ms_customquantitation.hpp

/*
##############################################################################
# file: ms_customquantitation.hpp                                               #
# 'msparser' toolkit                                                         #
# Quantitation for Reporter and Multiplex protocols                          #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2013 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Author: francoisr@matrixscience.com $ #
#       $Date: 2018-11-22 11:02:10 +0000 $ #
#   $Revision: b577d675f5daad88ac6730bda521ef7317380154 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/
 
#ifndef MS_CUSTOMQUANTITATION_HPP
#define MS_CUSTOMQUANTITATION_HPP
 
 
// Includes from the standard template library
#include <string>
#include <vector>
#include <utility>
 
namespace msparser_internal {
    struct peptide_ratio_data_t;
}
 
namespace matrix_science {
    class ms_peptide_quant_ratio;
    class ms_quantitation;
    class ms_peptidesummary;
    class ms_ms2quantitation;
    class ms_protein;
    class ms_peptide_quant_key;
    class ms_peptide_quant_key_vector;
    class ms_quant_average;
 
 
    class MS_MASCOTRESFILE_API ms_customquantitation: public ms_quantitation
    {
        public:
            explicit ms_customquantitation(const ms_quant_method &qm);
 
            explicit ms_customquantitation(const ms_peptidesummary &initFrom);
 
            ms_customquantitation(const ms_peptidesummary &initFrom, const ms_quant_method &qm);
 
            explicit ms_customquantitation(const ms_ms2quantitation &copyFrom);
 
            virtual ~ms_customquantitation();
 
            virtual bool hasPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) const;
            virtual ms_peptide_quant_ratio getPeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName) const;
 
            virtual bool isPeptideRatioExcluded(const ms_peptide_quant_key &key, const std::string &ratioName) const;
            virtual void setPeptideRatioIncluded(const ms_peptide_quant_key &key, const std::string &ratioName);
            virtual void setPeptideRatioExcluded(const ms_peptide_quant_key &key, const std::string &ratioName);
 
            virtual void setProteinRatioType(const char *value);
 
            virtual void setQuantOutliers(const ms_quant_outliers *);
 
            virtual ms_protein_quant_ratio getProteinRatio(const std::string &accession, int dbIdx, const std::string &ratioName) const;
 
            virtual ms_protein_quant_ratio getProteinRatio(const std::string &accession, int dbIdx, const std::string &ratioName, const ms_peptide_quant_key_vector &includeKeys, const ms_peptide_quant_key_vector &excludeKeys) const;
 
            void addPeptideRatio(const ms_peptide_quant_ratio &ratio);
 
            void removePeptideRatio(const ms_peptide_quant_key &key, const std::string &ratioName);
 
            void clearPeptideRatios();
 
            void addPeptideQuantKey(const std::string &accession, int dbIdx, const ms_peptide_quant_key &key);
 
            void addPeptideQuantKeys(const std::string &accession, int dbIdx, const std::vector<ms_peptide_quant_key> &keys);
 
            void addPeptideQuantKeys(const std::string &accession, int dbIdx, const ms_peptide_quant_key_vector &keys);
 
            void removePeptideQuantKey(const std::string &accession, int dbIdx, const ms_peptide_quant_key &key);
 
            void clearPeptideQuantKeys(const std::string &accession, int dbIdx);
 
            double getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType) const;
 
            double getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType, const ms_peptide_quant_key_vector &keys) const;
 
            double getUnnormalisedAveragePeptideRatio(const std::string &ratioName, const std::string &averageType, const std::string &accession, int dbIdx) const;
 
        protected:
            virtual void getSortedFinitePeptideRatioValues(const std::string &ratioName, const std::set<ms_peptide_quant_key> &keys, const std::set<ms_peptide_quant_key> &includeKeys, const std::set<ms_peptide_quant_key> &excludeKEys, std::vector<double> &values, std::vector<double> &weights, std::vector<ms_peptide_quant_key> &activeKeys, std::map<ms_peptide_quant_key, int> &inactiveKeys) const;
 
            void addPeptideQuantKeySibling(const ms_peptide_quant_key & originalKey, const ms_peptide_quant_key & newKey);
            void removePeptideQuantKeySibling(const ms_peptide_quant_key & newKey);
 
        private:
            ms_customquantitation(const ms_customquantitation &copyFrom);
            ms_customquantitation& operator=(const ms_customquantitation &right);
 
            typedef std::string ratio_name_t;
 
            typedef std::map< ms_peptide_quant_key, msparser_internal::peptide_ratio_data_t* > peptide_quant_key_to_ratio_pointer_t;
            typedef std::multimap< msparser_internal::peptide_ratio_data_t*, ms_peptide_quant_key > ratio_pointer_to_peptide_quant_key_t;
 
            typedef std::map< ratio_name_t, peptide_quant_key_to_ratio_pointer_t > ratio_name_to_peptide_quant_key_map_t;
            typedef std::map< ratio_name_t, ratio_pointer_to_peptide_quant_key_t > ratio_name_to_pointer_map_t;
 
            bool lookupPeptideRatioNondestructive(const ms_peptide_quant_key &key, const std::string &ratioName, peptide_quant_key_to_ratio_pointer_t **qpmap, msparser_internal::peptide_ratio_data_t **rp);
            bool lookupPeptideRatioNondestructive(const ms_peptide_quant_key &key, const std::string &ratioName, const peptide_quant_key_to_ratio_pointer_t **qpmap = NULL, const msparser_internal::peptide_ratio_data_t **rp = NULL) const;
 
            bool insertPeptideRatio(const ms_peptide_quant_ratio &ratio);
            msparser_internal::peptide_ratio_data_t* insertPeptideRatio(const std::string &ratioName, bool isMissing, const ms_peptide_quant_key &key, bool isInfinite, bool isExcluded, double value, double weight);
            void deleteAlias(const std::string &ratioName, const ms_peptide_quant_key &key);
            void deleteAliases(const std::string &ratioName, const ms_peptide_quant_key &key);
            void deallocatePeptideRatios();
 
            double calculateAverageRatio(const std::vector<double> &values, const std::string &kind) const;
 
            std::set< msparser_internal::peptide_ratio_data_t* > peptideRatioPool_;
            ratio_name_to_peptide_quant_key_map_t ratioNameToPeptideQuantKeyMap_;
            ratio_name_to_pointer_map_t ratioNameToPointerMap_;
 
            enum SUPPORTED_PROTEIN_RATIO_TYPE {
                PROTEIN_RATIO_TYPE_MEDIAN = 0,
                PROTEIN_RATIO_TYPE_AVERAGE,
                PROTEIN_RATIO_TYPE_WEIGHTED
            };
 
            int proteinRatioType_;
 
            bool initialiseProteinMappingFromResultsFile(const ms_peptidesummary &pepsum);
            bool initialisePeptideQuantKeys(const ms_peptidesummary &pepsum, const ms_protein *protein);
 
    }; // end of quantitation_group
}   // matrix_science namespace
 
#endif // MS_CUSTOMQUANTITATION_HPP
 
/*------------------------------- End of File -------------------------------*/