OpenMS  3.0.0
PeakFileOptions.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
39 
40 #include <vector>
41 
42 namespace OpenMS
43 {
47  class OPENMS_DLLAPI PeakFileOptions
48  {
49 public:
55  PeakFileOptions& operator=(const PeakFileOptions&) = default;
57  ~PeakFileOptions();
58 
60 
61  void setMetadataOnly(bool only);
64  bool getMetadataOnly() const;
65 
67  void setForceMQCompatability(bool forceMQ);
69  bool getForceMQCompatability() const;
70 
72  void setForceTPPCompatability(bool forceTPP);
74  bool getForceTPPCompatability() const;
76 
78 
79  void setWriteSupplementalData(bool write);
82  bool getWriteSupplementalData() const;
84 
86 
87  void setRTRange(const DRange<1> & range);
90  bool hasRTRange() const;
92  const DRange<1> & getRTRange() const;
94 
96 
97  void setMZRange(const DRange<1> & range);
100  bool hasMZRange() const;
102  const DRange<1> & getMZRange() const;
104 
106 
107  void setIntensityRange(const DRange<1> & range);
110  bool hasIntensityRange() const;
112  const DRange<1> & getIntensityRange() const;
114 
123  void setMSLevels(const std::vector<Int> & levels);
126  void addMSLevel(int level);
128  void clearMSLevels();
130  bool hasMSLevels() const;
132  bool containsMSLevel(int level) const;
134  const std::vector<Int> & getMSLevels() const;
136 
143  //Sets if data should be compressed when writing
144  void setCompression(bool compress);
146  bool getCompression() const;
148 
151  void setAlwaysAppendData(bool only);
153  bool getAlwaysAppendData() const;
155  void setFillData(bool only);
157  bool getFillData() const;
159  void setSkipXMLChecks(bool only);
161  bool getSkipXMLChecks() const;
162 
165  void setSortSpectraByMZ(bool sort);
167  bool getSortSpectraByMZ() const;
169  void setSortChromatogramsByRT(bool sort);
171  bool getSortChromatogramsByRT() const;
172 
182  //Sets if mz-data and rt-data should be stored with 32bit or 64bit precision
183  void setMz32Bit(bool mz_32_bit);
184  //returns @c true, if mz-data and rt-data should be stored with 32bit precision
185  bool getMz32Bit() const;
186  //Sets if intensity data should be stored with 32bit or 64bit precision
187  void setIntensity32Bit(bool int_32_bit);
188  //returns @c true, if intensity data should be stored with 32bit precision
189  bool getIntensity32Bit() const;
191 
193  bool getWriteIndex() const;
195  void setWriteIndex(bool write_index);
196 
198  MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime() const;
200  void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config);
202  MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity() const;
204  void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config);
206  MSNumpressCoder::NumpressConfig getNumpressConfigurationFloatDataArray() const;
208  void setNumpressConfigurationFloatDataArray(MSNumpressCoder::NumpressConfig config);
209 
220  Size getMaxDataPoolSize() const;
223  void setMaxDataPoolSize(Size size);
225 
227  bool getPrecursorMZSelectedIon() const;
228 
230  void setPrecursorMZSelectedIon(bool choice);
231 
233  bool hasFilters() const;
234 
235 private:
248  std::vector<Int> ms_levels_;
261  };
262 
263 } // namespace OpenMS
264 
OpenMS::PeakFileOptions::force_tpp_compatibility_
bool force_tpp_compatibility_
for mzML-writing only: work around some bugs in TPP file parsers
Definition: PeakFileOptions.h:238
OpenMS::PeakFileOptions::has_rt_range_
bool has_rt_range_
Definition: PeakFileOptions.h:240
DRange.h
OpenMS::PeakFileOptions::skip_xml_checks_
bool skip_xml_checks_
Definition: PeakFileOptions.h:251
OpenMS::PeakFileOptions::mz_range_
DRange< 1 > mz_range_
Definition: PeakFileOptions.h:246
OpenMS::PeakFileOptions::sort_spectra_by_mz_
bool sort_spectra_by_mz_
Definition: PeakFileOptions.h:252
OpenMS::DRange< 1 >
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::PeakFileOptions::ms_levels_
std::vector< Int > ms_levels_
Definition: PeakFileOptions.h:248
OpenMS::PeakFileOptions::always_append_data_
bool always_append_data_
Definition: PeakFileOptions.h:250
OpenMS::PeakFileOptions::write_supplemental_data_
bool write_supplemental_data_
Definition: PeakFileOptions.h:239
OpenMS::PeakFileOptions::mz_32_bit_
bool mz_32_bit_
Definition: PeakFileOptions.h:243
OpenMS::PeakFileOptions::metadata_only_
bool metadata_only_
Definition: PeakFileOptions.h:236
OpenMS::PeakFileOptions::precursor_mz_selected_ion_
bool precursor_mz_selected_ion_
Definition: PeakFileOptions.h:260
OpenMS::PeakFileOptions::has_mz_range_
bool has_mz_range_
Definition: PeakFileOptions.h:241
OpenMS::PeakFileOptions::rt_range_
DRange< 1 > rt_range_
Definition: PeakFileOptions.h:245
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::PeakFileOptions::write_index_
bool write_index_
Definition: PeakFileOptions.h:255
OpenMS::PeakFileOptions::int_32_bit_
bool int_32_bit_
Definition: PeakFileOptions.h:244
OpenMS::PeakFileOptions::intensity_range_
DRange< 1 > intensity_range_
Definition: PeakFileOptions.h:247
OpenMS::PeakFileOptions::np_config_mz_
MSNumpressCoder::NumpressConfig np_config_mz_
Definition: PeakFileOptions.h:256
OpenMS::PeakFileOptions::zlib_compression_
bool zlib_compression_
Definition: PeakFileOptions.h:249
MSNumpressCoder.h
OpenMS::PeakFileOptions::force_maxquant_compatibility_
bool force_maxquant_compatibility_
for mzXML-writing only: set a fixed vendor (Thermo Scientific), mass analyzer (FTMS)
Definition: PeakFileOptions.h:237
OpenMS::PeakFileOptions::has_intensity_range_
bool has_intensity_range_
Definition: PeakFileOptions.h:242
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::PeakFileOptions::sort_chromatograms_by_rt_
bool sort_chromatograms_by_rt_
Definition: PeakFileOptions.h:253
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:88
OpenMS::PeakFileOptions::np_config_int_
MSNumpressCoder::NumpressConfig np_config_int_
Definition: PeakFileOptions.h:257
OpenMS::PeakFileOptions::np_config_fda_
MSNumpressCoder::NumpressConfig np_config_fda_
Definition: PeakFileOptions.h:258
OpenMS::PeakFileOptions::maximal_data_pool_size_
Size maximal_data_pool_size_
Definition: PeakFileOptions.h:259
OpenMS::PeakFileOptions::fill_data_
bool fill_data_
Definition: PeakFileOptions.h:254