35 #ifndef OPENMS_VISUAL_LAYERDATA_H
36 #define OPENMS_VISUAL_LAYERDATA_H
46 #include <boost/shared_ptr.hpp>
88 std::bitset<SIZE_OF_FLAGS>
flags;
248 this->
getPeakData()->metaValueExists(
"is_chromatogram") &&
249 this->
getPeakData()->getMetaValue(
"is_chromatogram").toBool();
255 this->
getPeakData()->setMetaValue(
"is_chromatogram",
"true");
263 this->
getPeakData()->removeMetaValue(
"is_chromatogram");
Flags
Flags that determine which information is shown.
Definition: LayerData.h:75
Consensus features: Show elements.
Definition: LayerData.h:82
static const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]
Label names.
Definition: LayerData.h:102
Features: Convex hulls of single mass traces.
Definition: LayerData.h:78
MSSpectrum< PeakType > SpectrumType
Spectrum Type.
Definition: MSExperiment.h:91
FeatureMapSharedPtrType features
feature data
Definition: LayerData.h:308
const Annotations1DContainer & getCurrentAnnotations() const
Returns a const reference to the annotations of the current spectrum (1d view)
Definition: LayerData.h:200
std::bitset< SIZE_OF_FLAGS > flags
Actual state of each flag.
Definition: LayerData.h:88
Features: Overall convex hull.
Definition: LayerData.h:77
Definition: LayerData.h:84
A more convenient string class.
Definition: String.h:56
LabelType label
Label type.
Definition: LayerData.h:304
const ConsensusMapSharedPtrType & getConsensusMap() const
Returns a const reference to the consensus feature data.
Definition: LayerData.h:164
const FeatureMapSharedPtrType & getFeatureMap() const
Returns a const reference to the current feature data.
Definition: LayerData.h:152
DataType
Dataset types.
Definition: LayerData.h:64
bool modified
Flag that indicates that the layer data was modified since loading it.
Definition: LayerData.h:301
FeatureMapSharedPtrType & getFeatureMap()
Returns a const reference to the current feature data.
Definition: LayerData.h:158
void remove_chromatogram_flag()
Definition: LayerData.h:259
ExperimentType::SpectrumType & getCurrentSpectrum()
Returns a mutable reference to the current spectrum (1d view)
Definition: LayerData.h:224
MSExperiment ExperimentType
Main data type (experiment)
Definition: LayerData.h:117
All peptide hits of the first identification run are used.
Definition: LayerData.h:97
Size getCurrentSpectrumIndex() const
Get the index of the current spectrum.
Definition: LayerData.h:230
std::ostream & operator<<(std::ostream &os, const ItraqQuantifier::ItraqQuantifierStats &stats)
A container for consensus elements.
Definition: ConsensusMap.h:60
Undefined data type indicating an error.
Definition: LayerData.h:71
Peptide identification data.
Definition: LayerData.h:70
Annotations1DContainer & getCurrentAnnotations()
Returns a mutable reference to the annotations of the current spectrum (1d view)
Definition: LayerData.h:206
boost::shared_ptr< ExperimentType > ExperimentSharedPtrType
SharedPtr on MSExperiment.
Definition: LayerData.h:120
Chromatogram data.
Definition: LayerData.h:69
std::vector< Annotations1DContainer > annotations_1d
Annotations of all spectra of the experiment (1D view)
Definition: LayerData.h:295
ExperimentSharedPtrType & getPeakData()
Returns a mutable reference to the current peak data.
Definition: LayerData.h:182
The 'label' meta information is used.
Definition: LayerData.h:95
String name
layer name
Definition: LayerData.h:277
bool flipped
if this layer is flipped (1d mirror view)
Definition: LayerData.h:271
ExperimentSharedPtrType & getChromatogramData()
Returns a mutable reference to the current chromatogram data.
Definition: LayerData.h:194
ExperimentSharedPtrType chromatograms
chromatogram data
Definition: LayerData.h:317
Param param
Layer parameters.
Definition: LayerData.h:286
const ExperimentSharedPtrType & getPeakData() const
Returns a const reference to the current peak data.
Definition: LayerData.h:176
Feature data.
Definition: LayerData.h:67
Annotations1DContainer & getAnnotations(Size spectrum_index)
Returns a mutable reference to the annotations of the current spectrum (1d view)
Definition: LayerData.h:218
boost::shared_ptr< ConsensusMap > ConsensusMapSharedPtrType
SharedPtr on consensus features.
Definition: LayerData.h:114
Consensus feature data.
Definition: LayerData.h:68
ConsensusMapSharedPtrType & getConsensusMap()
Returns current consensus map (mutable)
Definition: LayerData.h:170
String filename
file name of the file the data comes from (if available)
Definition: LayerData.h:280
const ExperimentSharedPtrType & getChromatogramData() const
Returns a const reference to the current chromatogram data.
Definition: LayerData.h:188
Size current_spectrum_
Index of the current spectrum.
Definition: LayerData.h:320
void set_chromatogram_flag()
Definition: LayerData.h:253
ExperimentSharedPtrType peaks
peak data
Definition: LayerData.h:314
boost::shared_ptr< FeatureMap<> > FeatureMapSharedPtrType
SharedPtr on feature map.
Definition: LayerData.h:108
ConsensusMap ConsensusMapType
consensus features
Definition: LayerData.h:111
const Annotations1DContainer & getAnnotations(Size spectrum_index) const
Returns a const reference to the annotations of the current spectrum (1d view)
Definition: LayerData.h:212
bool chromatogram_flag_set() const
Check whether the current layer is a chromatogram.
Definition: LayerData.h:245
Management and storage of parameters / INI files.
Definition: Param.h:69
Representation of a mass spectrometry experiment.
Definition: MSExperiment.h:68
Peaks: Show projections.
Definition: LayerData.h:81
bool modifiable
Flag that indicates if the layer data can be modified (so far used for features only) ...
Definition: LayerData.h:298
Peaks: Mark precursor peaks of MS/MS scans.
Definition: LayerData.h:80
void setCurrentSpectrumIndex(Size index)
Set the index of the current spectrum.
Definition: LayerData.h:236
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
std::vector< PeptideIdentification > peptides
peptide identifications
Definition: LayerData.h:283
DataFilters filters
Filters to apply before painting.
Definition: LayerData.h:292
LayerData()
Default constructor.
Definition: LayerData.h:125
DataType type
data type (peak or feature data)
Definition: LayerData.h:274
LabelType
Label used in visualization.
Definition: LayerData.h:91
The best peptide hit of the first identification run is used.
Definition: LayerData.h:96
Spectrum profile or centroided data.
Definition: LayerData.h:66
const ExperimentType::SpectrumType & getCurrentSpectrum() const
Returns a const reference to the current spectrum (1d view)
DataFilter array providing some convenience functions.
Definition: DataFilters.h:53
A gradient of multiple colors and arbitrary distances between colors.
Definition: MultiGradient.h:65
The element number is used.
Definition: LayerData.h:94
MultiGradient gradient
Gradient for 2D and 3D views.
Definition: LayerData.h:289
Container for annotations to content of Spectrum1DCanvas.
Definition: Annotations1DContainer.h:54
No label is displayed.
Definition: LayerData.h:93
ConsensusMapSharedPtrType consensus
consensus feature data
Definition: LayerData.h:311
Features: Unassigned peptide hits.
Definition: LayerData.h:79
bool visible
if this layer is visible
Definition: LayerData.h:268
Definition: LayerData.h:98
Class that stores the data for one layer.
Definition: LayerData.h:58
Identifications: m/z source.
Definition: LayerData.h:83
FeatureMap FeatureMapType
Features.
Definition: LayerData.h:105