OpenMS  3.0.0
LayerDataBase.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
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34 
35 #pragma once
36 
38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
39 
41 
44 
52 //#include <OpenMS/VISUAL/Painter1DBase.h>
55 
56 #include <boost/shared_ptr.hpp>
57 
58 #include <bitset>
59 #include <vector>
60 
61 class QWidget;
62 
63 namespace OpenMS
64 {
65  class LayerStatistics;
66  class OSWData;
67  class Painter1DBase;
68 
97  class OPENMS_GUI_DLLAPI LayerDataBase
98  {
99  public:
102  enum DataType
105  {
111  DT_UNKNOWN
112  };
113 
115  enum Flags
116  {
125  SIZE_OF_FLAGS
126  };
127 
129  std::bitset<SIZE_OF_FLAGS> flags;
130 
133  {
139  SIZE_OF_LABEL_TYPE
140  };
141 
143  static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE];
144 
147 
149  typedef boost::shared_ptr<FeatureMap> FeatureMapSharedPtrType;
150 
153 
155  typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType;
156 
159 
161  typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType;
162 
163  typedef boost::shared_ptr<const ExperimentType> ConstExperimentSharedPtrType;
164 
166  typedef boost::shared_ptr<OnDiscMSExperiment> ODExperimentSharedPtrType;
167 
169  typedef boost::shared_ptr<OSWData> OSWDataSharedPtrType;
170 
172 
174  LayerDataBase() = delete;
176  LayerDataBase(const DataType type) : type(type) {};
178  LayerDataBase(const LayerDataBase& ld) = delete;
180  LayerDataBase& operator=(const LayerDataBase& ld) = delete;
182  LayerDataBase(LayerDataBase&& ld) = default;
184  LayerDataBase& operator=(LayerDataBase&& ld) = default;
186  virtual ~LayerDataBase() = default;
187 
188  virtual std::unique_ptr<Painter1DBase> getPainter1D() const = 0;
189 
190 
193  {
194  return features_;
195  }
196 
199  {
200  return features_;
201  }
202 
205  {
206  return consensus_map_;
207  }
208 
211  {
212  return consensus_map_;
213  }
214 
224  const ConstExperimentSharedPtrType getPeakData() const;
225 
236  {
237  return peak_map_;
238  }
239 
244  {
245  peak_map_ = p;
246  updateCache_();
247  }
248 
251  {
252  on_disc_peaks = p;
253  }
254 
257  {
258  return on_disc_peaks;
259  }
260 
263  {
264  return chromatogram_map_;
265  }
266 
269  {
270  return chromatogram_map_;
271  }
272 
275  OSWDataSharedPtrType& getChromatogramAnnotation();
276 
279  const OSWDataSharedPtrType& getChromatogramAnnotation() const;
280 
282  void setChromatogramAnnotation(OSWData&& data);
283 
287  bool annotate(const std::vector<PeptideIdentification>& identifications,
288  const std::vector<ProteinIdentification>& protein_identifications);
289 
290 
293  {
294  return annotations_1d[current_spectrum_idx_];
295  }
296 
299  {
300  return annotations_1d[current_spectrum_idx_];
301  }
302 
304  const Annotations1DContainer& getAnnotations(Size spectrum_index) const
305  {
306  return annotations_1d[spectrum_index];
307  }
308 
311  {
312  return annotations_1d[spectrum_index];
313  }
314 
320  const ExperimentType::SpectrumType& getCurrentSpectrum() const;
321 
323  {
324  cached_spectrum_.sortByPosition();
325  }
326 
328  const ExperimentType::SpectrumType getSpectrum(Size spectrum_idx) const;
329 
332  {
333  return current_spectrum_idx_;
334  }
335 
338  {
339  current_spectrum_idx_ = index;
340  updateCache_();
341  }
342 
343 
348  {
349  ExperimentSharedPtrType exp_sptr(getChromatogramData().get() == nullptr ||
350  getChromatogramData().get()->getNrChromatograms() == 0 ?
351  getPeakDataMuteable() :
352  getChromatogramData());
353  return exp_sptr;
354  }
355 
357  bool isIonMobilityData() const
358  {
359  return this->getPeakData()->size() > 0 &&
360  this->getPeakData()->metaValueExists("is_ion_mobility") &&
361  this->getPeakData()->getMetaValue("is_ion_mobility").toBool();
362  }
363 
365  {
366  peak_map_->setMetaValue("is_ion_mobility", "true");
367  }
368 
370  bool isDIAData() const
371  {
372  return this->getPeakData()->size() > 0 &&
373  this->getPeakData()->metaValueExists("is_dia_data") &&
374  this->getPeakData()->getMetaValue("is_dia_data").toBool();
375  }
376 
379  {
380  peak_map_->setMetaValue("is_dia_data", "true");
381  }
382 
392  {
393  return this->getPeakData()->size() > 0 &&
394  this->getPeakData()->metaValueExists("is_chromatogram") &&
395  this->getPeakData()->getMetaValue("is_chromatogram").toBool();
396  }
397 
400  {
401  peak_map_->setMetaValue("is_chromatogram", "true");
402  }
403 
406  {
407  if (this->chromatogram_flag_set())
408  {
409  peak_map_->removeMetaValue("is_chromatogram");
410  }
411  }
412 
416  virtual void updateRanges() = 0;
417 
419  float getMinIntensity() const;
420 
422  float getMaxIntensity() const;
423 
425 
428  virtual RangeAllType getRange() const = 0;
429 
431  virtual std::unique_ptr<LayerStatistics> getStats() const = 0;
432 
435  void synchronizePeakAnnotations();
436 
438  void removePeakAnnotationsFromPeptideHit(const std::vector<Annotation1DItem*>& selected_annotations);
439 
441  bool visible = true;
442 
444  bool flipped = false;
445 
447  DataType type = DT_UNKNOWN;
448 
449  private:
452 
453  public:
454  const String& getName() const
455  {
456  return name_;
457  }
458  void setName(const String& new_name)
459  {
460  name_ = new_name;
461  }
462 
465 
468 
471 
474 
476  std::vector<Annotations1DContainer> annotations_1d = std::vector<Annotations1DContainer>(1);
477 
479  std::vector<QColor> peak_colors_1d;
480 
482  bool modifiable = false;
483 
485  bool modified = false;
486 
488  LabelType label = L_NONE;
489 
491  int peptide_id_index = -1;
492  int peptide_hit_index = -1;
493 
495  String getDecoratedName() const;
496 
497  protected:
499  void updateCache_();
500 
502  void updatePeptideHitAnnotations_(PeptideHit& hit);
503 
506 
509 
512 
515 
518 
521 
523  Size current_spectrum_idx_ = 0;
524 
527  };
528 
532  {
533  public:
541  LayerAnnotatorBase(const FileTypeList& supported_types, const String& file_dialog_text, QWidget* gui_lock);
542 
547  bool annotateWithFileDialog(LayerDataBase& layer, LogWindow& log, const String& current_path) const;
548 
552  bool annotateWithFilename(LayerDataBase& layer, LogWindow& log, const String& filename) const;
553 
557  static std::unique_ptr<LayerAnnotatorBase> getAnnotatorWhichSupports(const FileTypes::Type& type);
558 
560  static std::unique_ptr<LayerAnnotatorBase> getAnnotatorWhichSupports(const String& filename);
561 
562  protected:
565  virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const = 0;
566 
569  QWidget* gui_lock_ = nullptr;
570  };
571 
575  {
576  public:
579  "Select peptide identification data", gui_lock)
580  {
581  }
582 
583  protected:
586  virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const;
587  };
588 
592  {
593  public:
596  "Select AccurateMassSearch's featureXML file", gui_lock)
597  {
598  }
599 
600  protected:
603  virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const;
604  };
605 
609  {
610  public:
612  LayerAnnotatorBase(std::vector<FileTypes::Type>{FileTypes::OSW},
613  "Select OpenSwath/pyProphet output file", gui_lock)
614  {
615  }
616 
617  protected:
620  virtual bool annotateWorker_(LayerDataBase& layer, const String& filename, LogWindow& log) const;
621  };
622 
624  OPENMS_GUI_DLLAPI std::ostream& operator<<(std::ostream& os, const LayerDataBase& rhs);
625 
626 }// namespace OpenMS
627 
OpenMS::LayerDataBase::F_HULL
Features: Overall convex hull.
Definition: LayerDataBase.h:117
OpenMS::LayerAnnotatorBase::gui_lock_
QWidget * gui_lock_
optional widget which will be locked when calling annotateWorker_() in child-classes
Definition: LayerDataBase.h:569
OpenMS::MultiGradient
A gradient of multiple colors and arbitrary distances between colors.
Definition: MultiGradient.h:67
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
OpenMS::LayerDataBase::getChromatogramData
const ExperimentSharedPtrType & getChromatogramData() const
Returns a mutable reference to the current chromatogram data.
Definition: LayerDataBase.h:262
OpenMS::LayerDataBase::peak_colors_1d
std::vector< QColor > peak_colors_1d
Peak colors of the currently shown spectrum.
Definition: LayerDataBase.h:479
OpenMS::LayerDataBase::L_INDEX
The element number is used.
Definition: LayerDataBase.h:135
OpenMS::LayerDataBase::I_PEPTIDEMZ
Identifications: m/z source.
Definition: LayerDataBase.h:123
OpenMS::LogWindow
A log window (QTextEdit) with convenience functions.
Definition: LogWindow.h:53
OpenMS::LayerDataBase::L_ID
The best peptide hit of the first identification run is used.
Definition: LayerDataBase.h:137
OpenMS::LayerDataBase::filename
String filename
file name of the file the data comes from (if available)
Definition: LayerDataBase.h:464
OpenMS::LayerDataBase::C_ELEMENTS
Consensus features: Show elements.
Definition: LayerDataBase.h:122
OpenMS::LayerAnnotatorPeptideID::annotateWorker_
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const
OpenMS::LayerDataBase::setOnDiscPeakData
void setOnDiscPeakData(ODExperimentSharedPtrType p)
Set the current on-disc data.
Definition: LayerDataBase.h:250
OpenMS::LayerAnnotatorAMS
Definition: LayerDataBase.h:591
OpenMS::LayerDataBase::isIonMobilityData
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerDataBase.h:357
OpenMS::LayerDataBase::getFullChromData
ExperimentSharedPtrType getFullChromData()
Definition: LayerDataBase.h:347
OpenMS::LayerDataBase::getName
const String & getName() const
Definition: LayerDataBase.h:454
OpenMS::LayerDataBase::param
Param param
Layer parameters.
Definition: LayerDataBase.h:467
OpenMS::LayerDataBase::getAnnotations
const Annotations1DContainer & getAnnotations(Size spectrum_index) const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:304
OpenMS::LayerDataBase::setPeakData
void setPeakData(ExperimentSharedPtrType p)
Set the current in-memory peak data.
Definition: LayerDataBase.h:243
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::LayerDataBase::LayerDataBase
LayerDataBase(const DataType type)
C'tor for child classes.
Definition: LayerDataBase.h:176
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
LogWindow.h
OpenMS::LayerDataBase::OSWDataSharedPtrType
boost::shared_ptr< OSWData > OSWDataSharedPtrType
SharedPtr on OSWData.
Definition: LayerDataBase.h:169
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::LayerAnnotatorBase
Definition: LayerDataBase.h:531
OpenMS::LayerDataBase::labelAsIonMobilityData
void labelAsIonMobilityData() const
Definition: LayerDataBase.h:364
MultiGradient.h
OpenMS::LayerDataBase::P_PRECURSORS
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerDataBase.h:120
OpenMS::FileTypes::MZIDENTML
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
OpenMS::LayerDataBase::gradient
MultiGradient gradient
Gradient for 2D and 3D views.
Definition: LayerDataBase.h:470
OpenMS::LayerDataBase::L_META_LABEL
The 'label' meta information is used.
Definition: LayerDataBase.h:136
OpenMS::LayerDataBase::DT_CONSENSUS
Consensus feature data.
Definition: LayerDataBase.h:109
OpenMS::LayerDataBase::getCurrentAnnotations
Annotations1DContainer & getCurrentAnnotations()
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:298
QWidget
OpenMS::LayerDataBase::L_NONE
No label is displayed.
Definition: LayerDataBase.h:134
OpenMS::LayerDataBase::DT_CHROMATOGRAM
Chromatogram data.
Definition: LayerDataBase.h:107
OpenMS::LayerDataBase::setName
void setName(const String &new_name)
Definition: LayerDataBase.h:458
OpenMS::LayerDataBase::DataType
DataType
Definition: LayerDataBase.h:104
OpenMS::LayerAnnotatorBase::LayerAnnotatorBase
LayerAnnotatorBase(const FileTypeList &supported_types, const String &file_dialog_text, QWidget *gui_lock)
C'tor with params.
OpenMS::LayerDataBase::sortCurrentSpectrumByPosition
void sortCurrentSpectrumByPosition()
Definition: LayerDataBase.h:322
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::RangeManager
Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra.
Definition: RangeManager.h:588
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
OpenMS::LayerDataBase::F_UNASSIGNED
Features: Unassigned peptide hits.
Definition: LayerDataBase.h:119
OpenMS::LayerDataBase::P_PROJECTIONS
Peaks: Show projections.
Definition: LayerDataBase.h:121
OpenMS::LayerDataBase::DT_IDENT
Peptide identification data.
Definition: LayerDataBase.h:110
OpenMS::LayerDataBase::getConsensusMap
ConsensusMapSharedPtrType & getConsensusMap()
Returns current consensus map (mutable)
Definition: LayerDataBase.h:210
OpenMS::LayerAnnotatorBase::getAnnotatorWhichSupports
static std::unique_ptr< LayerAnnotatorBase > getAnnotatorWhichSupports(const FileTypes::Type &type)
OpenMS::OnDiscMSExperiment
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:66
OpenMS::LayerDataBase::DT_PEAK
Spectrum profile or centroided data.
Definition: LayerDataBase.h:106
FeatureMap.h
OpenMS::LayerDataBase::ExperimentSharedPtrType
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerDataBase.h:161
ProteinIdentification.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::LayerAnnotatorOSW::LayerAnnotatorOSW
LayerAnnotatorOSW(QWidget *gui_lock)
Definition: LayerDataBase.h:611
Param.h
DataFilters.h
OpenMS::LayerDataBase::DT_FEATURE
Feature data.
Definition: LayerDataBase.h:108
OpenMS::Internal::SpectrumType
MSSpectrum SpectrumType
Definition: MzDataHandler.h:60
OpenMS::LayerDataBase::getFeatureMap
FeatureMapSharedPtrType & getFeatureMap()
Returns a const reference to the current feature data.
Definition: LayerDataBase.h:198
OpenMS::LayerAnnotatorOSW
Definition: LayerDataBase.h:608
OpenMS::LayerDataBase::getFeatureMap
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerDataBase.h:192
OpenMS::LayerDataBase::labelAsDIAData
void labelAsDIAData()
Label the current layer as DIA (SWATH-MS) data.
Definition: LayerDataBase.h:378
OpenMS::LayerAnnotatorPeptideID::LayerAnnotatorPeptideID
LayerAnnotatorPeptideID(QWidget *gui_lock)
Definition: LayerDataBase.h:577
OpenMS::LayerAnnotatorBase::annotateWithFileDialog
bool annotateWithFileDialog(LayerDataBase &layer, LogWindow &log, const String &current_path) const
OpenMS::LayerDataBase::ConsensusMapType
ConsensusMap ConsensusMapType
consensus features
Definition: LayerDataBase.h:152
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::LayerDataBase::L_ID_ALL
All peptide hits of the first identification run are used.
Definition: LayerDataBase.h:138
OpenMS::FileTypes::OSW
OpenSWATH OpenSWATH report (OSW) SQLite DB.
Definition: FileTypes.h:104
OpenMS::LayerDataBase::filters
DataFilters filters
Filters to apply before painting.
Definition: LayerDataBase.h:473
OpenMS::LayerDataBase::F_HULLS
Features: Convex hulls of single mass traces.
Definition: LayerDataBase.h:118
OpenMS::LayerDataBase::chrom_annotation_
OSWDataSharedPtrType chrom_annotation_
Chromatogram annotation data.
Definition: LayerDataBase.h:520
MSExperiment.h
OpenMS::LayerDataBase::I_LABELS
Identifications: Show labels (not sequences)
Definition: LayerDataBase.h:124
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::DataFilters
DataFilter array providing some convenience functions.
Definition: DataFilters.h:51
OpenMS::LayerDataBase::isDIAData
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerDataBase.h:370
Annotations1DContainer.h
OpenMS::LayerAnnotatorAMS::annotateWorker_
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const
OpenMS::LayerDataBase::FeatureMapType
FeatureMap FeatureMapType
Features.
Definition: LayerDataBase.h:146
OpenMS::LayerDataBase::ConsensusMapSharedPtrType
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerDataBase.h:155
OpenMS::LayerAnnotatorPeptideID
Definition: LayerDataBase.h:574
OpenMS::LayerDataBase::FeatureMapSharedPtrType
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerDataBase.h:149
OpenMS::LayerDataBase::remove_chromatogram_flag
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerDataBase.h:405
OpenMS::LayerDataBase::getConsensusMap
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerDataBase.h:204
String.h
OpenMS::supported_types
const FileTypeList supported_types({ FileTypes::MZML, FileTypes::MZXML, FileTypes::MZDATA, FileTypes::SQMASS, FileTypes::FEATUREXML, FileTypes::CONSENSUSXML, FileTypes::IDXML, FileTypes::DTA, FileTypes::DTA2D, FileTypes::MGF, FileTypes::MS2, FileTypes::MSP, FileTypes::BZ2, FileTypes::GZ })
supported types which can be opened with File–>Open
OpenMS::LayerDataBase::getOnDiscPeakData
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerDataBase.h:256
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::LayerDataBase::flags
std::bitset< SIZE_OF_FLAGS > flags
Actual state of each flag.
Definition: LayerDataBase.h:129
OpenMS::LayerDataBase::ExperimentType
PeakMap ExperimentType
Main data type (experiment)
Definition: LayerDataBase.h:158
OpenMS::LayerDataBase::ConstExperimentSharedPtrType
boost::shared_ptr< const ExperimentType > ConstExperimentSharedPtrType
Definition: LayerDataBase.h:163
OpenMS::OSWData
Holds all or partial information from an OSW file.
Definition: OSWData.h:304
OpenMS::LayerDataBase::ODExperimentSharedPtrType
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerDataBase.h:166
OpenMS::LayerDataBase::getCurrentSpectrumIndex
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum (1D view)
Definition: LayerDataBase.h:331
OpenMS::LayerDataBase
Class that stores the data for one layer.
Definition: LayerDataBase.h:97
OpenMS::LayerAnnotatorBase::annotateWithFilename
bool annotateWithFilename(LayerDataBase &layer, LogWindow &log, const String &filename) const
OpenMS::FileTypes
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:52
OpenMS::LayerAnnotatorBase::annotateWorker_
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const =0
OpenMS::LayerAnnotatorAMS::LayerAnnotatorAMS
LayerAnnotatorAMS(QWidget *gui_lock)
Definition: LayerDataBase.h:594
OpenMS::LayerDataBase::Flags
Flags
Flags that determine which information is shown.
Definition: LayerDataBase.h:115
PeptideIdentification.h
OpenMS::LayerDataBase::set_chromatogram_flag
void set_chromatogram_flag()
set the chromatogram flag
Definition: LayerDataBase.h:399
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::LayerAnnotatorOSW::annotateWorker_
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const
OnDiscMSExperiment.h
OpenMS::LayerDataBase::cached_spectrum_
ExperimentType::SpectrumType cached_spectrum_
Current cached spectrum.
Definition: LayerDataBase.h:526
OpenMS::LayerDataBase::getCurrentAnnotations
const Annotations1DContainer & getCurrentAnnotations() const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:292
OpenMS::LayerDataBase::LabelType
LabelType
Label used in visualization.
Definition: LayerDataBase.h:132
OpenMS::LayerAnnotatorBase::supported_types_
const FileTypeList supported_types_
Definition: LayerDataBase.h:567
OpenMS::LayerAnnotatorBase::file_dialog_text_
const String file_dialog_text_
Definition: LayerDataBase.h:568
StandardTypes.h
OpenMS::LayerDataBase::chromatogram_flag_set
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerDataBase.h:391
OpenMS::LayerDataBase::getChromatogramData
ExperimentSharedPtrType & getChromatogramData()
Returns a mutable reference to the current chromatogram data.
Definition: LayerDataBase.h:268
OpenMS::Annotations1DContainer
Container for annotations to content of Plot1DCanvas.
Definition: Annotations1DContainer.h:53
OpenMS::LayerDataBase::setCurrentSpectrumIndex
void setCurrentSpectrumIndex(Size index)
Set the index of the current spectrum (1D view)
Definition: LayerDataBase.h:337
OpenMS::LayerDataBase::getPeakDataMuteable
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerDataBase.h:235
OpenMS::LayerDataBase::getAnnotations
Annotations1DContainer & getAnnotations(Size spectrum_index)
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:310
OpenMS::LayerDataBase::name_
String name_
layer name
Definition: LayerDataBase.h:451
OpenMS::FileTypeList
holds a vector of known file types, e.g. as a way to specify supported input formats
Definition: FileTypes.h:149
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55