ms_inputquery.hpp

/*
##############################################################################
# file: ms_inputquery.hpp                                                    #
# 'msparser' toolkit                                                         #
# Encapsulates a query from the mascot results file                          #
##############################################################################
# COPYRIGHT NOTICE                                                           #
# Copyright 1998-2002 Matrix Science Limited  All Rights Reserved.           #
#                                                                            #
##############################################################################
#    $Archive:: /MowseBranches/ms_mascotresfile_1.2/include/ms_inputquery. $ #
#     $Author: villek@matrixscience.com $ #
#       $Date: 2024-09-23 15:56:58 +0100 $ #
#   $Revision: 47700ac4361244fc5a56b7330a3249bd6fbbe674 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
# $NoKeywords::                                                            $ #
##############################################################################
*/
 
#ifndef MS_INPUTQUERY_HPP
#define MS_INPUTQUERY_HPP
 
 
#include <string>
 
namespace msparser_internal
{
    class ms_inputquerybase;
    class ms_inputquery_dat;
    class ms_inputquery_msr;
}
namespace matrix_science
{
 
    class MS_MASCOTRESFILE_API ms_inputquery  
    {
    public:
 
        ms_inputquery(const ms_mascotresfilebase &resfile, const int q);
        
        ~ms_inputquery() = default;
 
        int getQueryNumber() const;
 
#ifndef DOXYGEN_SHOULD_SKIP_THIS
        static std::vector<std::string> splitIT_MODS(std::string itmods);
#endif
        
#ifndef SWIGCSHARP
        std::string getStringTitle(bool unescaped) const;
#else
        std::wstring getStringTitle(bool unescaped) const
        {
          return getStringTitleWide(unescaped);
        };
#endif
        std::string getCharge() const;
#ifndef SWIG
        bool getAverageCharge(int* averageCharge, double * averageChargeDbl = 0) const;
#else // SWIG Multiple return values
        bool getAverageCharge(int * OUTPUT, double * OUTPUT=0) const;
#endif
        std::string getSeq(int seq_no) const;
        
        std::string getComp(int comp_no) const;
        
        std::string getTag(int tag_no) const;
        
        double getMassMin() const;
        
        double getMassMax() const;
        
        double getIonMobility() const;
        
        int getNumVals() const;
        
        int getNumUsed() const;
        
        std::string getStringIons1(bool includeCharges = false) const;
        
        std::string getStringIons2(bool includeCharges = false) const;
 
        std::string getStringIons3(bool includeCharges = false) const;
        
        double getIntMax() const;
        
        double getIntMin() const;
        
        std::vector<std::pair<double,double> > getPeakList(const int ions) const;
        
        double getPeakMass(const int ions, const int peakNo) const;
        
        double getPeakIntensity(const int ions, const int peakNo) const;
        
        int getPeakCharge(const int ions, const int peakNo) const;
        
        int getNumberOfPeaks(const int ions) const;
        
        double getTotalIonsIntensity() const;
        
        double getPepTol() const;
        
        std::string getPepTolUnits() const;
        
        std::string getPepTolString() const;
        
        std::string getINSTRUMENT(const bool unescaped = true) const;
        
        std::string getRULES() const;
        
        double getMinInternalMass() const;
        
        double getMaxInternalMass() const;
        
        std::string getIT_MODS(const bool unescaped = true) const;
        
        int getNumberOfLocalVarMods() const;
        
        std::string getLocalVarModName(const int num) const;
        
        std::string getScanNumbers(const int rawFileIdx = -1) const;
        
        void getScanNumbers(std::vector<int> &index, std::vector<std::string> &scans) const;
        
        std::string getRawScans(const int rawFileIdx = -1) const;
 
        void getRawScans(std::vector<int> &index, std::vector<std::string> &rawscans) const;
 
        std::string getRetentionTimes(const int rawFileIdx = -1) const;
 
        void getRetentionTimes(std::vector<int> &index, std::vector<std::string> &times) const;
 
        std::string getRawfile() const;
 
        std::string getLocus() const;
 
        int getIndex() const;
 
        bool hasINTERNALS() const;
 
    protected:
 
        ms_inputquery(std::shared_ptr<msparser_internal::ms_inputquerybase>);
 
    private:
 
        std::wstring getStringTitleWide(bool unescaped) const;
    
        std::shared_ptr<msparser_internal::ms_inputquerybase> impl_;
    }; // end of resfile_group
}   // matrix_science namespace
 
#endif // !defined(MS_INPUTQUERY_HPP)