ms_ms1quant_time_align.hpp

/*
##############################################################################
# File:  ms_ms1quant_time_align.hpp                                          #
# Mascot Parser toolkit                                                      #
# Class for accessing the time alignemnt data produced by Distiller for LFQ  #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2022 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Source: parser/inc/ms_ms1quant_time_align.hpp $
#    $Author: dcreasy@matrixscience.com $
#      $Date: 2025-01-12 19:32:12 +0000 $
#  $Revision: fe1e6417cc2b0f4dc9283fa86a1c13c112ed1988 | MSPARSER_REL_3_1_0-2025-07-27-0-gea47708fac $
##############################################################################
*/
 
#ifndef MS_MS1QUANT_TIME_ALIGN_HPP
#define MS_MS1QUANT_TIME_ALIGN_HPP
 
 
// Includes from the standard template library
#include <string>
 
namespace matrix_science
{
    //=========================================================================
    class ms_ms1quant_time_align_body;
 
 
    class MS_MASCOTRESFILE_API ms_ms1quant_time_align :
        public ms_handle, public ms_errors
    {
        public:
            enum status_t {
                ST_TA_NO_DATA,          
                ST_TA_LOADED_FROM_XML,  
                ST_TA_LOADED_FROM_CDB,  
                ST_TA_CALCULATED        
            };
 
            enum warningMessage_t {
                TA_WM_NO_SHARED_PEPTIDES_BETWEEN_P1_AND_P2,           
                TA_WM_LOW_NUM_SHARED_PEPTIDES_BETWEEN_P1_AND_P2,      
                TA_WM_SUBPRJ_HAS_NO_SHARED_PEPTIDES,                  
                TA_WM_USER_SPEC_AUTO_BUT_USING_UNSUPERVISED,          
                TA_WM_LAST
            };
 
            ms_ms1quant_time_align(const int binSize = 12);
 
            ms_ms1quant_time_align(const ms_ms1quant_time_align_body & body);
 
            bool loadXmlFile(const std::string & xmlFilename, const std::string & schemaDirectory);
 
            bool saveXmlFile(const std::string & xmlFilename, const std::string & schemaDirectory) const;
 
            double getRToffset(const int myProjectId, const int otherProjectId, const double rtInOtherProject, const double mOverZ) const;
 
            double getEstimatedFeatureWidth(const int subProjectId, const double mOverZ, const double rt) const;
 
#ifndef SWIG
            ms_ms1quant_time_align_limits & getCombinedLimits(const int fractionNum);
#endif
 
            ms_ms1quant_time_align_limits getCombinedLimits(const int fractionNum) const;
 
            int getBinSize() const;
 
#ifndef SWIG
            std::vector<std::vector<std::vector<double>>> & getFinalResults();
 
            std::vector<std::vector<std::vector<double>>>& getShiftsToConsensus();
 
            std::vector<std::vector<std::vector<double>>>& getShiftsFromConsensus();
#endif
            const std::vector<std::vector<std::vector<double>>> & getFinalResults() const;
 
            const std::vector<std::vector<std::vector<double>>>& getShiftsToConsensus() const;
 
            const std::vector<std::vector<std::vector<double>>>& getShiftsFromConsensus() const;
 
            typedef std::vector<std::vector<std::map<double, double>>> featureWidths_t;
 
#ifndef SWIG
            featureWidths_t & getFeatureWidths();
#endif
            void setAverageFeatureWidths(const std::vector<double> & featureWidths);
 
            const featureWidths_t & getFeatureWidths() const;
 
#ifndef SWIG
            bool getEvaluation(const int subProject, double & meanErrorsRaw, double & meanErrorsAligned, double & stdevErrorsRaw, double & stdevErrorsAligned, double & pearsonCoefficientRaw, double & pearsonCoefficientAligned);
#else // SWIG Multiple return values
            bool getEvaluation(const int subProject, double & OUTPUT, double & OUTPUT, double & OUTPUT, double & OUTPUT, double & OUTPUT, double & OUTPUT);
#endif
 
            void setStatus(status_t status);
 
            status_t getStatus(void) const;
 
            std::string getStatusAsText(void) const;
 
            void setAlgorithmName(const char* algorithmName);
 
            std::string getAlgorithmName() const;
 
            const std::vector<int> getSubProjectToFractionMap() const;
 
#ifndef SWIG
            ms_ms1quant_time_align_body * body();
            const ms_ms1quant_time_align_body * body() const;
#endif
            typedef std::map<int, std::vector<int>> fractionToSubProject_t;
 
            fractionToSubProject_t getFractionToSubProjectMap() const;
 
            bool calculateFromConsensuValues(bool replaceExisting = false);
 
            int getNumSharedPeptides(const int subProject1, const int subProject2) const;
 
            void setNumSharedPeptides(const int subProject1, const int subProject2, int count);
 
            int getMaxPossibleSharedPeptides(const int fractionNum) const;
 
            void setMaxPossibleSharedPeptides(const int fractionNum, const int value);
 
            std::string getWarningMessages(const warningMessage_t messageType, const int fractionNum) const;
 
            void setWarningMessages(const warningMessage_t messageType, const int fractionNum, const std::string& message);
 
        protected:
            void setUpFractions(const std::vector<int> & subProjectToFraction);
 
            void setEvaluation(int subProject, double meanErrorsRaw, double meanErrorsAligned, double stdevErrorsRaw, double stdevErrorsAligned, double pearsonCoefficientRaw, double pearsonCoefficientAligned);
    };
 // end of quantitation_group
    //=========================================================================
 
} // namespace matrix_science
 
 
#endif // MS_MS1QUANT_TIME_ALIGN_HPP
 
/*------------------------------- End of File -------------------------------*/