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OpenMS
3.0.0
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38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
56 #include <boost/shared_ptr.hpp>
65 class LayerStatistics;
143 static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE];
188 virtual std::unique_ptr<Painter1DBase> getPainter1D()
const = 0;
206 return consensus_map_;
212 return consensus_map_;
224 const ConstExperimentSharedPtrType getPeakData()
const;
258 return on_disc_peaks;
264 return chromatogram_map_;
270 return chromatogram_map_;
275 OSWDataSharedPtrType& getChromatogramAnnotation();
279 const OSWDataSharedPtrType& getChromatogramAnnotation()
const;
282 void setChromatogramAnnotation(
OSWData&& data);
287 bool annotate(
const std::vector<PeptideIdentification>& identifications,
288 const std::vector<ProteinIdentification>& protein_identifications);
294 return annotations_1d[current_spectrum_idx_];
300 return annotations_1d[current_spectrum_idx_];
306 return annotations_1d[spectrum_index];
312 return annotations_1d[spectrum_index];
324 cached_spectrum_.sortByPosition();
333 return current_spectrum_idx_;
339 current_spectrum_idx_ = index;
350 getChromatogramData().get()->getNrChromatograms() == 0 ?
351 getPeakDataMuteable() :
352 getChromatogramData());
359 return this->getPeakData()->size() > 0 &&
360 this->getPeakData()->metaValueExists(
"is_ion_mobility") &&
361 this->getPeakData()->getMetaValue(
"is_ion_mobility").toBool();
366 peak_map_->setMetaValue(
"is_ion_mobility",
"true");
372 return this->getPeakData()->size() > 0 &&
373 this->getPeakData()->metaValueExists(
"is_dia_data") &&
374 this->getPeakData()->getMetaValue(
"is_dia_data").toBool();
380 peak_map_->setMetaValue(
"is_dia_data",
"true");
393 return this->getPeakData()->size() > 0 &&
394 this->getPeakData()->metaValueExists(
"is_chromatogram") &&
395 this->getPeakData()->getMetaValue(
"is_chromatogram").toBool();
401 peak_map_->setMetaValue(
"is_chromatogram",
"true");
407 if (this->chromatogram_flag_set())
409 peak_map_->removeMetaValue(
"is_chromatogram");
416 virtual void updateRanges() = 0;
419 float getMinIntensity()
const;
422 float getMaxIntensity()
const;
431 virtual std::unique_ptr<LayerStatistics> getStats()
const = 0;
435 void synchronizePeakAnnotations();
438 void removePeakAnnotationsFromPeptideHit(
const std::vector<Annotation1DItem*>& selected_annotations);
444 bool flipped =
false;
476 std::vector<Annotations1DContainer> annotations_1d = std::vector<Annotations1DContainer>(1);
482 bool modifiable =
false;
485 bool modified =
false;
491 int peptide_id_index = -1;
492 int peptide_hit_index = -1;
495 String getDecoratedName()
const;
502 void updatePeptideHitAnnotations_(
PeptideHit& hit);
523 Size current_spectrum_idx_ = 0;
579 "Select peptide identification data", gui_lock)
586 virtual bool annotateWorker_(LayerDataBase& layer,
const String& filename, LogWindow& log)
const;
596 "Select AccurateMassSearch's featureXML file", gui_lock)
603 virtual bool annotateWorker_(LayerDataBase& layer,
const String& filename, LogWindow& log)
const;
613 "Select OpenSwath/pyProphet output file", gui_lock)
620 virtual bool annotateWorker_(LayerDataBase& layer,
const String& filename, LogWindow& log)
const;
624 OPENMS_GUI_DLLAPI std::ostream&
operator<<(std::ostream& os,
const LayerDataBase& rhs);
Features: Overall convex hull.
Definition: LayerDataBase.h:117
QWidget * gui_lock_
optional widget which will be locked when calling annotateWorker_() in child-classes
Definition: LayerDataBase.h:569
A gradient of multiple colors and arbitrary distances between colors.
Definition: MultiGradient.h:67
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
const ExperimentSharedPtrType & getChromatogramData() const
Returns a mutable reference to the current chromatogram data.
Definition: LayerDataBase.h:262
std::vector< QColor > peak_colors_1d
Peak colors of the currently shown spectrum.
Definition: LayerDataBase.h:479
The element number is used.
Definition: LayerDataBase.h:135
Identifications: m/z source.
Definition: LayerDataBase.h:123
A log window (QTextEdit) with convenience functions.
Definition: LogWindow.h:53
The best peptide hit of the first identification run is used.
Definition: LayerDataBase.h:137
String filename
file name of the file the data comes from (if available)
Definition: LayerDataBase.h:464
Consensus features: Show elements.
Definition: LayerDataBase.h:122
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const
void setOnDiscPeakData(ODExperimentSharedPtrType p)
Set the current on-disc data.
Definition: LayerDataBase.h:250
Definition: LayerDataBase.h:591
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerDataBase.h:357
ExperimentSharedPtrType getFullChromData()
Definition: LayerDataBase.h:347
const String & getName() const
Definition: LayerDataBase.h:454
Param param
Layer parameters.
Definition: LayerDataBase.h:467
const Annotations1DContainer & getAnnotations(Size spectrum_index) const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:304
void setPeakData(ExperimentSharedPtrType p)
Set the current in-memory peak data.
Definition: LayerDataBase.h:243
A more convenient string class.
Definition: String.h:58
LayerDataBase(const DataType type)
C'tor for child classes.
Definition: LayerDataBase.h:176
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
boost::shared_ptr< OSWData > OSWDataSharedPtrType
SharedPtr on OSWData.
Definition: LayerDataBase.h:169
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Definition: LayerDataBase.h:531
void labelAsIonMobilityData() const
Definition: LayerDataBase.h:364
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerDataBase.h:120
mzIdentML (HUPO PSI AnalysisXML followup format) (.mzid)
Definition: FileTypes.h:75
MultiGradient gradient
Gradient for 2D and 3D views.
Definition: LayerDataBase.h:470
The 'label' meta information is used.
Definition: LayerDataBase.h:136
Consensus feature data.
Definition: LayerDataBase.h:109
Annotations1DContainer & getCurrentAnnotations()
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:298
No label is displayed.
Definition: LayerDataBase.h:134
Chromatogram data.
Definition: LayerDataBase.h:107
void setName(const String &new_name)
Definition: LayerDataBase.h:458
DataType
Definition: LayerDataBase.h:104
LayerAnnotatorBase(const FileTypeList &supported_types, const String &file_dialog_text, QWidget *gui_lock)
C'tor with params.
void sortCurrentSpectrumByPosition()
Definition: LayerDataBase.h:322
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Handles the management of a multidimensional range, e.g. RangeMZ and RangeIntensity for spectra.
Definition: RangeManager.h:588
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
Features: Unassigned peptide hits.
Definition: LayerDataBase.h:119
Peaks: Show projections.
Definition: LayerDataBase.h:121
Peptide identification data.
Definition: LayerDataBase.h:110
ConsensusMapSharedPtrType & getConsensusMap()
Returns current consensus map (mutable)
Definition: LayerDataBase.h:210
static std::unique_ptr< LayerAnnotatorBase > getAnnotatorWhichSupports(const FileTypes::Type &type)
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:66
Spectrum profile or centroided data.
Definition: LayerDataBase.h:106
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerDataBase.h:161
Type
Actual file types enum.
Definition: FileTypes.h:56
LayerAnnotatorOSW(QWidget *gui_lock)
Definition: LayerDataBase.h:611
Feature data.
Definition: LayerDataBase.h:108
MSSpectrum SpectrumType
Definition: MzDataHandler.h:60
FeatureMapSharedPtrType & getFeatureMap()
Returns a const reference to the current feature data.
Definition: LayerDataBase.h:198
Definition: LayerDataBase.h:608
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerDataBase.h:192
void labelAsDIAData()
Label the current layer as DIA (SWATH-MS) data.
Definition: LayerDataBase.h:378
LayerAnnotatorPeptideID(QWidget *gui_lock)
Definition: LayerDataBase.h:577
bool annotateWithFileDialog(LayerDataBase &layer, LogWindow &log, const String ¤t_path) const
ConsensusMap ConsensusMapType
consensus features
Definition: LayerDataBase.h:152
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
A container for consensus elements.
Definition: ConsensusMap.h:82
All peptide hits of the first identification run are used.
Definition: LayerDataBase.h:138
OpenSWATH OpenSWATH report (OSW) SQLite DB.
Definition: FileTypes.h:104
DataFilters filters
Filters to apply before painting.
Definition: LayerDataBase.h:473
Features: Convex hulls of single mass traces.
Definition: LayerDataBase.h:118
OSWDataSharedPtrType chrom_annotation_
Chromatogram annotation data.
Definition: LayerDataBase.h:520
Identifications: Show labels (not sequences)
Definition: LayerDataBase.h:124
A container for features.
Definition: FeatureMap.h:98
DataFilter array providing some convenience functions.
Definition: DataFilters.h:51
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerDataBase.h:370
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const
FeatureMap FeatureMapType
Features.
Definition: LayerDataBase.h:146
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerDataBase.h:155
Definition: LayerDataBase.h:574
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerDataBase.h:149
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerDataBase.h:405
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerDataBase.h:204
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
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerDataBase.h:256
Management and storage of parameters / INI files.
Definition: Param.h:69
std::bitset< SIZE_OF_FLAGS > flags
Actual state of each flag.
Definition: LayerDataBase.h:129
PeakMap ExperimentType
Main data type (experiment)
Definition: LayerDataBase.h:158
boost::shared_ptr< const ExperimentType > ConstExperimentSharedPtrType
Definition: LayerDataBase.h:163
Holds all or partial information from an OSW file.
Definition: OSWData.h:304
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerDataBase.h:166
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum (1D view)
Definition: LayerDataBase.h:331
Class that stores the data for one layer.
Definition: LayerDataBase.h:97
bool annotateWithFilename(LayerDataBase &layer, LogWindow &log, const String &filename) const
Centralizes the file types recognized by FileHandler.
Definition: FileTypes.h:52
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const =0
LayerAnnotatorAMS(QWidget *gui_lock)
Definition: LayerDataBase.h:594
Flags
Flags that determine which information is shown.
Definition: LayerDataBase.h:115
void set_chromatogram_flag()
set the chromatogram flag
Definition: LayerDataBase.h:399
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
virtual bool annotateWorker_(LayerDataBase &layer, const String &filename, LogWindow &log) const
ExperimentType::SpectrumType cached_spectrum_
Current cached spectrum.
Definition: LayerDataBase.h:526
const Annotations1DContainer & getCurrentAnnotations() const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:292
LabelType
Label used in visualization.
Definition: LayerDataBase.h:132
const FileTypeList supported_types_
Definition: LayerDataBase.h:567
const String file_dialog_text_
Definition: LayerDataBase.h:568
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerDataBase.h:391
ExperimentSharedPtrType & getChromatogramData()
Returns a mutable reference to the current chromatogram data.
Definition: LayerDataBase.h:268
Container for annotations to content of Plot1DCanvas.
Definition: Annotations1DContainer.h:53
void setCurrentSpectrumIndex(Size index)
Set the index of the current spectrum (1D view)
Definition: LayerDataBase.h:337
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerDataBase.h:235
Annotations1DContainer & getAnnotations(Size spectrum_index)
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerDataBase.h:310
String name_
layer name
Definition: LayerDataBase.h:451
holds a vector of known file types, e.g. as a way to specify supported input formats
Definition: FileTypes.h:149
Representation of a peptide hit.
Definition: PeptideHit.h:55