE_WEIGHTED = 2
            };

            static std::string lookupWhyUnavailable(int reason);

//Warning 325: Nested struct not currently supported
#ifndef SWIG
            typedef struct { int why; const char *str; } reason_why_t;
            static const reason_why_t reason_why_db[];
#endif


            ms_protein_quant_ratio(const std::string &accession, int dbIdx, const std::string &ratioName, double value, double stdev, double stderror, double hypothesisPvalue, double normalityPvalue, const std::vector<ms_peptide_quant_key> &activeKeys, const std::map<ms_peptide_quant_key, int> &inactiveKeys);

            ms_peptide_quant_key_vector collectKeys(int type) const;

            bool isMissing_;

            std::string accession_;
            int dbIdx_;
            std::string ratioName_;

            double value_;

            double stdev_;
            double stderror_;
            int whyStdevUnavailable_;

            double hypothesisPvalue_;
            int whyHypothesisPUnavailable_;

            double normalityPvalue_;
            int whyNormalityPUnavailable_;

            unsigned int sampleSize_;

            std::vector<ms_peptide_quant_key> activeKeys_;
            std::map<ms_peptide_quant_key, int> inactiveKeys_;
    }; // end of quantitation_group
}   // matrix_science namespace

#endif // MS_PROTEIN_QUANT_RATIO_HPP

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