OpenMS  2.6.0
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();
56 
58 
59  void setMetadataOnly(bool only);
62  bool getMetadataOnly() const;
63 
65  void setForceMQCompatability(bool forceMQ);
67  bool getForceMQCompatability() const;
68 
70  void setForceTPPCompatability(bool forceTPP);
72  bool getForceTPPCompatability() const;
74 
76 
77  void setWriteSupplementalData(bool write);
80  bool getWriteSupplementalData() const;
82 
84 
85  void setRTRange(const DRange<1> & range);
88  bool hasRTRange() const;
90  const DRange<1> & getRTRange() const;
92 
94 
95  void setMZRange(const DRange<1> & range);
98  bool hasMZRange() const;
100  const DRange<1> & getMZRange() const;
102 
104 
105  void setIntensityRange(const DRange<1> & range);
108  bool hasIntensityRange() const;
110  const DRange<1> & getIntensityRange() const;
112 
121  void setMSLevels(const std::vector<Int> & levels);
124  void addMSLevel(int level);
126  void clearMSLevels();
128  bool hasMSLevels() const;
130  bool containsMSLevel(int level) const;
132  const std::vector<Int> & getMSLevels() const;
134 
141  //Sets if data should be compressed when writing
142  void setCompression(bool compress);
143  //returns @c true, if data should be compressed when writing
144  bool getCompression() const;
146 
149  void setAlwaysAppendData(bool only);
151  bool getAlwaysAppendData() const;
153  void setFillData(bool only);
155  bool getFillData() const;
157  void setSkipXMLChecks(bool only);
159  bool getSkipXMLChecks() const;
160 
163  void setSortSpectraByMZ(bool sort);
165  bool getSortSpectraByMZ() const;
167  void setSortChromatogramsByRT(bool sort);
169  bool getSortChromatogramsByRT() const;
170 
180  //Sets if mz-data and rt-data should be stored with 32bit or 64bit precision
181  void setMz32Bit(bool mz_32_bit);
182  //returns @c true, if mz-data and rt-data should be stored with 32bit precision
183  bool getMz32Bit() const;
184  //Sets if intensity data should be stored with 32bit or 64bit precision
185  void setIntensity32Bit(bool int_32_bit);
186  //returns @c true, if intensity data should be stored with 32bit precision
187  bool getIntensity32Bit() const;
189 
191  bool getWriteIndex() const;
193  void setWriteIndex(bool write_index);
194 
196  MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime() const;
198  void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config);
200  MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity() const;
202  void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config);
204  MSNumpressCoder::NumpressConfig getNumpressConfigurationFloatDataArray() const;
206  void setNumpressConfigurationFloatDataArray(MSNumpressCoder::NumpressConfig config);
207 
218  Size getMaxDataPoolSize() const;
221  void setMaxDataPoolSize(Size size);
223 
225  bool getPrecursorMZSelectedIon() const;
226 
228  void setPrecursorMZSelectedIon(bool choice);
229 
231  bool hasFilters();
232 
233 private:
246  std::vector<Int> ms_levels_;
259  };
260 
261 } // namespace OpenMS
262 
OpenMS::PeakFileOptions::force_tpp_compatibility_
bool force_tpp_compatibility_
for mzML-writing only: work around some bugs in TPP file parsers
Definition: PeakFileOptions.h:236
OpenMS::PeakFileOptions::has_rt_range_
bool has_rt_range_
Definition: PeakFileOptions.h:238
DRange.h
OpenMS::PeakFileOptions::skip_xml_checks_
bool skip_xml_checks_
Definition: PeakFileOptions.h:249
OpenMS::PeakFileOptions::mz_range_
DRange< 1 > mz_range_
Definition: PeakFileOptions.h:244
OpenMS::PeakFileOptions::sort_spectra_by_mz_
bool sort_spectra_by_mz_
Definition: PeakFileOptions.h:250
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:246
OpenMS::PeakFileOptions::always_append_data_
bool always_append_data_
Definition: PeakFileOptions.h:248
OpenMS::PeakFileOptions::write_supplemental_data_
bool write_supplemental_data_
Definition: PeakFileOptions.h:237
OpenMS::PeakFileOptions::mz_32_bit_
bool mz_32_bit_
Definition: PeakFileOptions.h:241
OpenMS::PeakFileOptions::metadata_only_
bool metadata_only_
Definition: PeakFileOptions.h:234
OpenMS::PeakFileOptions::precursor_mz_selected_ion_
bool precursor_mz_selected_ion_
Definition: PeakFileOptions.h:258
OpenMS::PeakFileOptions::has_mz_range_
bool has_mz_range_
Definition: PeakFileOptions.h:239
OpenMS::PeakFileOptions::rt_range_
DRange< 1 > rt_range_
Definition: PeakFileOptions.h:243
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeakFileOptions::write_index_
bool write_index_
Definition: PeakFileOptions.h:253
OpenMS::PeakFileOptions::int_32_bit_
bool int_32_bit_
Definition: PeakFileOptions.h:242
OpenMS::PeakFileOptions::intensity_range_
DRange< 1 > intensity_range_
Definition: PeakFileOptions.h:245
OpenMS::PeakFileOptions::np_config_mz_
MSNumpressCoder::NumpressConfig np_config_mz_
Definition: PeakFileOptions.h:254
OpenMS::PeakFileOptions::zlib_compression_
bool zlib_compression_
Definition: PeakFileOptions.h:247
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:235
OpenMS::PeakFileOptions::has_intensity_range_
bool has_intensity_range_
Definition: PeakFileOptions.h:240
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:251
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:87
OpenMS::PeakFileOptions::np_config_int_
MSNumpressCoder::NumpressConfig np_config_int_
Definition: PeakFileOptions.h:255
OpenMS::PeakFileOptions::np_config_fda_
MSNumpressCoder::NumpressConfig np_config_fda_
Definition: PeakFileOptions.h:256
OpenMS::PeakFileOptions::maximal_data_pool_size_
Size maximal_data_pool_size_
Definition: PeakFileOptions.h:257
OpenMS::PeakFileOptions::fill_data_
bool fill_data_
Definition: PeakFileOptions.h:252