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OpenMS
2.5.0
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38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
50 #include <boost/shared_ptr.hpp>
308 if ((*
peaks)[spectrum_idx].size() > 0)
310 return (*
peaks)[spectrum_idx];
316 return (*
peaks)[spectrum_idx];
336 this->
getPeakData()->metaValueExists(
"is_ion_mobility") &&
337 this->
getPeakData()->getMetaValue(
"is_ion_mobility").toBool();
342 peaks->setMetaValue(
"is_ion_mobility",
"true");
349 this->
getPeakData()->metaValueExists(
"is_dia_data") &&
350 this->
getPeakData()->getMetaValue(
"is_dia_data").toBool();
356 peaks->setMetaValue(
"is_dia_data",
"true");
370 this->
getPeakData()->metaValueExists(
"is_chromatogram") &&
371 this->
getPeakData()->getMetaValue(
"is_chromatogram").toBool();
377 peaks->setMetaValue(
"is_chromatogram",
"true");
385 peaks->removeMetaValue(
"is_chromatogram");
A gradient of multiple colors and arbitrary distances between colors.
Definition: MultiGradient.h:67
std::vector< PeptideIdentification > peptides
peptide identifications
Definition: LayerData.h:420
String name
layer name
Definition: LayerData.h:414
ODExperimentSharedPtrType on_disc_peaks
on disc peak data
Definition: LayerData.h:468
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:149
bool modified
Flag that indicates that the layer data was modified since loading it.
Definition: LayerData.h:441
static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]
Label names.
Definition: LayerData.h:131
The 'label' meta information is used.
Definition: LayerData.h:124
FeatureMapSharedPtrType features
feature data
Definition: LayerData.h:459
boost::shared_ptr< FeatureMap > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:137
Consensus feature data.
Definition: LayerData.h:97
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:143
Peaks: Show projections.
Definition: LayerData.h:109
void sortCurrentSpectrumByPosition()
Definition: LayerData.h:298
const Annotations1DContainer & getCurrentAnnotations() const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:268
boost::shared_ptr< const ExperimentType > ConstExperimentSharedPtrType
Definition: LayerData.h:151
No label is displayed.
Definition: LayerData.h:122
const ODExperimentSharedPtrType & getOnDiscPeakData() const
Returns a mutable reference to the on-disc data.
Definition: LayerData.h:250
A more convenient string class.
Definition: String.h:58
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerData.h:189
Annotations1DContainer & getAnnotations(Size spectrum_index)
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:286
DataFilters filters
Filters to apply before painting.
Definition: LayerData.h:429
Size current_spectrum_
Index of the current spectrum.
Definition: LayerData.h:474
std::vector< QColor > peak_colors_1d
Peak colors of the currently shown spectrum.
Definition: LayerData.h:435
ConsensusMap ConsensusMapType
consensus features
Definition: LayerData.h:140
bool flipped
if this layer is flipped (1d mirror view)
Definition: LayerData.h:408
const ExperimentSharedPtrType & getChromatogramData() const
Returns a mutable reference to the current chromatogram data.
Definition: LayerData.h:256
Flags
Flags that determine which information is shown.
Definition: LayerData.h:103
Identifications: Show labels (not sequences)
Definition: LayerData.h:112
void setOnDiscPeakData(ODExperimentSharedPtrType p)
Set the current on-disc data.
Definition: LayerData.h:244
LayerData()
Default constructor.
Definition: LayerData.h:159
MSSpectrum SpectrumType
Spectrum Type.
Definition: MSExperiment.h:101
Feature data.
Definition: LayerData.h:96
MultiGradient gradient
Gradient for 2D and 3D views.
Definition: LayerData.h:426
The element number is used.
Definition: LayerData.h:123
void set_chromatogram_flag()
set the chromatogram flag
Definition: LayerData.h:375
const ConstExperimentSharedPtrType getPeakData() const
Returns a const reference to the current in-memory peak data.
Undefined data type indicating an error.
Definition: LayerData.h:99
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Spectrum profile or centroided data.
Definition: LayerData.h:94
Definition: LayerData.h:113
Features: Unassigned peptide hits.
Definition: LayerData.h:107
Peptide identification data.
Definition: LayerData.h:98
String filename
file name of the file the data comes from (if available)
Definition: LayerData.h:417
void remove_chromatogram_flag()
remove the chromatogram flag
Definition: LayerData.h:381
void updateRanges()
Update ranges of all data structures.
const ExperimentType::SpectrumType & getCurrentSpectrum() const
Returns a const reference to the current spectrum (1D view)
Class that stores the data for one layer.
Definition: LayerData.h:85
ConsensusMapSharedPtrType & getConsensusMap()
Returns current consensus map (mutable)
Definition: LayerData.h:207
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerData.h:201
ExperimentSharedPtrType & getChromatogramData()
Returns a mutable reference to the current chromatogram data.
Definition: LayerData.h:262
void updateCache_()
Update current cached spectrum for easy retrieval.
void updatePeptideHitAnnotations_(PeptideHit &hit)
updates the PeakAnnotations in the current PeptideHit with manually changed annotations
Identifications: m/z source.
Definition: LayerData.h:111
const ExperimentSharedPtrType & getPeakDataMuteable()
Returns a mutable reference to the current in-memory peak data.
Definition: LayerData.h:232
FeatureMap FeatureMapType
Features.
Definition: LayerData.h:134
ExperimentSharedPtrType peaks
peak data
Definition: LayerData.h:465
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
Consensus features: Show elements.
Definition: LayerData.h:110
ExperimentType::SpectrumType cached_spectrum_
Current cached spectrum.
Definition: LayerData.h:477
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum (1D view)
Definition: LayerData.h:320
bool visible
if this layer is visible
Definition: LayerData.h:405
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerData.h:367
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
bool modifiable
Flag that indicates if the layer data can be modified (so far used for features only)
Definition: LayerData.h:438
A container for consensus elements.
Definition: ConsensusMap.h:79
void sortByPosition()
Lexicographically sorts the peaks by their position.
void removePeakAnnotationsFromPeptideHit(const std::vector< Annotation1DItem * > &selected_annotations)
remove peak annotations in the given list from the currently active PeptideHit
std::vector< Annotations1DContainer > annotations_1d
Annotations of all spectra of the experiment (1D view)
Definition: LayerData.h:432
int peptide_id_index
Selected peptide id and hit index (-1 if none is selected)
Definition: LayerData.h:447
The best peptide hit of the first identification run is used.
Definition: LayerData.h:125
PeakMap ExperimentType
Main data type (experiment)
Definition: LayerData.h:146
Param param
Layer parameters.
Definition: LayerData.h:423
Features: Convex hulls of single mass traces.
Definition: LayerData.h:106
A container for features.
Definition: FeatureMap.h:95
DataFilter array providing some convenience functions.
Definition: DataFilters.h:50
bool isIonMobilityData() const
Check whether the current layer should be represented as ion mobility.
Definition: LayerData.h:333
FeatureMapSharedPtrType & getFeatureMap()
Returns a const reference to the current feature data.
Definition: LayerData.h:195
void labelAsDIAData()
Label the current layer as DIA (SWATH-MS) data.
Definition: LayerData.h:354
All peptide hits of the first identification run are used.
Definition: LayerData.h:126
std::bitset< SIZE_OF_FLAGS > flags
Actual state of each flag.
Definition: LayerData.h:117
ExperimentSharedPtrType chromatograms
chromatogram data
Definition: LayerData.h:471
int peptide_hit_index
Definition: LayerData.h:448
void labelAsIonMobilityData() const
Definition: LayerData.h:340
LabelType label
Label type.
Definition: LayerData.h:444
Definition: LayerData.h:127
DataType
Definition: LayerData.h:92
Management and storage of parameters / INI files.
Definition: Param.h:73
void setCurrentSpectrumIndex(Size index)
Set the index of the current spectrum (1D view)
Definition: LayerData.h:326
void setPeakData(ExperimentSharedPtrType p)
Set the current in-memory peak data.
Definition: LayerData.h:237
ConsensusMapSharedPtrType consensus
consensus feature data
Definition: LayerData.h:462
DataType type
data type (peak or feature data)
Definition: LayerData.h:411
LabelType
Label used in visualization.
Definition: LayerData.h:120
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
const Annotations1DContainer & getAnnotations(Size spectrum_index) const
Returns a const reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:280
Features: Overall convex hull.
Definition: LayerData.h:105
boost::shared_ptr< OnDiscMSExperiment > ODExperimentSharedPtrType
SharedPtr on On-Disc MSExperiment.
Definition: LayerData.h:154
Annotations1DContainer & getCurrentAnnotations()
Returns a mutable reference to the annotations of the current spectrum (1D view)
Definition: LayerData.h:274
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerData.h:108
Container for annotations to content of Spectrum1DCanvas.
Definition: Annotations1DContainer.h:53
bool isDIAData() const
Check whether the current layer contains DIA (SWATH-MS) data.
Definition: LayerData.h:346
Chromatogram data.
Definition: LayerData.h:95
void synchronizePeakAnnotations()
Representation of a peptide hit.
Definition: PeptideHit.h:54