| OpenMS 2.5.0

LayerData.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.
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 // OpenMS_GUI config
38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
39
40 #include <OpenMS/KERNEL/StandardTypes.h>
41 #include <OpenMS/KERNEL/MSExperiment.h>
42 #include <OpenMS/KERNEL/OnDiscMSExperiment.h>
43 #include <OpenMS/KERNEL/FeatureMap.h>
44 #include <OpenMS/KERNEL/ConsensusMap.h>
45 #include <OpenMS/DATASTRUCTURES/String.h>
46 #include <OpenMS/VISUAL/MultiGradient.h>
47 #include <OpenMS/VISUAL/ANNOTATION/Annotations1DContainer.h>
48 #include <OpenMS/FILTERING/DATAREDUCTION/DataFilters.h>
49
50 #include <boost/shared_ptr.hpp>
51
52 #include <vector>
53 #include <bitset>
54
55 namespace OpenMS
56 {
85 class LayerData
86 {
87 public:
90 enum DataType
93 {
94 DT_PEAK,
95 DT_CHROMATOGRAM,
96 DT_FEATURE,
97 DT_CONSENSUS,
98 DT_IDENT,
99 DT_UNKNOWN
100 };
101
103 enum Flags
104 {
105 F_HULL,
106 F_HULLS,
107 F_UNASSIGNED,
108 P_PRECURSORS,
109 P_PROJECTIONS,
110 C_ELEMENTS,
111 I_PEPTIDEMZ,
112 I_LABELS,
113 SIZE_OF_FLAGS
114 };
115
117 std::bitset<SIZE_OF_FLAGS> flags;
118
120 enum LabelType
121 {
122 L_NONE,
123 L_INDEX,
124 L_META_LABEL,
125 L_ID,
126 L_ID_ALL,
127 SIZE_OF_LABEL_TYPE
128 };
129
131 static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE];
132
134 typedef FeatureMap FeatureMapType;
135
137 typedef boost::shared_ptr<FeatureMap > FeatureMapSharedPtrType;
138
140 typedef ConsensusMap ConsensusMapType;
141
143 typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType;
144
146 typedef PeakMap ExperimentType;
147
149 typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType;
150
151 typedef boost::shared_ptr<const ExperimentType> ConstExperimentSharedPtrType;
152
154 typedef boost::shared_ptr<OnDiscMSExperiment> ODExperimentSharedPtrType;
155
157
159 LayerData() :
160 flags(),
161 visible(true),
162 flipped(false),
163 type(DT_UNKNOWN),
164 name(),
165 filename(),
166 peptides(),
167 param(),
168 gradient(),
169 filters(),
170 annotations_1d(),
171 peak_colors_1d(),
172 modifiable(false),
173 modified(false),
174 label(L_NONE),
175 peptide_id_index(-1),
176 peptide_hit_index(-1),
177 features(new FeatureMapType()),
178 consensus(new ConsensusMapType()),
179 peaks(new ExperimentType()),
180 on_disc_peaks(new OnDiscMSExperiment()),
181 chromatograms(new ExperimentType()),
182 current_spectrum_(0),
183 cached_spectrum_()
184 {
185 annotations_1d.resize(1);
186 }
187
189 const FeatureMapSharedPtrType & getFeatureMap() const
190 {
191 return features;
192 }
193
195 FeatureMapSharedPtrType & getFeatureMap()
196 {
197 return features;
198 }
199
201 const ConsensusMapSharedPtrType & getConsensusMap() const
202 {
203 return consensus;
204 }
205
207 ConsensusMapSharedPtrType & getConsensusMap()
208 {
209 return consensus;
210 }
211
221 const ConstExperimentSharedPtrType getPeakData() const;
222
232 const ExperimentSharedPtrType & getPeakDataMuteable() {return peaks;}
233
237 void setPeakData(ExperimentSharedPtrType p)
238 {
239 peaks = p;
240 updateCache_();
241 }
242
244 void setOnDiscPeakData(ODExperimentSharedPtrType p)
245 {
246 on_disc_peaks = p;
247 }
248
250 const ODExperimentSharedPtrType & getOnDiscPeakData() const
251 {
252 return on_disc_peaks;
253 }
254
256 const ExperimentSharedPtrType & getChromatogramData() const
257 {
258 return chromatograms;
259 }
260
262 ExperimentSharedPtrType & getChromatogramData()
263 {
264 return chromatograms;
265 }
266
268 const Annotations1DContainer & getCurrentAnnotations() const
269 {
270 return annotations_1d[current_spectrum_];
271 }
272
274 Annotations1DContainer & getCurrentAnnotations()
275 {
276 return annotations_1d[current_spectrum_];
277 }
278
280 const Annotations1DContainer & getAnnotations(Size spectrum_index) const
281 {
282 return annotations_1d[spectrum_index];
283 }
284
286 Annotations1DContainer & getAnnotations(Size spectrum_index)
287 {
288 return annotations_1d[spectrum_index];
289 }
290
296 const ExperimentType::SpectrumType & getCurrentSpectrum() const;
297
298 void sortCurrentSpectrumByPosition()
299 {
300 cached_spectrum_.sortByPosition();
301 }
302
304 const ExperimentType::SpectrumType getSpectrum(Size spectrum_idx) const
305 {
306 if (spectrum_idx == current_spectrum_) return cached_spectrum_;
307
308 if ((*peaks)[spectrum_idx].size() > 0)
309 {
310 return (*peaks)[spectrum_idx];
311 }
312 else if (!on_disc_peaks->empty())
313 {
314 return on_disc_peaks->getSpectrum(spectrum_idx);
315 }
316 return (*peaks)[spectrum_idx];
317 }
318
320 Size getCurrentSpectrumIndex() const
321 {
322 return current_spectrum_;
323 }
324
326 void setCurrentSpectrumIndex(Size index)
327 {
328 current_spectrum_ = index;
329 updateCache_();
330 }
331
333 bool isIonMobilityData() const
334 {
335 return this->getPeakData()->size() > 0 &&
336 this->getPeakData()->metaValueExists("is_ion_mobility") &&
337 this->getPeakData()->getMetaValue("is_ion_mobility").toBool();
338 }
339
340 void labelAsIonMobilityData() const
341 {
342 peaks->setMetaValue("is_ion_mobility", "true");
343 }
344
346 bool isDIAData() const
347 {
348 return this->getPeakData()->size() > 0 &&
349 this->getPeakData()->metaValueExists("is_dia_data") &&
350 this->getPeakData()->getMetaValue("is_dia_data").toBool();
351 }
352
354 void labelAsDIAData()
355 {
356 peaks->setMetaValue("is_dia_data", "true");
357 }
358
367 bool chromatogram_flag_set() const
368 {
369 return this->getPeakData()->size() > 0 &&
370 this->getPeakData()->metaValueExists("is_chromatogram") &&
371 this->getPeakData()->getMetaValue("is_chromatogram").toBool();
372 }
373
375 void set_chromatogram_flag()
376 {
377 peaks->setMetaValue("is_chromatogram", "true");
378 }
379
381 void remove_chromatogram_flag()
382 {
383 if (this->chromatogram_flag_set())
384 {
385 peaks->removeMetaValue("is_chromatogram");
386 }
387 }
388
395 void updateRanges();
396
399 void synchronizePeakAnnotations();
400
402 void removePeakAnnotationsFromPeptideHit(const std::vector<Annotation1DItem*>& selected_annotations);
403
405 bool visible;
406
408 bool flipped;
409
411 DataType type;
412
414 String name;
415
417 String filename;
418
420 std::vector<PeptideIdentification> peptides;
421
423 Param param;
424
426 MultiGradient gradient;
427
429 DataFilters filters;
430
432 std::vector<Annotations1DContainer> annotations_1d;
433
435 std::vector<QColor> peak_colors_1d;
436
438 bool modifiable;
439
441 bool modified;
442
444 LabelType label;
445
447 int peptide_id_index;
448 int peptide_hit_index;
449
450 private:
451
453 void updateCache_();
454
456 void updatePeptideHitAnnotations_(PeptideHit& hit);
457
459 FeatureMapSharedPtrType features;
460
462 ConsensusMapSharedPtrType consensus;
463
465 ExperimentSharedPtrType peaks;
466
468 ODExperimentSharedPtrType on_disc_peaks;
469
471 ExperimentSharedPtrType chromatograms;
472
474 Size current_spectrum_;
475
477 ExperimentType::SpectrumType cached_spectrum_;
478
479 };
480
482 OPENMS_GUI_DLLAPI std::ostream & operator<<(std::ostream & os, const LayerData & rhs);
483
484 } //namespace
485
OpenMS::OnDiscMSExperiment
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
OpenMS::LayerData::FeatureMapType
FeatureMap FeatureMapType
Features.
Definition: LayerData.h:134
Annotations1DContainer.h
OpenMS::LayerData::set_chromatogram_flag
void set_chromatogram_flag()
set the chromatogram flag
Definition: LayerData.h:375
OpenMS::LayerData::peptides
std::vector< PeptideIdentification > peptides
peptide identifications
Definition: LayerData.h:420
OpenMS::LayerData::setOnDiscPeakData
void setOnDiscPeakData(ODExperimentSharedPtrType p)
Set the current on-disc data.
Definition: LayerData.h:244
OpenMS::LayerData::remove_chromatogram_flag
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerData.h:381
OpenMS::String
A more convenient string class.
Definition: String.h:58
MultiGradient.h
OpenMS::LayerData::getPeakData
const ConstExperimentSharedPtrType getPeakData() const
Returns a const reference to the current in-memory peak data.
OpenMS::LayerData::L_ID_ALL
All peptide hits of the first identification run are used.
Definition: LayerData.h:126
OpenMS::LayerData
Class that stores the data for one layer.
Definition: LayerData.h:85
OpenMS::LayerData::on_disc_peaks
ODExperimentSharedPtrType on_disc_peaks
on disc peak data
Definition: LayerData.h:468
OpenMS::LayerData::name
String name
layer name
Definition: LayerData.h:414
OpenMS::LayerData::labelAsIonMobilityData
void labelAsIonMobilityData() const
Definition: LayerData.h:340
OpenMS::LayerData::C_ELEMENTS
Consensus features: Show elements.
Definition: LayerData.h:110
OpenMS::LayerData::getFeatureMap
FeatureMapSharedPtrType & getFeatureMap()
Returns a const reference to the current feature data.
Definition: LayerData.h:195
DataFilters.h
OpenMS::LayerData::SIZE_OF_FLAGS
Definition: LayerData.h:113
OpenMS::LayerData::isIonMobilityData
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerData.h:333
OpenMS::LayerData::synchronizePeakAnnotations
void synchronizePeakAnnotations()
OpenMS::LayerData::L_META_LABEL
The &#39;label&#39; meta information is used.
Definition: LayerData.h:124
OpenMS::LayerData::peak_colors_1d
std::vector< QColor > peak_colors_1d
Peak colors of the currently shown spectrum.
Definition: LayerData.h:435
OpenMS::LayerData::getChromatogramData
const ExperimentSharedPtrType & getChromatogramData() const
Returns a mutable reference to the current chromatogram data.
Definition: LayerData.h:256
OpenMS::LayerData::getSpectrum
const ExperimentType::SpectrumType getSpectrum(Size spectrum_idx) const
Returns a const-copy of the required spectrum which is guaranteed to be populated with raw data...
Definition: LayerData.h:304
OpenMS::LayerData::DT_CHROMATOGRAM
Chromatogram data.
Definition: LayerData.h:95
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::LayerData::visible
bool visible
if this layer is visible
Definition: LayerData.h:405
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::LayerData::I_LABELS
Identifications: Show labels (not sequences)
Definition: LayerData.h:112
StandardTypes.h
OpenMS::LayerData::getFeatureMap
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerData.h:189
OpenMS::LayerData::peptide_hit_index
int peptide_hit_index
Definition: LayerData.h:448
OpenMS::LayerData::ConsensusMapType
ConsensusMap ConsensusMapType
consensus features
Definition: LayerData.h:140
OpenMS::LayerData::LayerData
LayerData()
Default constructor.
Definition: LayerData.h:159
OpenMS::LayerData::L_ID
The best peptide hit of the first identification run is used.
Definition: LayerData.h:125
OpenMS::LayerData::P_PROJECTIONS
Peaks: Show projections.
Definition: LayerData.h:109
OpenMS::LayerData::label
LabelType label
Label type.
Definition: LayerData.h:444
OpenMS::LayerData::F_HULLS
Features: Convex hulls of single mass traces.
Definition: LayerData.h:106
OpenMS::LayerData::peptide_id_index
int peptide_id_index
Selected peptide id and hit index (-1 if none is selected)
Definition: LayerData.h:447
OpenMS::LayerData::consensus
ConsensusMapSharedPtrType consensus
consensus feature data
Definition: LayerData.h:462
OpenMS::LayerData::updateCache_
void updateCache_()
Update current cached spectrum for easy retrieval.
OpenMS::LayerData::ExperimentType
PeakMap ExperimentType
Main data type (experiment)
Definition: LayerData.h:146
OpenMS::LayerData::DT_CONSENSUS
Consensus feature data.
Definition: LayerData.h:97
OpenMS::LayerData::F_HULL
Features: Overall convex hull.
Definition: LayerData.h:105
OpenMS::LayerData::chromatograms
ExperimentSharedPtrType chromatograms
chromatogram data
Definition: LayerData.h:471
ConsensusMap.h
OpenMS::LayerData::F_UNASSIGNED
Features: Unassigned peptide hits.
Definition: LayerData.h:107
OpenMS::LayerData::ODExperimentSharedPtrType
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerData.h:154
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::LayerData::chromatogram_flag_set
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerData.h:367
FeatureMap.h
OpenMS::MSExperiment::SpectrumType
MSSpectrum SpectrumType
Spectrum Type.
Definition: MSExperiment.h:101
OpenMS::LayerData::sortCurrentSpectrumByPosition
void sortCurrentSpectrumByPosition()
Definition: LayerData.h:298
String.h
OpenMS::LayerData::getPeakDataMuteable
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerData.h:232
OpenMS::LayerData::ExperimentSharedPtrType
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:149
OpenMS::LayerData::type
DataType type
data type (peak or feature data)
Definition: LayerData.h:411
OpenMS::LayerData::filters
DataFilters filters
Filters to apply before painting.
Definition: LayerData.h:429
OpenMS::LayerData::getConsensusMap
ConsensusMapSharedPtrType & getConsensusMap()
Returns current consensus map (mutable)
Definition: LayerData.h:207
OpenMS::LayerData::updatePeptideHitAnnotations_
void updatePeptideHitAnnotations_(PeptideHit &hit)
updates the PeakAnnotations in the current PeptideHit with manually changed annotations ...
OpenMS::LayerData::DT_UNKNOWN
Undefined data type indicating an error.
Definition: LayerData.h:99
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::LayerData::features
FeatureMapSharedPtrType features
feature data
Definition: LayerData.h:459
OpenMS::LayerData::getChromatogramData
ExperimentSharedPtrType & getChromatogramData()
Returns a mutable reference to the current chromatogram data.
Definition: LayerData.h:262
MSExperiment.h
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:54
OpenMS::LayerData::Flags
Flags
Flags that determine which information is shown.
Definition: LayerData.h:103
OpenMS::LayerData::LabelType
LabelType
Label used in visualization.
Definition: LayerData.h:120
OpenMS::LayerData::flags
std::bitset< SIZE_OF_FLAGS > flags
Actual state of each flag.
Definition: LayerData.h:117
OpenMS::MultiGradient
A gradient of multiple colors and arbitrary distances between colors.
Definition: MultiGradient.h:67
OpenMS::LayerData::getCurrentSpectrum
const ExperimentType::SpectrumType & getCurrentSpectrum() const
Returns a const reference to the current spectrum (1D view)
OpenMS::LayerData::flipped
bool flipped
if this layer is flipped (1d mirror view)
Definition: LayerData.h:408
OpenMS::LayerData::getAnnotations
Annotations1DContainer & getAnnotations(Size spectrum_index)
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:286
OpenMS::LayerData::isDIAData
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerData.h:346
OpenMS::LayerData::L_NONE
No label is displayed.
Definition: LayerData.h:122
OpenMS::LayerData::current_spectrum_
Size current_spectrum_
Index of the current spectrum.
Definition: LayerData.h:474
OpenMS::LayerData::getConsensusMap
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerData.h:201
OpenMS::LayerData::annotations_1d
std::vector< Annotations1DContainer > annotations_1d
Annotations of all spectra of the experiment (1D view)
Definition: LayerData.h:432
OpenMS::LayerData::NamesOfLabelType
static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]
Label names.
Definition: LayerData.h:131
OpenMS::LayerData::getCurrentAnnotations
Annotations1DContainer & getCurrentAnnotations()
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:274
OpenMS::LayerData::updateRanges
void updateRanges()
Update ranges of all data structures.
OnDiscMSExperiment.h
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::LayerData::ConsensusMapSharedPtrType
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:143
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::LayerData::getAnnotations
const Annotations1DContainer & getAnnotations(Size spectrum_index) const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:280
OpenMS::LayerData::modified
bool modified
Flag that indicates that the layer data was modified since loading it.
Definition: LayerData.h:441
OpenMS::LayerData::FeatureMapSharedPtrType
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:137
OpenMS::LayerData::SIZE_OF_LABEL_TYPE
Definition: LayerData.h:127
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::LayerData::labelAsDIAData
void labelAsDIAData()
Label the current layer as DIA (SWATH-MS) data.
Definition: LayerData.h:354
OpenMS::Annotations1DContainer
Container for annotations to content of Spectrum1DCanvas.
Definition: Annotations1DContainer.h:53
OpenMS::LayerData::cached_spectrum_
ExperimentType::SpectrumType cached_spectrum_
Current cached spectrum.
Definition: LayerData.h:477
OpenMS::LayerData::DataType
DataType
Definition: LayerData.h:92
OpenMS::LayerData::setCurrentSpectrumIndex
void setCurrentSpectrumIndex(Size index)
Set the index of the current spectrum (1D view)
Definition: LayerData.h:326
OpenMS::LayerData::I_PEPTIDEMZ
Identifications: m/z source.
Definition: LayerData.h:111
OpenMS::LayerData::peaks
ExperimentSharedPtrType peaks
peak data
Definition: LayerData.h:465
OpenMS::LayerData::gradient
MultiGradient gradient
Gradient for 2D and 3D views.
Definition: LayerData.h:426
OpenMS::LayerData::modifiable
bool modifiable
Flag that indicates if the layer data can be modified (so far used for features only) ...
Definition: LayerData.h:438
OpenMS::LayerData::setPeakData
void setPeakData(ExperimentSharedPtrType p)
Set the current in-memory peak data.
Definition: LayerData.h:237
OpenMS::LayerData::ConstExperimentSharedPtrType
boost::shared_ptr< const ExperimentType > ConstExperimentSharedPtrType
Definition: LayerData.h:151
OpenMS::LayerData::param
Param param
Layer parameters.
Definition: LayerData.h:423
OpenMS::LayerData::DT_PEAK
Spectrum profile or centroided data.
Definition: LayerData.h:94
OpenMS::LayerData::filename
String filename
file name of the file the data comes from (if available)
Definition: LayerData.h:417
OpenMS::LayerData::DT_IDENT
Peptide identification data.
Definition: LayerData.h:98
OpenMS::LayerData::getCurrentSpectrumIndex
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum (1D view)
Definition: LayerData.h:320
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::DataFilters
DataFilter array providing some convenience functions.
Definition: DataFilters.h:50
OpenMS::LayerData::L_INDEX
The element number is used.
Definition: LayerData.h:123
OpenMS::LayerData::getOnDiscPeakData
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerData.h:250
OpenMS::LayerData::getCurrentAnnotations
const Annotations1DContainer & getCurrentAnnotations() const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:268
OpenMS::LayerData::DT_FEATURE
Feature data.
Definition: LayerData.h:96
OpenMS::LayerData::P_PRECURSORS
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerData.h:108
OpenMS::LayerData::removePeakAnnotationsFromPeptideHit
void removePeakAnnotationsFromPeptideHit(const std::vector< Annotation1DItem *> &selected_annotations)
remove peak annotations in the given list from the currently active PeptideHit