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_().
| 
 | inline | 
Returns a const reference to the annotations of the current spectrum (1d view)
References LayerData::annotations_1d.
| 
 | inline | 
Returns a mutable reference to the annotations of the current spectrum (1d view)
References LayerData::annotations_1d.
| 
 | inline | 
Returns a const reference to the current chromatogram data.
References LayerData::chromatograms.
| 
 | inline | 
Returns a mutable reference to the current chromatogram data.
References LayerData::chromatograms.
| 
 | inline | 
Returns a const reference to the consensus feature data.
References LayerData::consensus.
Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), and TOPPViewBase::runTOPPTool_().
| 
 | inline | 
Returns current consensus map (mutable)
References LayerData::consensus.
| 
 | inline | 
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_().
| 
 | inline | 
Returns a const reference to the current feature data.
References LayerData::features.
| 
 | inline | 
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().
| 
 | inline | 
Returns a mutable reference to the current peak data.
References LayerData::peaks.
| 
 | inline | 
References LayerData::chromatogram_flag_set(), and LayerData::getPeakData().
Referenced by TOPPViewBase::runTOPPTool_().
| 
 | inline | 
References LayerData::getPeakData().
| 
 | inline | 
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().
| 
 | private | 
chromatogram data
Referenced by LayerData::getChromatogramData().
| 
 | private | 
consensus feature data
Referenced by LayerData::getConsensusMap().
| 
 | private | 
Index of the current spectrum.
Referenced by LayerData::getCurrentAnnotations(), LayerData::getCurrentSpectrum(), LayerData::getCurrentSpectrumIndex(), and LayerData::setCurrentSpectrumIndex().
| 
 | 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().
| 
 | 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 |