SpectrumAccessSqMass.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <OpenMS/FORMAT/HANDLERS/MzMLSqliteHandler.h>
 
#include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
 
#include <memory>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SpectrumAccessSqMass :
    public OpenSwath::ISpectrumAccess
  {
 
public:
    typedef OpenMS::MSSpectrum MSSpectrumType;
    typedef OpenMS::MSChromatogram MSChromatogramType;
 
    SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler);
 
    SpectrumAccessSqMass(const OpenMS::Internal::MzMLSqliteHandler& handler, const std::vector<int> & indices);
 
    SpectrumAccessSqMass(const SpectrumAccessSqMass& sp, const std::vector<int>& indices);
 
    ~SpectrumAccessSqMass() override;
 
    SpectrumAccessSqMass(const SpectrumAccessSqMass & rhs);
 
    std::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
 
    OpenSwath::SpectrumPtr getSpectrumById(int id) override;
 
    OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override;
 
    void getAllSpectra(std::vector< OpenSwath::SpectrumPtr > & spectra, std::vector< OpenSwath::SpectrumMeta > & spectra_meta) const;
 
    std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
 
    size_t getNrSpectra() const override;
 
    OpenSwath::ChromatogramPtr getChromatogramById(int id) override;
 
    size_t getNrChromatograms() const override;
 
    std::string getChromatogramNativeID(int id) const override;
 
private:
 
    OpenMS::Internal::MzMLSqliteHandler handler_;
    std::vector<int> sidx_;
  };
} //end namespace OpenMS