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PeakFileOptions.h
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34 
35 #ifndef OPENMS_FORMAT_OPTIONS_PEAKFILEOPTIONS_H
36 #define OPENMS_FORMAT_OPTIONS_PEAKFILEOPTIONS_H
37 
40 
41 #include <vector>
42 
43 namespace OpenMS
44 {
48  class OPENMS_DLLAPI PeakFileOptions
49  {
50 public:
56  ~PeakFileOptions();
57 
59 
60  void setMetadataOnly(bool only);
63  bool getMetadataOnly() const;
64 
66  void setForceMQCompatability(bool forceMQ);
68  bool getForceMQCompatability() const;
69 
71  void setForceTPPCompatability(bool forceTPP);
73  bool getForceTPPCompatability() const;
75 
77 
78  void setWriteSupplementalData(bool write);
81  bool getWriteSupplementalData() const;
83 
85 
86  void setRTRange(const DRange<1> & range);
89  bool hasRTRange() const;
91  const DRange<1> & getRTRange() const;
93 
95 
96  void setMZRange(const DRange<1> & range);
99  bool hasMZRange() const;
101  const DRange<1> & getMZRange() const;
103 
105 
106  void setIntensityRange(const DRange<1> & range);
109  bool hasIntensityRange() const;
111  const DRange<1> & getIntensityRange() const;
113 
122  void setMSLevels(const std::vector<Int> & levels);
125  void addMSLevel(int level);
127  void clearMSLevels();
129  bool hasMSLevels() const;
131  bool containsMSLevel(int level) const;
133  const std::vector<Int> & getMSLevels() const;
135 
142  //Sets if data should be compressed when writing
143  void setCompression(bool compress);
144  //returns @c true, if data should be compressed when writing
145  bool getCompression() const;
147 
150  void setSizeOnly(bool only);
152  bool getSizeOnly() const;
154  void setAlwaysAppendData(bool only);
156  bool getAlwaysAppendData() const;
158  void setFillData(bool only);
160  bool getFillData() const;
162  void setSkipXMLChecks(bool only);
164  bool getSkipXMLChecks() const;
165 
168  void setSortSpectraByMZ(bool sort);
170  bool getSortSpectraByMZ() const;
172  void setSortChromatogramsByRT(bool sort);
174  bool getSortChromatogramsByRT() const;
175 
185  //Sets if mz-data and rt-data should be stored with 32bit or 64bit precision
186  void setMz32Bit(bool mz_32_bit);
187  //returns @c true, if mz-data and rt-data should be stored with 32bit precision
188  bool getMz32Bit() const;
189  //Sets if intensity data should be stored with 32bit or 64bit precision
190  void setIntensity32Bit(bool int_32_bit);
191  //returns @c true, if intensity data should be stored with 32bit precision
192  bool getIntensity32Bit() const;
194 
196  bool getWriteIndex() const;
198  void setWriteIndex(bool write_index);
199 
201  MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime() const;
203  void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config);
205  MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity() const;
207  void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config);
208 
219  Size getMaxDataPoolSize() const;
222  void setMaxDataPoolSize(Size size);
224 
225 private:
227  bool force_maxquant_compatibility_; //< for mzXML-writing only: set a fixed vendor (Thermo Scientific), mass analyzer (FTMS)
228  bool force_tpp_compatibility_; //< for mzML-writing only: work around some bugs in TPP file parsers
238  std::vector<Int> ms_levels_;
250 
251  };
252 
253 } // namespace OpenMS
254 
255 #endif // OPENMS_FORMAT_OPTIONS_PEAKFILEOPTIONS_H
MSNumpressCoder::NumpressConfig np_config_mz_
Definition: PeakFileOptions.h:247
bool has_intensity_range_
Definition: PeakFileOptions.h:232
bool metadata_only_
Definition: PeakFileOptions.h:226
bool skip_xml_checks_
Definition: PeakFileOptions.h:242
DRange< 1 > rt_range_
Definition: PeakFileOptions.h:235
Size maximal_data_pool_size_
Definition: PeakFileOptions.h:249
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
bool fill_data_
Definition: PeakFileOptions.h:245
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:69
MSNumpressCoder::NumpressConfig np_config_int_
Definition: PeakFileOptions.h:248
bool int_32_bit_
Definition: PeakFileOptions.h:234
bool write_supplemental_data_
Definition: PeakFileOptions.h:229
DRange< 1 > mz_range_
Definition: PeakFileOptions.h:236
bool sort_chromatograms_by_rt_
Definition: PeakFileOptions.h:244
bool force_maxquant_compatibility_
Definition: PeakFileOptions.h:227
bool write_index_
Definition: PeakFileOptions.h:246
bool always_append_data_
Definition: PeakFileOptions.h:241
bool has_rt_range_
Definition: PeakFileOptions.h:230
bool has_mz_range_
Definition: PeakFileOptions.h:231
DRange< 1 > intensity_range_
Definition: PeakFileOptions.h:237
bool sort_spectra_by_mz_
Definition: PeakFileOptions.h:243
bool size_only_
Definition: PeakFileOptions.h:240
bool zlib_compression_
Definition: PeakFileOptions.h:239
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
bool force_tpp_compatibility_
Definition: PeakFileOptions.h:228
Options for loading files containing peak data.
Definition: PeakFileOptions.h:48
bool mz_32_bit_
Definition: PeakFileOptions.h:233
std::vector< Int > ms_levels_
Definition: PeakFileOptions.h:238

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13