Class that stores the data for one layer. More...
#include <OpenMS/VISUAL/LayerData.h>
Public Member Functions | |
| LayerData () | |
| Default constructor. More... | |
| const ExperimentType::SpectrumType & | getCurrentSpectrum () const |
| Returns a const reference to the current spectrum (1d view) More... | |
| const FeatureMapSharedPtrType & | getFeatureMap () const |
| Returns a const reference to the current feature data. More... | |
| FeatureMapSharedPtrType & | getFeatureMap () |
| Returns a const reference to the current feature data. More... | |
| const ConsensusMapSharedPtrType & | getConsensusMap () const |
| Returns a const reference to the consensus feature data. More... | |
| ConsensusMapSharedPtrType & | getConsensusMap () |
| Returns current consensus map (mutable) More... | |
| const ExperimentSharedPtrType & | getPeakData () const |
| Returns a const reference to the current peak data. More... | |
| ExperimentSharedPtrType & | getPeakData () |
| Returns a mutable reference to the current peak data. More... | |
| const ExperimentSharedPtrType & | getChromatogramData () const |
| Returns a const reference to the current chromatogram data. More... | |
| ExperimentSharedPtrType & | getChromatogramData () |
| Returns a mutable reference to the current chromatogram data. More... | |
| const Annotations1DContainer & | getCurrentAnnotations () const |
| Returns a const reference to the annotations of the current spectrum (1d view) More... | |
| Annotations1DContainer & | getCurrentAnnotations () |
| Returns a mutable reference to the annotations of the current spectrum (1d view) More... | |
| const Annotations1DContainer & | getAnnotations (Size spectrum_index) const |
| Returns a const reference to the annotations of the current spectrum (1d view) More... | |
| Annotations1DContainer & | getAnnotations (Size spectrum_index) |
| Returns a mutable reference to the annotations of the current spectrum (1d view) More... | |
| ExperimentType::SpectrumType & | getCurrentSpectrum () |
| Returns a mutable reference to the current spectrum (1d view) More... | |
| Size | getCurrentSpectrumIndex () const |
| Get the index of the current spectrum. More... | |
| void | setCurrentSpectrumIndex (Size index) |
| Set the index of the current spectrum. More... | |
| bool | chromatogram_flag_set () const |
| Check whether the current layer is a chromatogram. More... | |
| void | set_chromatogram_flag () |
| void | remove_chromatogram_flag () |
Public Attributes | |
| bool | visible |
| if this layer is visible More... | |
| bool | flipped |
| if this layer is flipped (1d mirror view) More... | |
| DataType | type |
| data type (peak or feature data) More... | |
| String | name |
| layer name More... | |
| String | filename |
| file name of the file the data comes from (if available) More... | |
| std::vector < PeptideIdentification > | peptides |
| peptide identifications More... | |
| Param | param |
| Layer parameters. More... | |
| MultiGradient | gradient |
| Gradient for 2D and 3D views. More... | |
| DataFilters | filters |
| Filters to apply before painting. More... | |
| std::vector < Annotations1DContainer > | annotations_1d |
| Annotations of all spectra of the experiment (1D view) More... | |
| bool | modifiable |
| Flag that indicates if the layer data can be modified (so far used for features only) More... | |
| bool | modified |
| Flag that indicates that the layer data was modified since loading it. More... | |
| LabelType | label |
| Label type. More... | |
Private Attributes | |
| FeatureMapSharedPtrType | features |
| feature data More... | |
| ConsensusMapSharedPtrType | consensus |
| consensus feature data More... | |
| ExperimentSharedPtrType | peaks |
| peak data More... | |
| ExperimentSharedPtrType | chromatograms |
| chromatogram data More... | |
| Size | current_spectrum_ |
| Index of the current spectrum. More... | |
Class that stores the data for one layer.
| typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType |
SharedPtr on consensus features.
| typedef ConsensusMap ConsensusMapType |
consensus features
| typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType |
SharedPtr on MSExperiment.
| typedef MSExperiment ExperimentType |
Main data type (experiment)
| typedef boost::shared_ptr<FeatureMap<> > FeatureMapSharedPtrType |
SharedPtr on feature map.
| typedef FeatureMap FeatureMapType |
Features.
| enum DataType |
Dataset types.
| Enumerator | |
|---|---|
| DT_PEAK |
Spectrum profile or centroided data. |
| DT_FEATURE |
Feature data. |
| DT_CONSENSUS |
Consensus feature data. |
| DT_CHROMATOGRAM |
Chromatogram data. |
| DT_IDENT |
Peptide identification data. |
| DT_UNKNOWN |
Undefined data type indicating an error. |
| enum Flags |
Flags that determine which information is shown.
| enum LabelType |
Label used in visualization.
|
inline |
Default constructor.
References LayerData::annotations_1d.
|
inline |
Check whether the current layer is a chromatogram.
References LayerData::getPeakData().
Referenced by LayerData::remove_chromatogram_flag(), and TOPPViewBase::runTOPPTool_().
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inline |
Returns a const reference to the annotations of the current spectrum (1d view)
References LayerData::annotations_1d.
|
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Returns a mutable reference to the annotations of the current spectrum (1d view)
References LayerData::annotations_1d.
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Returns a const reference to the current chromatogram data.
References LayerData::chromatograms.
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inline |
Returns a mutable reference to the current chromatogram data.
References LayerData::chromatograms.
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inline |
Returns a const reference to the consensus feature data.
References LayerData::consensus.
Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), and TOPPViewBase::runTOPPTool_().
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inline |
Returns current consensus map (mutable)
References LayerData::consensus.
|
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Returns a const reference to the annotations of the current spectrum (1d view)
References LayerData::annotations_1d, and LayerData::current_spectrum_.
|
inline |
Returns a mutable reference to the annotations of the current spectrum (1d view)
References LayerData::annotations_1d, and LayerData::current_spectrum_.
| const ExperimentType::SpectrumType& getCurrentSpectrum | ( | ) | const |
Returns a const reference to the current spectrum (1d view)
|
inline |
Returns a mutable reference to the current spectrum (1d view)
References LayerData::current_spectrum_, and LayerData::peaks.
|
inline |
Get the index of the current spectrum.
References LayerData::current_spectrum_.
Referenced by TOPPViewBase::runTOPPTool_().
|
inline |
Returns a const reference to the current feature data.
References LayerData::features.
Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), and TOPPViewBase::runTOPPTool_().
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inline |
Returns a const reference to the current feature data.
References LayerData::features.
|
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Returns a const reference to the current peak data.
References LayerData::peaks.
Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateWithID(), LayerData::chromatogram_flag_set(), TOPPViewBase::copyLayer(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerZoomChanged(), LayerData::remove_chromatogram_flag(), TOPPViewBase::runTOPPTool_(), LayerData::set_chromatogram_flag(), TOPPViewBase::showCurrentPeaksAs2D(), and TOPPViewBase::showCurrentPeaksAs3D().
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Returns a mutable reference to the current peak data.
References LayerData::peaks.
|
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References LayerData::chromatogram_flag_set(), and LayerData::getPeakData().
Referenced by TOPPViewBase::runTOPPTool_().
|
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References LayerData::getPeakData().
|
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Set the index of the current spectrum.
References LayerData::current_spectrum_.
| std::vector<Annotations1DContainer> annotations_1d |
Annotations of all spectra of the experiment (1D view)
Referenced by LayerData::getAnnotations(), LayerData::getCurrentAnnotations(), and LayerData::LayerData().
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private |
chromatogram data
Referenced by LayerData::getChromatogramData().
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private |
consensus feature data
Referenced by LayerData::getConsensusMap().
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private |
Index of the current spectrum.
Referenced by LayerData::getCurrentAnnotations(), LayerData::getCurrentSpectrum(), LayerData::getCurrentSpectrumIndex(), and LayerData::setCurrentSpectrumIndex().
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private |
feature data
Referenced by LayerData::getFeatureMap().
| String filename |
file name of the file the data comes from (if available)
Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), TOPPViewBase::getFilenamesOfOpenFiles_(), TOPPViewBase::showCurrentPeaksAs2D(), and TOPPViewBase::showCurrentPeaksAs3D().
| DataFilters filters |
Filters to apply before painting.
Referenced by TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), and TOPPViewBase::updateFilterBar().
| std::bitset<SIZE_OF_FLAGS> flags |
Actual state of each flag.
| bool flipped |
if this layer is flipped (1d mirror view)
Referenced by TOPPViewBase::updateLayerBar().
| MultiGradient gradient |
Gradient for 2D and 3D views.
| LabelType label |
Label type.
Referenced by TOPPViewBase::updateToolBar().
| bool modifiable |
Flag that indicates if the layer data can be modified (so far used for features only)
| bool modified |
Flag that indicates that the layer data was modified since loading it.
Referenced by TOPPViewBase::updateLayerBar().
| String name |
|
static |
Label names.
Referenced by TOPPViewBase::changeLabel(), and TOPPViewBase::TOPPViewBase().
| Param param |
Layer parameters.
Referenced by TOPPViewBase::loadFiles(), TOPPViewBase::setIntensityMode(), and TOPPViewBase::updateLayerBar().
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private |
peak data
Referenced by LayerData::getCurrentSpectrum(), and LayerData::getPeakData().
| std::vector<PeptideIdentification> peptides |
peptide identifications
Referenced by TOPPViewBase::copyLayer().
| DataType type |
data type (peak or feature data)
Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::updateToolBar().
| bool visible |
if this layer is visible
Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::editMetadata(), TOPPViewBase::layerVisibilityChange(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::showTOPPDialog_(), and TOPPViewBase::updateLayerBar().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5 |