Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
PeakFileOptions.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2015.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
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.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Andreas Bertsch $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
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;
65 
67 
68  void setWriteSupplementalData(bool write);
71  bool getWriteSupplementalData() const;
73 
75 
76  void setRTRange(const DRange<1> & range);
79  bool hasRTRange() const;
81  const DRange<1> & getRTRange() const;
83 
85 
86  void setMZRange(const DRange<1> & range);
89  bool hasMZRange() const;
91  const DRange<1> & getMZRange() const;
93 
95 
96  void setIntensityRange(const DRange<1> & range);
99  bool hasIntensityRange() const;
101  const DRange<1> & getIntensityRange() const;
103 
112  void setMSLevels(const std::vector<Int> & levels);
115  void addMSLevel(int level);
117  void clearMSLevels();
119  bool hasMSLevels() const;
121  bool containsMSLevel(int level) const;
123  const std::vector<Int> & getMSLevels() const;
125 
132  //Sets if data should be compressed when writing
133  void setCompression(bool compress);
134  //returns @c true, if data should be compressed when writing
135  bool getCompression() const;
137 
140  void setSizeOnly(bool only);
142  bool getSizeOnly() const;
144  void setAlwaysAppendData(bool only);
146  bool getAlwaysAppendData() const;
148  void setFillData(bool only);
150  bool getFillData() const;
152  void setSkipXMLChecks(bool only);
154  bool getSkipXMLChecks() const;
155 
158  void setSortSpectraByMZ(bool sort);
160  bool getSortSpectraByMZ() const;
162  void setSortChromatogramsByRT(bool sort);
164  bool getSortChromatogramsByRT() const;
165 
172  //Sets if mz-data should be stored with 32bit or 64bit precision
173  void setMz32Bit(bool mz_32_bit);
174  //returns @c true, if mz-data should be stored with 32bit precision
175  bool getMz32Bit() const;
176  //Sets if intensity data should be stored with 32bit or 64bit precision
177  void setIntensity32Bit(bool int_32_bit);
178  //returns @c true, if intensity data should be stored with 32bit precision
179  bool getIntensity32Bit() const;
181 
183  bool getWriteIndex() const;
185  void setWriteIndex(bool write_index);
186 
188  MSNumpressCoder::NumpressConfig getNumpressConfigurationMassTime() const;
190  void setNumpressConfigurationMassTime(MSNumpressCoder::NumpressConfig config);
192  MSNumpressCoder::NumpressConfig getNumpressConfigurationIntensity() const;
194  void setNumpressConfigurationIntensity(MSNumpressCoder::NumpressConfig config);
195 
206  Size getMaxDataPoolSize() const;
209  void setMaxDataPoolSize(Size size);
211 
212 private:
223  std::vector<Int> ms_levels_;
235  };
236 
237 } // namespace OpenMS
238 
239 #endif // OPENMS_FORMAT_OPTIONS_PEAKFILEOPTIONS_H
MSNumpressCoder::NumpressConfig np_config_mz_
Definition: PeakFileOptions.h:232
bool has_intensity_range_
Definition: PeakFileOptions.h:217
bool metadata_only_
Definition: PeakFileOptions.h:213
bool skip_xml_checks_
Definition: PeakFileOptions.h:227
DRange< 1 > rt_range_
Definition: PeakFileOptions.h:220
Size maximal_data_pool_size_
Definition: PeakFileOptions.h:234
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
bool fill_data_
Definition: PeakFileOptions.h:230
Configuration class for MSNumpress.
Definition: MSNumpressCoder.h:65
MSNumpressCoder::NumpressConfig np_config_int_
Definition: PeakFileOptions.h:233
bool int_32_bit_
Definition: PeakFileOptions.h:219
bool write_supplemental_data_
Definition: PeakFileOptions.h:214
DRange< 1 > mz_range_
Definition: PeakFileOptions.h:221
bool sort_chromatograms_by_rt_
Definition: PeakFileOptions.h:229
bool write_index_
Definition: PeakFileOptions.h:231
bool always_append_data_
Definition: PeakFileOptions.h:226
bool has_rt_range_
Definition: PeakFileOptions.h:215
bool has_mz_range_
Definition: PeakFileOptions.h:216
DRange< 1 > intensity_range_
Definition: PeakFileOptions.h:222
bool sort_spectra_by_mz_
Definition: PeakFileOptions.h:228
bool size_only_
Definition: PeakFileOptions.h:225
bool zlib_compression_
Definition: PeakFileOptions.h:224
Options for loading files containing peak data.
Definition: PeakFileOptions.h:48
bool mz_32_bit_
Definition: PeakFileOptions.h:218
std::vector< Int > ms_levels_
Definition: PeakFileOptions.h:223

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:27 using doxygen 1.8.9.1