PeakFileOptions.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// --------------------------------------------------------------------------
// $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 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 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;
 
private:
    bool metadata_only_;
    bool force_maxquant_compatibility_; 
    bool force_tpp_compatibility_; 
    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_;
    bool always_append_data_;
    bool skip_xml_checks_;
    bool sort_spectra_by_mz_;
    bool sort_chromatograms_by_rt_;
    bool fill_data_;
    bool write_index_;
    MSNumpressCoder::NumpressConfig np_config_mz_;
    MSNumpressCoder::NumpressConfig np_config_int_;
    MSNumpressCoder::NumpressConfig np_config_fda_;
    Size maximal_data_pool_size_;
    bool precursor_mz_selected_ion_;
  };
 
} // namespace OpenMS