ms_fragment.hpp

/*
##############################################################################
# File: ms_fragment.hpp                                                      #
# Mascot Parser toolkit                                                      #
# Encapsulates a single fragment ion                                         #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2012 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Source: parser/inc/ms_fragment.hpp $
#    $Author: villek@matrixscience.com $ 
#      $Date: 2019-10-25 16:58:28 +0100 $ 
#  $Revision: 729a9d2d2b60ca4ca4ccf3b95c449b13288dba7d | MSPARSER_REL_2_8_1-0-gea32989045 $
##############################################################################
*/


#if !defined(ms_fragment_INCLUDED_)
#define ms_fragment_INCLUDED_


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


namespace matrix_science {

    class MS_MASCOTRESFILE_API ms_fragment
    {
    public:

        enum LABEL_FORMAT {
            LABEL_FORMAT_TRADITIONAL = 0, 
            LABEL_FORMAT_PEPTIDE_VIEW = 1 
        };

        ms_fragment();

        ms_fragment(const ms_fragment &src);

#ifndef SWIG

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

        void copyFrom(const ms_fragment* src);

        ms_fragment(const int    seriesID, 
                    const double massValue, 
                    const double nlValue, 
                    const int    col, 
                    const int    chargeState = 1, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const ms_peptide::PSM psmComponent,
                    const int    seriesID, 
                    const double massValue, 
                    const double nlValue, 
                    const int    col,
                    const int    chargeState, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const char * seriesName, 
                    const double massValue, 
                    const double nlValue, 
                    const int    col, 
                    const int    chargeState = 1, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const ms_peptide::PSM psmComponent,
                    const char * seriesName, 
                    const double massValue, 
                    const double nlValue, 
                    const int    col, 
                    const int    chargeState, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const int    seriesID, 
                    const double massValue,
                    const double nlValue,
                    const char * peptideStr,
                    const int    startPos, 
                    const int    endPos, 
                    const int    chargeState = 1, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const ms_peptide::PSM psmComponent,
                    const int    seriesID, 
                    const double massValue,
                    const double nlValue,
                    const char * peptideStr,
                    const int    startPos, 
                    const int    endPos, 
                    const int    chargeState, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const char   residueName, 
                    const double massValue, 
                    const double nlValue, 
                    const int    col = -1, 
                    const int    chargeState = 1, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const ms_peptide::PSM psmComponent,
                    const char   residueName, 
                    const double massValue, 
                    const double nlValue, 
                    const int    col, 
                    const int    chargeState, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        ms_fragment(const double massValue, 
                    const double nlValue, 
                    const int    chargeState, 
                    const double matchedExptMass = 0,
                    const double matchedExptIntensity = 0);

        bool isFromAlpha() const;

        bool isFromBeta() const;

        bool isRegular() const;

        bool isNTerminal() const;

        bool isCTerminal() const;

        bool isInternal() const;

        bool isImmonium() const;

        bool isPrecursorNL() const;

        double getMass() const;

        double getNeutralLoss() const;

        std::string getLabel(const LABEL_FORMAT fmt = LABEL_FORMAT_TRADITIONAL) const;

        std::string getPeptideSubstring() const;

        std::string getSeriesName() const;

        int getColumn() const;

        int getStart() const;

        int getEnd() const;

        int getCharge() const;

        void clearMatchedIon();

        void setMatchedIon(const double mass, const double intensity);

        double getMatchedIonMass() const;

        double getMatchedIonIntensity() const;

        int getAllMatchedIons(std::vector<double> & masses, std::vector<double> & intensities) const;

    protected:
        enum ION_TYPE {ION_TYPE_UNKNOWN,
                       ION_TYPE_REGULAR,
                       ION_TYPE_INTERNAL,
                       ION_TYPE_IMMONIUM,
                       ION_TYPE_PRECURSOR_NL};
        enum ION_TERMINUS {ION_TERM_AMBIGUOUS,
                           ION_TERM_N,
                           ION_TERM_C};
        ms_peptide::PSM psmComponent_;
        double      mass_;
        double      nl_;
        std::string labelTraditional_;
        std::string labelPeptideView_;
        std::string peptideSubstring_;
        std::string series_;
        int         start_;
        int         end_;
        int         charge_;
        ION_TYPE    type_;
        ION_TERMINUS terminus_;
        bool        matchedValueSet_;
        double      matchedExptMass_;
        double      matchedExptIntensity_;
        std::vector<double> matchedExptMasses_;
        std::vector<double> matchedExptIntensities_;

    private:
        void initRegularFragment(const ms_peptide::PSM psmComponent,
                                 const int seriesID,
                                 const double massValue,
                                 const double nlValue,
                                 const int col,
                                 const int chargeState,
                                 const double matchedExptMass,
                                 const double matchedExptIntensity);

        void initRegularFragment(const ms_peptide::PSM psmComponent,
                                 const char* seriesName,
                                 const double massValue, 
                                 const double nlValue,
                                 const int col, 
                                 const int chargeState, 
                                 const double matchedExptMass,
                                 const double matchedExptIntensity);

        void initInternalFragment(const ms_peptide::PSM psmComponent,
                                  const int seriesID,
                                  const double massValue,
                                  const double nlValue,
                                  const char* peptideStr,
                                  const int startPos,
                                  const int endPos,
                                  const int chargeState,
                                  const double matchedExptMass,
                                  const double matchedExptIntensity);

        void initImmoniumFragment(const ms_peptide::PSM psmComponent,
                                  const char residueName,
                                  const double massValue,
                                  const double nlValue,
                                  const int col,
                                  const int chargeState,
                                  const double matchedExptMass,
                                  const double matchedExptIntensity);

    }; //class ms_fragment // end of mass_calculation_group
} // matrix_science

#endif // !defined(ms_fragment_INCLUDED_)