SpectrumSettings.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/METADATA/InstrumentSettings.h>
#include <OpenMS/METADATA/AcquisitionInfo.h>
#include <OpenMS/METADATA/SourceFile.h>
#include <OpenMS/METADATA/Precursor.h>
#include <OpenMS/METADATA/Product.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/DataProcessing.h>

#include <map>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI SpectrumSettings :
    public MetaInfoInterface
  {

public:

    enum SpectrumType
    {
      UNKNOWN,          
      CENTROID,         
      PROFILE,          
      SIZE_OF_SPECTRUMTYPE
    };
    static const std::string NamesOfSpectrumType[SIZE_OF_SPECTRUMTYPE];

    SpectrumSettings();
    SpectrumSettings(const SpectrumSettings & source);
    ~SpectrumSettings();

    // Assignment operator
    SpectrumSettings & operator=(const SpectrumSettings & source);

    bool operator==(const SpectrumSettings & rhs) const;
    bool operator!=(const SpectrumSettings & rhs) const;

    void unify(const SpectrumSettings & rhs);

    SpectrumType getType() const;
    void setType(SpectrumType type);

    const String & getNativeID() const;
    void setNativeID(const String & native_id);

    const String & getComment() const;
    void setComment(const String & comment);

    const InstrumentSettings & getInstrumentSettings() const;
    InstrumentSettings & getInstrumentSettings();
    void setInstrumentSettings(const InstrumentSettings & instrument_settings);

    const AcquisitionInfo & getAcquisitionInfo() const;
    AcquisitionInfo & getAcquisitionInfo();
    void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);

    const SourceFile & getSourceFile() const;
    SourceFile & getSourceFile();
    void setSourceFile(const SourceFile & source_file);

    const std::vector<Precursor> & getPrecursors() const;
    std::vector<Precursor> & getPrecursors();
    void setPrecursors(const std::vector<Precursor> & precursors);

    const std::vector<Product> & getProducts() const;
    std::vector<Product> & getProducts();
    void setProducts(const std::vector<Product> & products);

    const std::vector<PeptideIdentification> & getPeptideIdentifications() const;
    std::vector<PeptideIdentification> & getPeptideIdentifications();
    void setPeptideIdentifications(const std::vector<PeptideIdentification> & identifications);

    void setDataProcessing(const std::vector< DataProcessingPtr > & data_processing);

    std::vector< DataProcessingPtr > & getDataProcessing();

    const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing() const;

protected:

    SpectrumType type_;
    String native_id_;
    String comment_;
    InstrumentSettings instrument_settings_;
    SourceFile source_file_;
    AcquisitionInfo acquisition_info_;
    std::vector<Precursor> precursors_;
    std::vector<Product> products_;
    std::vector<PeptideIdentification> identification_;
    std::vector< DataProcessingPtr > data_processing_;
  };

  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const SpectrumSettings & spec);

} // namespace OpenMS