OpenMS  2.4.0
LayerData.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 2002-2018.
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: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 // OpenMS_GUI config
38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
39 
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
92  {
99  };
100 
102  enum Flags
103  {
112  };
113 
115  std::bitset<SIZE_OF_FLAGS> flags;
116 
119  {
126  };
127 
129  static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE];
130 
133 
135  typedef boost::shared_ptr<FeatureMap > FeatureMapSharedPtrType;
136 
139 
141  typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType;
142 
145 
147  typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType;
148 
149  typedef boost::shared_ptr<const ExperimentType> ConstExperimentSharedPtrType;
150 
152  typedef boost::shared_ptr<OnDiscMSExperiment> ODExperimentSharedPtrType;
153 
155 
158  flags(),
159  visible(true),
160  flipped(false),
161  type(DT_UNKNOWN),
162  name(),
163  filename(),
164  peptides(),
165  param(),
166  gradient(),
167  filters(),
168  annotations_1d(),
169  peak_colors_1d(),
170  modifiable(false),
171  modified(false),
172  label(L_NONE),
173  peptide_id_index(-1),
174  peptide_hit_index(-1),
175  features(new FeatureMapType()),
177  peaks(new ExperimentType()),
182  {
183  annotations_1d.resize(1);
184  }
185 
188  {
189  return features;
190  }
191 
194  {
195  return features;
196  }
197 
200  {
201  return consensus;
202  }
203 
206  {
207  return consensus;
208  }
209 
220 
231 
236  {
237  peaks = p;
238  updateCache_();
239  }
240 
243  {
244  on_disc_peaks = p;
245  }
246 
249  {
250  return on_disc_peaks;
251  }
252 
255  {
256  return chromatograms;
257  }
258 
261  {
262  return chromatograms;
263  }
264 
267  {
269  }
270 
273  {
275  }
276 
278  const Annotations1DContainer & getAnnotations(Size spectrum_index) const
279  {
280  return annotations_1d[spectrum_index];
281  }
282 
285  {
286  return annotations_1d[spectrum_index];
287  }
288 
295 
297  {
299  }
300 
303  {
304  if (spectrum_idx == current_spectrum_) return cached_spectrum_;
305 
306  if ((*peaks)[spectrum_idx].size() > 0)
307  {
308  return (*peaks)[spectrum_idx];
309  }
310  else if (!on_disc_peaks->empty())
311  {
312  return on_disc_peaks->getSpectrum(spectrum_idx);
313  }
314  return (*peaks)[spectrum_idx];
315  }
316 
319  {
320  return current_spectrum_;
321  }
322 
325  {
326  current_spectrum_ = index;
327  updateCache_();
328  }
329 
331  bool isIonMobilityData() const
332  {
333  return this->getPeakData()->size() > 0 &&
334  this->getPeakData()->metaValueExists("is_ion_mobility") &&
335  this->getPeakData()->getMetaValue("is_ion_mobility").toBool();
336  }
337 
339  {
340  peaks->setMetaValue("is_ion_mobility", "true");
341  }
342 
344  bool isDIAData() const
345  {
346  return this->getPeakData()->size() > 0 &&
347  this->getPeakData()->metaValueExists("is_dia_data") &&
348  this->getPeakData()->getMetaValue("is_dia_data").toBool();
349  }
350 
353  {
354  peaks->setMetaValue("is_dia_data", "true");
355  }
356 
366  {
367  return this->getPeakData()->size() > 0 &&
368  this->getPeakData()->metaValueExists("is_chromatogram") &&
369  this->getPeakData()->getMetaValue("is_chromatogram").toBool();
370  }
371 
374  {
375  peaks->setMetaValue("is_chromatogram", "true");
376  }
377 
380  {
381  if (this->chromatogram_flag_set())
382  {
383  peaks->removeMetaValue("is_chromatogram");
384  }
385  }
386 
393  void updateRanges();
394 
398 
400  void removePeakAnnotationsFromPeptideHit(const std::vector<Annotation1DItem*>& selected_annotations);
401 
403  bool visible;
404 
406  bool flipped;
407 
410 
413 
416 
418  std::vector<PeptideIdentification> peptides;
419 
422 
425 
428 
430  std::vector<Annotations1DContainer> annotations_1d;
431 
433  std::vector<QColor> peak_colors_1d;
434 
437 
439  bool modified;
440 
443 
447 
448 private:
449 
451  void updateCache_();
452 
455 
458 
461 
464 
467 
470 
473 
476 
477  };
478 
480  OPENMS_GUI_DLLAPI std::ostream & operator<<(std::ostream & os, const LayerData & rhs);
481 
482 } //namespace
483 
Flags
Flags that determine which information is shown.
Definition: LayerData.h:102
const Annotations1DContainer & getAnnotations(Size spectrum_index) const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:278
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:135
void removePeakAnnotationsFromPeptideHit(const std::vector< Annotation1DItem *> &selected_annotations)
remove peak annotations in the given list from the currently active PeptideHit
Consensus features: Show elements.
Definition: LayerData.h:109
static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]
Label names.
Definition: LayerData.h:129
Features: Convex hulls of single mass traces.
Definition: LayerData.h:105
FeatureMapSharedPtrType features
feature data
Definition: LayerData.h:457
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerData.h:344
ExperimentType::SpectrumType cached_spectrum_
Current cached spectrum.
Definition: LayerData.h:475
std::bitset< SIZE_OF_FLAGS > flags
Actual state of each flag.
Definition: LayerData.h:115
Features: Overall convex hull.
Definition: LayerData.h:104
Definition: LayerData.h:111
A more convenient string class.
Definition: String.h:57
LabelType label
Label type.
Definition: LayerData.h:442
PeakMap ExperimentType
Main data type (experiment)
Definition: LayerData.h:144
void sortByPosition()
Lexicographically sorts the peaks by their position.
const ExperimentType::SpectrumType & getCurrentSpectrum() const
Returns a const reference to the current spectrum (1D view)
void synchronizePeakAnnotations()
DataType
Dataset types.
Definition: LayerData.h:91
bool modified
Flag that indicates that the layer data was modified since loading it.
Definition: LayerData.h:439
A container for features.
Definition: FeatureMap.h:93
FeatureMapSharedPtrType & getFeatureMap()
Returns a const reference to the current feature data.
Definition: LayerData.h:193
void updateRanges()
Update ranges of all data structures.
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerData.h:379
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerData.h:331
All peptide hits of the first identification run are used.
Definition: LayerData.h:124
A container for consensus elements.
Definition: ConsensusMap.h:75
Undefined data type indicating an error.
Definition: LayerData.h:98
void setOnDiscPeakData(ODExperimentSharedPtrType p)
Set the current on-disc data.
Definition: LayerData.h:242
boost::shared_ptr< const ExperimentType > ConstExperimentSharedPtrType
Definition: LayerData.h:149
Peptide identification data.
Definition: LayerData.h:97
void updateCache_()
Update current cached spectrum for easy retrieval.
ODExperimentSharedPtrType on_disc_peaks
on disc peak data
Definition: LayerData.h:466
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
void labelAsDIAData()
Label the current layer as DIA (SWATH-MS) data.
Definition: LayerData.h:352
Annotations1DContainer & getCurrentAnnotations()
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:272
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:147
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerData.h:365
Chromatogram data.
Definition: LayerData.h:96
std::vector< Annotations1DContainer > annotations_1d
Annotations of all spectra of the experiment (1D view)
Definition: LayerData.h:430
const ExperimentSharedPtrType & getChromatogramData() const
Returns a mutable reference to the current chromatogram data.
Definition: LayerData.h:254
MSSpectrum SpectrumType
Spectrum Type.
Definition: MSExperiment.h:101
The &#39;label&#39; meta information is used.
Definition: LayerData.h:122
String name
layer name
Definition: LayerData.h:412
bool flipped
if this layer is flipped (1d mirror view)
Definition: LayerData.h:406
ExperimentSharedPtrType & getChromatogramData()
Returns a mutable reference to the current chromatogram data.
Definition: LayerData.h:260
const Annotations1DContainer & getCurrentAnnotations() const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:266
ExperimentSharedPtrType chromatograms
chromatogram data
Definition: LayerData.h:469
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
Param param
Layer parameters.
Definition: LayerData.h:421
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerData.h:187
Feature data.
Definition: LayerData.h:94
Annotations1DContainer & getAnnotations(Size spectrum_index)
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:284
const ConstExperimentSharedPtrType getPeakData() const
Returns a const reference to the current in-memory peak data.
void labelAsIonMobilityData() const
Definition: LayerData.h:338
Representation of a peptide hit.
Definition: PeptideHit.h:54
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:141
Consensus feature data.
Definition: LayerData.h:95
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
ConsensusMapSharedPtrType & getConsensusMap()
Returns current consensus map (mutable)
Definition: LayerData.h:205
std::vector< QColor > peak_colors_1d
Peak colors of the currently shown spectrum.
Definition: LayerData.h:433
String filename
file name of the file the data comes from (if available)
Definition: LayerData.h:415
Size current_spectrum_
Index of the current spectrum.
Definition: LayerData.h:472
void set_chromatogram_flag()
set the chromatogram flag
Definition: LayerData.h:373
ExperimentSharedPtrType peaks
peak data
Definition: LayerData.h:463
ConsensusMap ConsensusMapType
consensus features
Definition: LayerData.h:138
Management and storage of parameters / INI files.
Definition: Param.h:74
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Peaks: Show projections.
Definition: LayerData.h:108
bool modifiable
Flag that indicates if the layer data can be modified (so far used for features only) ...
Definition: LayerData.h:436
int peptide_hit_index
Definition: LayerData.h:446
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerData.h:107
void setCurrentSpectrumIndex(Size index)
Set the index of the current spectrum (1D view)
Definition: LayerData.h:324
int peptide_id_index
Selected peptide id and hit index (-1 if none is selected)
Definition: LayerData.h:445
void setPeakData(ExperimentSharedPtrType p)
Set the current in-memory peak data.
Definition: LayerData.h:235
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerData.h:152
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< PeptideIdentification > peptides
peptide identifications
Definition: LayerData.h:418
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerData.h:199
DataFilters filters
Filters to apply before painting.
Definition: LayerData.h:427
LayerData()
Default constructor.
Definition: LayerData.h:157
DataType type
data type (peak or feature data)
Definition: LayerData.h:409
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:302
LabelType
Label used in visualization.
Definition: LayerData.h:118
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerData.h:248
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerData.h:230
The best peptide hit of the first identification run is used.
Definition: LayerData.h:123
Spectrum profile or centroided data.
Definition: LayerData.h:93
DataFilter array providing some convenience functions.
Definition: DataFilters.h:50
void sortCurrentSpectrumByPosition()
Definition: LayerData.h:296
A gradient of multiple colors and arbitrary distances between colors.
Definition: MultiGradient.h:67
The element number is used.
Definition: LayerData.h:121
MultiGradient gradient
Gradient for 2D and 3D views.
Definition: LayerData.h:424
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum (1D view)
Definition: LayerData.h:318
Container for annotations to content of Spectrum1DCanvas.
Definition: Annotations1DContainer.h:53
No label is displayed.
Definition: LayerData.h:120
ConsensusMapSharedPtrType consensus
consensus feature data
Definition: LayerData.h:460
Features: Unassigned peptide hits.
Definition: LayerData.h:106
bool visible
if this layer is visible
Definition: LayerData.h:403
Definition: LayerData.h:125
Class that stores the data for one layer.
Definition: LayerData.h:85
void updatePeptideHitAnnotations_(PeptideHit &hit)
updates the PeakAnnotations in the current PeptideHit with manually changed annotations ...
Identifications: m/z source.
Definition: LayerData.h:110
FeatureMap FeatureMapType
Features.
Definition: LayerData.h:132