libopenms-dev 1.11.1-3 / usr / include / OpenMS / FORMAT / OPTIONS / PeakFileOptions.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
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#ifndef OPENMS_FORMAT_OPTIONS_PEAKFILEOPTIONS_H
#define OPENMS_FORMAT_OPTIONS_PEAKFILEOPTIONS_H

#include <OpenMS/DATASTRUCTURES/DRange.h>

#include <vector>

namespace OpenMS
{
  /**
      @brief Options for loading files containing peak data.
  */
  class OPENMS_DLLAPI PeakFileOptions
  {
public:
    ///Default constructor
    PeakFileOptions();
    ///Copy constructor
    PeakFileOptions(const PeakFileOptions &);
    ///Destructor
    ~PeakFileOptions();

    ///@name Meta data option
    //@{
    ///sets whether or not to load only meta data
    void setMetadataOnly(bool only);
    ///returns whether or not to load only meta data
    bool getMetadataOnly() const;
    //@}

    ///@name Supplemental data option
    //@{
    ///sets whether or not to write supplemental peak data in MzData files
    void setWriteSupplementalData(bool write);
    ///returns whether or not to write supplemental peak data in MzData files
    bool getWriteSupplementalData() const;
    //@}

    ///@name RT range option
    //@{
    ///restricts the range of RT values for peaks to load
    void setRTRange(const DRange<1> & range);
    ///returns @c true if an RT range has been set
    bool hasRTRange() const;
    ///returns the RT range
    const DRange<1> & getRTRange() const;
    //@}

    ///@name m/z range option
    //@{
    ///restricts the range of MZ values for peaks to load
    void setMZRange(const DRange<1> & range);
    ///returns @c true if an MZ range has been set
    bool hasMZRange() const;
    ///returns the MZ range
    const DRange<1> & getMZRange() const;
    //@}

    ///@name Intensity range option
    //@{
    ///restricts the range of intensity values for peaks to load
    void setIntensityRange(const DRange<1> & range);
    ///returns @c true if an intensity range has been set
    bool hasIntensityRange() const;
    ///returns the intensity range
    const DRange<1> & getIntensityRange() const;
    //@}

    /**
        @name MS levels option

        With this option, MS level filters can be set.

        @note The original spectrum identifiers are stored as the nativeID of the spectrum.
    */
    //@{
    ///sets the desired MS levels for peaks to load
    void setMSLevels(const std::vector<Int> & levels);
    ///adds a desired MS level for peaks to load
    void addMSLevel(int level);
    ///clears the MS levels
    void clearMSLevels();
    ///returns @c true, if MS levels have been set
    bool hasMSLevels() const;
    ///returns @c true, if MS level @p level has been set
    bool containsMSLevel(int level) const;
    ///returns the set MS levels
    const std::vector<Int> & getMSLevels() const;
    //@}

    /**
        @name Compression options

        @note This option is ignored if the format does not support compression
    */
    //@{
    //Sets if data should be compressed when writing
    void setCompression(bool compress);
    //returns @c true, if data should be compressed when writing
    bool getCompression() const;
    //@}

    /**
        @name Precision options

        @note This option is ignored if the format does not support multiple precisions
    */
    //@{
    //Sets if mz-data should be stored with 32bit or 64bit precision
    void setMz32Bit(bool mz_32_bit);
    //returns @c true, if mz-data should be stored with 32bit precision
    bool getMz32Bit() const;
    //Sets if intensity data should be stored with 32bit or 64bit precision
    void setIntensity32Bit(bool int_32_bit);
    //returns @c true, if intensity data should be stored with 32bit precision
    bool getIntensity32Bit() const;
    //@}

private:
    bool metadata_only_;
    bool write_supplemental_data_;
    bool has_rt_range_;
    bool has_mz_range_;
    bool has_intensity_range_;
    bool mz_32_bit_;
    bool int_32_bit_;
    DRange<1> rt_range_;
    DRange<1> mz_range_;
    DRange<1> intensity_range_;
    std::vector<Int> ms_levels_;
    bool zlib_compression_;
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_OPTIONS_PEAKFILEOPTIONS_H