ms_mascotresults_params.hpp

/*
##############################################################################
# file: ms_mascotresults_params.hpp                                          #
# 'msparser' toolkit                                                         #
# Parameter storage for ms_peptidesummary and ms_proteinsummary              #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2018 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#     $Author: villek@matrixscience.com $ #
#       $Date: 2021-04-16 16:53:57 +0100 $ #
#   $Revision: 11d32bab75bd4a36805819329c7ad7887156b404 | MSPARSER_REL_2_8_1-0-gea32989045 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/

#ifndef MS_MASCOTRESULTS_PARAMS_HPP
#define MS_MASCOTRESULTS_PARAMS_HPP

namespace matrix_science {
    class ms_mascotresults;
    class ms_peptidesummary;

    class MS_MASCOTRESFILE_API ms_mascotresults_params
    {
        public:
            ms_mascotresults_params(const unsigned int flags = ms_mascotresults::MSRES_GROUP_PROTEINS,
                                    double             minProbability = 0.05,
                                    int                maxHitsToReport = 0,
                                    const char *       unigeneIndexFile = 0,
                                    double             ignoreIonsScoreBelow = 0.0,
                                    int                minPepLenInPepSummary = 0,
                                    const char *       singleHit = 0,
                                    const unsigned int flags2 = 0);

            virtual ~ms_mascotresults_params();

            ms_mascotresults_params(const ms_mascotresults_params & src);

#ifndef SWIG

            ms_mascotresults_params& operator=(const ms_mascotresults_params & right);
#endif

            void copyFrom(const ms_mascotresults_params * right);

            void setFlags(const unsigned int flags);

            void setFlag(const ms_mascotresults::FLAGS flag, bool enabled);

            unsigned int getFlags() const;

            void setFlags2(const unsigned int flags2);

            void setFlag2(const ms_peptidesummary::MSPEPSUM flag, bool enabled);

            unsigned int getFlags2() const;

            double getMinProbability() const;

            void setMinProbability(const double minProbability);

            double getTargetFDR() const;

            void setTargetFDR(double fdr);

            ms_mascotresults::DECOY_STATS_COUNT_TYPE getTargetFDRType() const;

            void setTargetFDRType(ms_mascotresults::DECOY_STATS_COUNT_TYPE fdrType);

            double getIgnoreIonsScoreBelow() const;

            void setIgnoreIonsScoreBelow(const double ignoreIonsScoreBelow);

            int getMinNumSigUniqueSequences() const;

            void setMinNumSigUniqueSequences(const int n);

            int getMaxHitsToReport() const;

            void setMaxHitsToReport(const int maxHitsToReport);

            int getMinPepLenInPeptideSummary() const;

            void setMinPepLenInPeptideSummary(const int minPepLenInPeptideSummary);

            std::string getUnigeneIndexFile() const;

            void setUnigeneIndexFile(const char* unigeneIndexFile);

            std::string getSingleHit() const;

            void setSingleHit(const char* singleHit);

            bool isUsePeptideSummary() const;

            void setUsePeptideSummary(const bool usePeptideSummary);

        private:
            unsigned int      flags_;
            double            minProbability_;
            double            targetFDR_;
            ms_mascotresults::DECOY_STATS_COUNT_TYPE targetFDRtype_;
            int               maxHitsToReport_;
            double            ignoreIonsScoreBelow_;
            std::string       unigeneIndexFile_;
            int               minPepLenInPepSummary_;
            std::string       singleHit_;
            unsigned int      flags2_;
            bool              usePeptideSummary_;   

            int               minNumSigUniqueSeqs_;
    };
 // end of resfile_group
}   // matrix_science namespace

#endif // MS_MASCOTRESULTS_PARAMS_HPP

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