| OpenMS 2.5.0

PeakFileOptions.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
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10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
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15 // without specific prior written permission.
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DRange.h>
38 #include <OpenMS/FORMAT/MSNumpressCoder.h>
39
40 #include <vector>
41
42 namespace OpenMS
43 {
47 class OPENMS_DLLAPI PeakFileOptions
48 {
49 public:
51 PeakFileOptions();
53 PeakFileOptions(const PeakFileOptions &);
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:
234 bool metadata_only_;
235 bool force_maxquant_compatibility_;
236 bool force_tpp_compatibility_;
237 bool write_supplemental_data_;
238 bool has_rt_range_;
239 bool has_mz_range_;
240 bool has_intensity_range_;
241 bool mz_32_bit_;
242 bool int_32_bit_;
243 DRange<1> rt_range_;
244 DRange<1> mz_range_;
245 DRange<1> intensity_range_;
246 std::vector<Int> ms_levels_;
247 bool zlib_compression_;
248 bool always_append_data_;
249 bool skip_xml_checks_;
250 bool sort_spectra_by_mz_;
251 bool sort_chromatograms_by_rt_;
252 bool fill_data_;
253 bool write_index_;
254 MSNumpressCoder::NumpressConfig np_config_mz_;
255 MSNumpressCoder::NumpressConfig np_config_int_;
256 MSNumpressCoder::NumpressConfig np_config_fda_;
257 Size maximal_data_pool_size_;
258 bool precursor_mz_selected_ion_;
259 };
260
261 } // namespace OpenMS
262
OpenMS::PeakFileOptions::write_supplemental_data_
bool write_supplemental_data_
Definition: PeakFileOptions.h:237
OpenMS::PeakFileOptions::write_index_
bool write_index_
Definition: PeakFileOptions.h:253
OpenMS::PeakFileOptions::np_config_fda_
MSNumpressCoder::NumpressConfig np_config_fda_
Definition: PeakFileOptions.h:256
MSNumpressCoder.h
DRange.h
OpenMS::PeakFileOptions::int_32_bit_
bool int_32_bit_
Definition: PeakFileOptions.h:242
OpenMS::PeakFileOptions::fill_data_
bool fill_data_
Definition: PeakFileOptions.h:252
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::rt_range_
DRange< 1 > rt_range_
Definition: PeakFileOptions.h:243
OpenMS::PeakFileOptions::metadata_only_
bool metadata_only_
Definition: PeakFileOptions.h:234
OpenMS::PeakFileOptions::np_config_int_
MSNumpressCoder::NumpressConfig np_config_int_
Definition: PeakFileOptions.h:255
OpenMS::PeakFileOptions::np_config_mz_
MSNumpressCoder::NumpressConfig np_config_mz_
Definition: PeakFileOptions.h:254
OpenMS::PeakFileOptions::intensity_range_
DRange< 1 > intensity_range_
Definition: PeakFileOptions.h:245
OpenMS::PeakFileOptions::zlib_compression_
bool zlib_compression_
Definition: PeakFileOptions.h:247
OpenMS::PeakFileOptions::mz_range_
DRange< 1 > mz_range_
Definition: PeakFileOptions.h:244
OpenMS::PeakFileOptions::mz_32_bit_
bool mz_32_bit_
Definition: PeakFileOptions.h:241
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DRange< 1 >
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_mz_range_
bool has_mz_range_
Definition: PeakFileOptions.h:239
OpenMS::PeakFileOptions::sort_spectra_by_mz_
bool sort_spectra_by_mz_
Definition: PeakFileOptions.h:250
OpenMS::PeakFileOptions::always_append_data_
bool always_append_data_
Definition: PeakFileOptions.h:248
OpenMS::PeakFileOptions::maximal_data_pool_size_
Size maximal_data_pool_size_
Definition: PeakFileOptions.h:257
OpenMS::PeakFileOptions::precursor_mz_selected_ion_
bool precursor_mz_selected_ion_
Definition: PeakFileOptions.h:258
OpenMS::PeakFileOptions::has_rt_range_
bool has_rt_range_
Definition: PeakFileOptions.h:238
OpenMS::PeakFileOptions::has_intensity_range_
bool has_intensity_range_
Definition: PeakFileOptions.h:240
OpenMS::PeakFileOptions::sort_chromatograms_by_rt_
bool sort_chromatograms_by_rt_
Definition: PeakFileOptions.h:251
OpenMS::PeakFileOptions::ms_levels_
std::vector< Int > ms_levels_
Definition: PeakFileOptions.h:246
OpenMS::MSNumpressCoder::NumpressConfig
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:87
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::PeakFileOptions::skip_xml_checks_
bool skip_xml_checks_
Definition: PeakFileOptions.h:249