PeakFileOptions.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: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DRange.h>
#include <OpenMS/FORMAT/MSNumpressCoder.h>
 
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI PeakFileOptions
  {
public:
    PeakFileOptions();
    PeakFileOptions(const PeakFileOptions &);
    PeakFileOptions& operator=(const PeakFileOptions&) = default;
    ~PeakFileOptions();
 
 
 
    void setMetadataOnly(bool only);
    bool getMetadataOnly() const;
 
    void setForceMQCompatability(bool forceMQ);
    bool getForceMQCompatability() const;
 
    void setForceTPPCompatability(bool forceTPP);
    bool getForceTPPCompatability() const;
 
 
 
    void setWriteSupplementalData(bool write);
    bool getWriteSupplementalData() const;
 
 
 
    void setRTRange(const DRange<1> & range);
    bool hasRTRange() const;
    const DRange<1> & getRTRange() const;
 
 
 
    void setMZRange(const DRange<1> & range);
    bool hasMZRange() const;
    const DRange<1> & getMZRange() const;
 
 
 
    void setIntensityRange(const DRange<1> & range);
    bool hasIntensityRange() const;
    const DRange<1> & getIntensityRange() const;
 
 
 
    void setPrecursorMZRange(const DRange<1> & range);
    bool hasPrecursorMZRange() const;
    const DRange<1> & getPrecursorMZRange() const;
 
 
 
    void setIMRange(const DRange<1> & range);
    bool hasIMRange() const;
    const DRange<1> & getIMRange() const;
 
    void setMSLevels(const std::vector<Int> & levels);
    void addMSLevel(int level);
    void clearMSLevels();
    bool hasMSLevels() const;
    bool containsMSLevel(int level) const;
    const std::vector<Int> & getMSLevels() const;
 
    //Sets if data should be compressed when writing
    void setCompression(bool compress);
    bool getCompression() const;
 
    void setZstdCompression(bool zstd);
    bool getZstdCompression() const;
 
    void setAlwaysAppendData(bool only);
    bool getAlwaysAppendData() const;
    void setFillData(bool only);
    bool getFillData() const;
    void setSkipXMLChecks(bool only);
    bool getSkipXMLChecks() const;
 
    void setSortSpectraByMZ(bool sort);
    bool getSortSpectraByMZ() const;
    void setSortChromatogramsByRT(bool sort);
    bool getSortChromatogramsByRT() const;
 
    //Sets if mz-data and rt-data should be stored with 32bit or 64bit precision
    void setMz32Bit(bool mz_32_bit);
    //returns @c true, if mz-data and rt-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;
 
    bool getWriteIndex() const;
    void setWriteIndex(bool write_index);
 
    MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime() const;
    void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config);
    MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity() const;
    void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config);
    MSNumpressCoder::NumpressConfig getNumpressConfigurationFloatDataArray() const;
    void setNumpressConfigurationFloatDataArray(MSNumpressCoder::NumpressConfig config);
 
    Size getMaxDataPoolSize() const;
    void setMaxDataPoolSize(Size size);
 
    bool getPrecursorMZSelectedIon() const;
 
    void setPrecursorMZSelectedIon(bool choice);
 
    bool hasFilters() const;
 
    void setSkipChromatograms(bool skip);
    bool getSkipChromatograms() const;
 
private:
    bool metadata_only_ = false;                
    bool force_maxquant_compatibility_ = false; 
    bool force_tpp_compatibility_ = false;      
    bool write_supplemental_data_ = true;
    bool has_rt_range_ = false;
    bool has_mz_range_ = false;
    bool has_intensity_range_ = false;
    bool has_precursor_mz_range_ = false;
    bool has_im_range_ = false;
    bool mz_32_bit_ = false;
    bool int_32_bit_ = true;
    DRange<1> rt_range_{};
    DRange<1> mz_range_{};
    DRange<1> intensity_range_{};
    DRange<1> precursor_mz_range_{};
    DRange<1> im_range_{};
    std::vector<Int> ms_levels_{};
    bool zlib_compression_ = false;
    bool zstd_compression_ = false;
    bool always_append_data_ = false;
    bool skip_xml_checks_ = false;
    bool sort_spectra_by_mz_ = true;
    bool sort_chromatograms_by_rt_ = true;
    bool fill_data_ = true;                     
    bool write_index_ = true;
    MSNumpressCoder::NumpressConfig np_config_mz_{};
    MSNumpressCoder::NumpressConfig np_config_int_{};
    MSNumpressCoder::NumpressConfig np_config_fda_{};
    Size maximal_data_pool_size_ = 100;
    bool precursor_mz_selected_ion_ = true;
    bool skip_chromatograms_ = false;
  };
 
} // namespace OpenMS