ms_distiller_data_search.hpp

/*
##############################################################################
# file: ms_distiller_data_search.hpp
# 'msparser' toolkit
# An extracted ion chromatogram
##############################################################################
# COPYRIGHT NOTICE
# Copyright 1998-2014 Matrix Science Limited  All Rights Reserved.
#
##############################################################################
* @(#)$Source: parser/inc/ms_distiller_data_search.hpp $
* @(#)$Revision: 1db06e98bca152b61622d19400e2b814164d92db | MSPARSER_REL_3_1_0-2025-07-27-0-gea47708fac $
* @(#)$Date: 2024-10-14 16:22:48 +0100 $
##############################################################################
 */
 
#ifndef MS_DISTILLER_DATA_SEARCH_HPP
#define MS_DISTILLER_DATA_SEARCH_HPP
 
 
// Includes from the standard template library
#include <string>
 
 
namespace msparser_internal
{
    class ms_XMLHelper;
    class ms_XMLElement;
}
 
namespace matrix_science
{
    class ms_quant_configfile;
 
 
    //=========================================================================
 
    class MS_MASCOTRESFILE_API ms_distiller_data_search
    {
        friend class ms_distiller_data;
 
        public:
 
 
            enum eScoring
            {
                eAuto = 0,            
                eMudpit = 1,          
                eStandard = 99999999, 
            };
 
 
            enum eGrouping
            {
                eGroupAuto = 0,     
                eGroupStandard = 1, 
                eGroupFamily = 2    
            };
 
 
            enum eSpectralLibrary
            {
                eUnknown = -1,   
                eFASTA = 0,      
                eLibrary = 1,    
                eIntegrated = 2, 
            };
 
            ms_distiller_data_search();
 
            ms_distiller_data_search(
                const std::string & taskId,
                bool isLoaded,
                const std::string & cacheFileName,
                const std::string & quantMethodXml,
                const std::string & mascotServerURL,
                const std::string & mascotServerVersion,
                unsigned int flags,
                unsigned int flags2,
                bool requireBoldRed,
                bool showSameset,
                double showSubset,
                bool loadUnassigned,
                double significanceThreshold,
                eScoring scoring,
                int reporttop,
                bool errTolPeptide,
                eGrouping proteinGrouping,
                bool percolator,
                double scoreExpectCutOff,
                bool showSamesetFamily,
                bool showSubsetFamily,
                eSpectralLibrary libraryDisplayOption,
                bool percolatorUseProteins,
                bool percolatorUseRT,
                int minPepLenInPepSummary,
                bool isTargetFDR = false,
                const std::string & targetFDRType = "",
                const std::string & targetFDRStr = "",
                const std::string & mlAdapterSettings = ""
            );
 
            // Copying constructor for c++ programs - don't document
            ms_distiller_data_search(const ms_distiller_data_search &src);
 
#ifndef SWIG
            // Assignment operator for c++ programs - don't document
            ms_distiller_data_search & operator=(const ms_distiller_data_search & right);
#endif
            std::string getTaskId() const;
 
            bool getLoaded() const;
 
            std::string getCacheFileName() const;
 
            std::string getQuantMethodXml() const;
 
            std::string getMascotServerURL() const;
 
            bool serverVersionNewerOrSameAs(int major, int minor, int patch) const;
 
            std::string getMascotSearchURL(const std::string & resultsFilePath) const;
 
            eGrouping getProteinGrouping() const;
 
            eScoring getScoring() const;
 
            double getScoreExpectCutOff() const;
 
            double getShowSubset() const;
 
            bool getShowSubsetFamily() const;
 
            bool getRequireBoldRed() const;
 
            double getSignificanceThreshold() const; // = minProbability
 
            int getReporttop() const;
 
            bool getPercolator() const;
 
            bool getPercolatorUseProteins() const;
 
            bool getPercolatorUseRT() const;
 
            bool getErrTolPeptide() const;
 
            unsigned int getPeptideSummaryFlags() const;
 
            unsigned getPeptideSummaryFlags2() const;
 
            bool getLoadUnassigned() const;
 
            bool getShowSamesets() const;
 
            bool getShowSamesetsFamily() const;
 
            int getMinPepLenInPepSummary() const;
 
            eSpectralLibrary getSpectralLibraryDisplayOption() const;
 
            bool isTargetFDR() const;
 
            std::string getTargetFDRType() const;
 
            std::string getTargetFDRStr() const;
 
            double getTargetFDR() const;
 
            ms_mascotresults::DECOY_STATS_COUNT_TYPE getFDRCountType() const;
 
            std::string getMachineLearningAdapterSettings() const;
 
        private:
            // Used internally to read from the rover_data XML file
            bool extractXml(msparser_internal::ms_XMLHelper & helper, msparser_internal::ms_XMLElement & element);
            void copyFrom(const ms_distiller_data_search * src);
            void setMissingBlueOptionValues(const std::string & mascotServerURL, 
                                            const std::string & mascotServerVersion,
                                            int minPepLenInPepSummary, 
                                            bool percolatorUseProteins, 
                                            bool percolatorUseRT);
 
            std::string taskId_;
            bool isLoaded_;
            std::string cacheFileName_;
            std::string quantMethodXml_;
            std::string mascotServerURL_;
            std::string mascotServerVersion_;
            unsigned int flags_;
            unsigned int flags2_;
 
            // From blueoptions (same order as schema)
            bool requireBoldRed_;
            bool showSameset_;
            double showSubset_;
            bool loadUnassigned_;
            double significanceThreshold_; // = minProbability
            eScoring scoring_;
            int reporttop_;
            bool errTolPeptide_;
            eGrouping proteinGrouping_;
            bool percolator_;
            double scoreExpectCutOff_;
            bool showSamesetFamily_;
            bool showSubsetFamily_;
            eSpectralLibrary libraryDisplayOption_;
            bool percolatorUseProteins_;
            bool percolatorUseRT_;
            int minPepLenInPepSummary_;
            std::string mlAdapterSettings_;
 
            // target fdr
            bool isTargetFDR_;
            std::string targetFDRType_;
            std::string targetFDRStr_;
            double targetFDR_;
    };
 // end of quantitation_group
    //=========================================================================
 
} // namespace matrix_science
 
#endif // MS_DISTILLER_DATA_SEARCH_HPP
 
/*------------------------------- End of File -------------------------------*/