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OnDiscMSExperiment.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/INTERFACES/DataStructures.h>
38
39 #include <OpenMS/KERNEL/MSExperiment.h>
40 #include <OpenMS/KERNEL/MSSpectrum.h>
41 #include <OpenMS/KERNEL/MSChromatogram.h>
42 #include <OpenMS/METADATA/ExperimentalSettings.h>
43 #include <OpenMS/FORMAT/HANDLERS/IndexedMzMLHandler.h>
44
45
46 #include <vector>
47 #include <algorithm>
48 #include <limits>
49
50 #include <boost/shared_ptr.hpp>
51
52 namespace OpenMS
53 {
68 class OPENMS_DLLAPI OnDiscMSExperiment
69 {
70
71 typedef ChromatogramPeak ChromatogramPeakT;
72 typedef Peak1D PeakT;
73
74 public:
75
81 OnDiscMSExperiment() {}
82
92 bool openFile(const String& filename, bool skipMetaData = false)
93 {
94 filename_ = filename;
95 indexed_mzml_file_.openFile(filename);
96 if (filename != "" && !skipMetaData)
97 {
98 loadMetaData_(filename);
99 }
100 return indexed_mzml_file_.getParsingSuccess();
101 }
102
104 OnDiscMSExperiment(const OnDiscMSExperiment& source) :
105 filename_(source.filename_),
106 indexed_mzml_file_(source.indexed_mzml_file_),
107 meta_ms_experiment_(source.meta_ms_experiment_)
108 {
109 }
110
118 bool operator==(const OnDiscMSExperiment& rhs) const
119 {
120 // check if file and meta information is the same
121 return filename_ == rhs.filename_ &&
122 (*meta_ms_experiment_) == (*rhs.meta_ms_experiment_);
123 // do not check if indexed_mzml_file_ is equal -> they have the same filename...
124 }
125
127 bool operator!=(const OnDiscMSExperiment& rhs) const
128 {
129 return !(operator==(rhs));
130 }
131
138 bool isSortedByRT() const
139 {
140 return meta_ms_experiment_->isSorted(false);
141 }
142
144 inline Size size() const
145 {
146 return getNrSpectra();
147 }
148
150 inline bool empty() const
151 {
152 return indexed_mzml_file_.getNrSpectra() == 0;
153 }
154
156 inline Size getNrSpectra() const
157 {
158 return indexed_mzml_file_.getNrSpectra();
159 }
160
162 inline Size getNrChromatograms() const
163 {
164 return indexed_mzml_file_.getNrChromatograms();
165 }
166
168 boost::shared_ptr<const ExperimentalSettings> getExperimentalSettings() const
169 {
170 return boost::static_pointer_cast<const ExperimentalSettings>(meta_ms_experiment_);
171 }
172
173 boost::shared_ptr<PeakMap> getMetaData() const
174 {
175 return meta_ms_experiment_;
176 }
177
179 inline MSSpectrum operator[](Size n)
180 {
181 return getSpectrum(n);
182 }
183
189 MSSpectrum getSpectrum(Size id)
190 {
191 MSSpectrum spectrum(meta_ms_experiment_->operator[](id));
192 indexed_mzml_file_.getMSSpectrumById(static_cast<int>(id), spectrum);
193 return spectrum;
194 }
195
199 OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
200 {
201 return indexed_mzml_file_.getSpectrumById(id);
202 }
203
209 MSChromatogram getChromatogram(Size id)
210 {
211 MSChromatogram chromatogram(meta_ms_experiment_->getChromatogram(id));
212 indexed_mzml_file_.getMSChromatogramById(static_cast<int>(id), chromatogram);
213 return chromatogram;
214 }
215
219 OpenMS::Interfaces::ChromatogramPtr getChromatogramById(Size id)
220 {
221 return indexed_mzml_file_.getChromatogramById(id);
222 }
223
225 void setSkipXMLChecks(bool skip)
226 {
227 indexed_mzml_file_.setSkipXMLChecks(skip);
228 }
229
230 private:
231
233 OnDiscMSExperiment& operator=(const OnDiscMSExperiment& /* source */);
234
235 void loadMetaData_(const String& filename);
236
237 protected:
238
240 String filename_;
242 Internal::IndexedMzMLHandler indexed_mzml_file_;
244 boost::shared_ptr<PeakMap> meta_ms_experiment_;
245 };
246
247 typedef OpenMS::OnDiscMSExperiment OnDiscPeakMap;
248
249 } // namespace OpenMS
250
251
OpenMS::OnDiscMSExperiment::PeakT
Peak1D PeakT
Definition: OnDiscMSExperiment.h:72
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
OpenMS::OnDiscMSExperiment
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
OpenMS::OnDiscMSExperiment::setSkipXMLChecks
void setSkipXMLChecks(bool skip)
sets whether to skip some XML checks and be fast instead
Definition: OnDiscMSExperiment.h:225
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ChromatogramPeak
A 1-dimensional raw data point or peak for chromatograms.
Definition: ChromatogramPeak.h:54
OpenMS::OnDiscMSExperiment::getNrSpectra
Size getNrSpectra() const
get the total number of spectra available
Definition: OnDiscMSExperiment.h:156
OpenMS::OnDiscMSExperiment::openFile
bool openFile(const String &filename, bool skipMetaData=false)
Open a specific file on disk.
Definition: OnDiscMSExperiment.h:92
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
OpenMS::OnDiscMSExperiment::getMetaData
boost::shared_ptr< PeakMap > getMetaData() const
Definition: OnDiscMSExperiment.h:173
OpenMS::OnDiscPeakMap
OpenMS::OnDiscMSExperiment OnDiscPeakMap
Definition: OnDiscMSExperiment.h:247
OpenMS::OnDiscMSExperiment::ChromatogramPeakT
ChromatogramPeak ChromatogramPeakT
Definition: OnDiscMSExperiment.h:71
OpenMS::OnDiscMSExperiment::getChromatogram
MSChromatogram getChromatogram(Size id)
returns a single chromatogram
Definition: OnDiscMSExperiment.h:209
OpenMS::OnDiscMSExperiment::operator==
bool operator==(const OnDiscMSExperiment &rhs) const
Equality operator.
Definition: OnDiscMSExperiment.h:118
OpenMS::OnDiscMSExperiment::meta_ms_experiment_
boost::shared_ptr< PeakMap > meta_ms_experiment_
The meta-data.
Definition: OnDiscMSExperiment.h:244
ExperimentalSettings.h
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::OnDiscMSExperiment::indexed_mzml_file_
Internal::IndexedMzMLHandler indexed_mzml_file_
The index of the underlying data file.
Definition: OnDiscMSExperiment.h:242
OpenMS::OnDiscMSExperiment::operator!=
bool operator!=(const OnDiscMSExperiment &rhs) const
Inequality operator.
Definition: OnDiscMSExperiment.h:127
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OnDiscMSExperiment::getSpectrumById
OpenMS::Interfaces::SpectrumPtr getSpectrumById(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:199
MSExperiment.h
OpenMS::OnDiscMSExperiment::getChromatogramById
OpenMS::Interfaces::ChromatogramPtr getChromatogramById(Size id)
returns a single chromatogram
Definition: OnDiscMSExperiment.h:219
MSSpectrum.h
OpenMS::OnDiscMSExperiment::empty
bool empty() const
returns whether spectra are empty
Definition: OnDiscMSExperiment.h:150
OpenMS::OnDiscMSExperiment::getNrChromatograms
Size getNrChromatograms() const
get the total number of chromatograms available
Definition: OnDiscMSExperiment.h:162
IndexedMzMLHandler.h
OpenMS::OnDiscMSExperiment::size
Size size() const
alias for getNrSpectra
Definition: OnDiscMSExperiment.h:144
OpenMS::OnDiscMSExperiment::getSpectrum
MSSpectrum getSpectrum(Size id)
returns a single spectrum
Definition: OnDiscMSExperiment.h:189
OpenMS::OnDiscMSExperiment::OnDiscMSExperiment
OnDiscMSExperiment(const OnDiscMSExperiment &source)
Copy constructor.
Definition: OnDiscMSExperiment.h:104
OpenMS::OnDiscMSExperiment::getExperimentalSettings
boost::shared_ptr< const ExperimentalSettings > getExperimentalSettings() const
returns the meta information of this experiment (const access)
Definition: OnDiscMSExperiment.h:168
OpenMS::Internal::IndexedMzMLHandler
A low-level class to read an indexedmzML file.
Definition: IndexedMzMLHandler.h:78
MSChromatogram.h
OpenMS::OnDiscMSExperiment::filename_
String filename_
The filename of the underlying data file.
Definition: OnDiscMSExperiment.h:240
OpenMS::OnDiscMSExperiment::operator[]
MSSpectrum operator[](Size n)
alias for getSpectrum
Definition: OnDiscMSExperiment.h:179
OpenMS::OnDiscMSExperiment::OnDiscMSExperiment
OnDiscMSExperiment()
Constructor.
Definition: OnDiscMSExperiment.h:81
OpenMS::Interfaces::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::Interfaces::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
DataStructures.h
OpenMS::OnDiscMSExperiment::isSortedByRT
bool isSortedByRT() const
Checks if all spectra are sorted with respect to ascending RT.
Definition: OnDiscMSExperiment.h:138
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806