LayerData Class Reference [Spectrum visualizaion widgets]

Class that stores the data for one layer. More...

#include <OpenMS/VISUAL/LayerData.h>

List of all members.

Public Member Functions
	LayerData ()
	Default constructor.
const ExperimentType::SpectrumType &	getCurrentSpectrum () const
	Returns a const reference to the current spectrum (1d view).
const FeatureMapSharedPtrType &	getFeatureMap () const
	Returns a const reference to the current feature data.
FeatureMapSharedPtrType &	getFeatureMap ()
	Returns a const reference to the current feature data.
const ConsensusMapSharedPtrType &	getConsensusMap () const
	Returns a const reference to the consensus feature data.
ConsensusMapSharedPtrType &	getConsensusMap ()
	Returns current consensus map (mutable).
const ExperimentSharedPtrType &	getPeakData () const
	Returns a const reference to the current peak data.
ExperimentSharedPtrType &	getPeakData ()
	Returns a mutable reference to the current peak data.
const ExperimentSharedPtrType &	getChromatogramData () const
	Returns a const reference to the current chromatogram data.
ExperimentSharedPtrType &	getChromatogramData ()
	Returns a mutable reference to the current chromatogram data.
const Annotations1DContainer &	getCurrentAnnotations () const
	Returns a const reference to the annotations of the current spectrum (1d view).
Annotations1DContainer &	getCurrentAnnotations ()
	Returns a mutable reference to the annotations of the current spectrum (1d view).
const Annotations1DContainer &	getAnnotations (Size spectrum_index) const
	Returns a const reference to the annotations of the current spectrum (1d view).
Annotations1DContainer &	getAnnotations (Size spectrum_index)
	Returns a mutable reference to the annotations of the current spectrum (1d view).
ExperimentType::SpectrumType &	getCurrentSpectrum ()
	Returns a mutable reference to the current spectrum (1d view).
Size	getCurrentSpectrumIndex () const
	Get the index of the current spectrum.
void	setCurrentSpectrumIndex (Size index)
	Set the index of the current spectrum.
bool	chromatogram_flag_set () const
	Check whether the current layer is a chromatogram.
void	set_chromatogram_flag ()
void	remove_chromatogram_flag ()
Public Attributes
bool	visible
	if this layer is visible
bool	flipped
	if this layer is flipped (1d mirror view)
DataType	type
	data type (peak or feature data)
String	name
	layer name
String	filename
	file name of the file the data comes from (if available)
std::vector < PeptideIdentification >	peptides
	peptide identifications
Param	param
	Layer parameters.
MultiGradient	gradient
	Gradient for 2D and 3D views.
DataFilters	filters
	Filters to apply before painting.
std::vector < Annotations1DContainer >	annotations_1d
	Annotations of all spectra of the experiment (1D view).
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.
LabelType	label
	Label type.
Private Attributes
FeatureMapSharedPtrType	features
	feature data
ConsensusMapSharedPtrType	consensus
	consensus feature data
ExperimentSharedPtrType	peaks
	peak data
ExperimentSharedPtrType	chromatograms
	chromatogram data
Size	current_spectrum_
	Index of the current spectrum.
Type definitions
enum	DataType {   DT_PEAK, DT_FEATURE, DT_CONSENSUS, DT_CHROMATOGRAM,   DT_IDENT, DT_UNKNOWN }
	Dataset types. More...
enum	Flags {   F_HULL, F_HULLS, F_UNASSIGNED, P_PRECURSORS,   P_PROJECTIONS, C_ELEMENTS, I_PEPTIDEMZ, SIZE_OF_FLAGS }
	Flags that determine which information is shown. More...
enum	LabelType {   L_NONE, L_INDEX, L_META_LABEL, L_ID,   L_ID_ALL, SIZE_OF_LABEL_TYPE }
	Label used in visualization. More...
typedef FeatureMap	FeatureMapType
	Features.
typedef boost::shared_ptr < FeatureMap<> >	FeatureMapSharedPtrType
	SharedPtr on feature map.
typedef ConsensusMap	ConsensusMapType
	consensus features
typedef boost::shared_ptr < ConsensusMap >	ConsensusMapSharedPtrType
	SharedPtr on consensus features.
typedef MSExperiment	ExperimentType
	Main data type (experiment).
typedef boost::shared_ptr < ExperimentType >	ExperimentSharedPtrType
	SharedPtr on MSExperiment.
std::bitset< SIZE_OF_FLAGS >	flags
	Actual state of each flag.
static const std::string	NamesOfLabelType [SIZE_OF_LABEL_TYPE]
	Label names.

---

Detailed Description

Class that stores the data for one layer.

---

Member Typedef Documentation

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.

---

Member Enumeration Documentation

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.

Enumerator:

F_HULL	Features: Overall convex hull.
F_HULLS	Features: Convex hulls of single mass traces.
F_UNASSIGNED	Features: Unassigned peptide hits.
P_PRECURSORS	Peaks: Mark precursor peaks of MS/MS scans.
P_PROJECTIONS	Peaks: Show projections.
C_ELEMENTS	Consensus features: Show elements.
I_PEPTIDEMZ	Identifications: m/z source.
SIZE_OF_FLAGS

enum LabelType

Label used in visualization.

Enumerator:

L_NONE	No label is displayed.
L_INDEX	The element number is used.
L_META_LABEL	The 'label' meta information is used.
L_ID	The best peptide hit of the first identification run is used.
L_ID_ALL	All peptide hits of the first identification run are used.
SIZE_OF_LABEL_TYPE

---

Constructor & Destructor Documentation

LayerData

(

)

[inline]

Default constructor.

References LayerData::annotations_1d.

---

Member Function Documentation

bool chromatogram_flag_set

(

)

const [inline]

Check whether the current layer is a chromatogram.

References LayerData::getPeakData().

Referenced by LayerData::remove_chromatogram_flag(), and TOPPViewBase::runTOPPTool_().

const Annotations1DContainer& getAnnotations

(

Size

spectrum_index

)

const [inline]

Returns a const reference to the annotations of the current spectrum (1d view).

References LayerData::annotations_1d.

Annotations1DContainer& getAnnotations

(

Size

spectrum_index

)

[inline]

Returns a mutable reference to the annotations of the current spectrum (1d view).

References LayerData::annotations_1d.

ExperimentSharedPtrType& getChromatogramData

(

)

[inline]

Returns a mutable reference to the current chromatogram data.

References LayerData::chromatograms.

const ExperimentSharedPtrType& getChromatogramData

(

)

const [inline]

Returns a const reference to the current chromatogram data.

References LayerData::chromatograms.

const ConsensusMapSharedPtrType& getConsensusMap

(

)

const [inline]

Returns a const reference to the consensus feature data.

References LayerData::consensus.

Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), and TOPPViewBase::runTOPPTool_().

ConsensusMapSharedPtrType& getConsensusMap

(

)

[inline]

Returns current consensus map (mutable).

References LayerData::consensus.

const Annotations1DContainer& getCurrentAnnotations

(

)

const [inline]

Returns a const reference to the annotations of the current spectrum (1d view).

References LayerData::annotations_1d, and LayerData::current_spectrum_.

Annotations1DContainer& getCurrentAnnotations

(

)

[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).

ExperimentType::SpectrumType& getCurrentSpectrum

(

)

[inline]

Returns a mutable reference to the current spectrum (1d view).

References LayerData::current_spectrum_, and LayerData::peaks.

Size getCurrentSpectrumIndex

(

)

const [inline]

Get the index of the current spectrum.

References LayerData::current_spectrum_.

Referenced by TOPPViewBase::runTOPPTool_().

const FeatureMapSharedPtrType& getFeatureMap

(

)

const [inline]

Returns a const reference to the current feature data.

References LayerData::features.

Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), and TOPPViewBase::runTOPPTool_().

FeatureMapSharedPtrType& getFeatureMap

(

)

[inline]

Returns a const reference to the current feature data.

References LayerData::features.

ExperimentSharedPtrType& getPeakData

(

)

[inline]

Returns a mutable reference to the current peak data.

References LayerData::peaks.

const ExperimentSharedPtrType& getPeakData

(

)

const [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().

void remove_chromatogram_flag

(

)

[inline]

References LayerData::chromatogram_flag_set(), and LayerData::getPeakData().

Referenced by TOPPViewBase::runTOPPTool_().

void set_chromatogram_flag

(

)

[inline]

References LayerData::getPeakData().

void setCurrentSpectrumIndex

(

Size

index

)

[inline]

Set the index of the current spectrum.

References LayerData::current_spectrum_.

---

Member Data Documentation

std::vector<Annotations1DContainer> annotations_1d

Annotations of all spectra of the experiment (1D view).

Referenced by LayerData::getAnnotations(), LayerData::getCurrentAnnotations(), and LayerData::LayerData().

ExperimentSharedPtrType chromatograms [private]

chromatogram data

Referenced by LayerData::getChromatogramData().

ConsensusMapSharedPtrType consensus [private]

consensus feature data

Referenced by LayerData::getConsensusMap().

Size current_spectrum_ [private]

Index of the current spectrum.

Referenced by LayerData::getCurrentAnnotations(), LayerData::getCurrentSpectrum(), LayerData::getCurrentSpectrumIndex(), and LayerData::setCurrentSpectrumIndex().

FeatureMapSharedPtrType features [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

layer name

Referenced by TOPPViewBase::addData(), TOPPViewBase::copyLayer(), TOPPViewBase::filterContextMenu(), TOPPViewBase::layerContextMenu(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::updateLayerBar().

const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE] [static]

Label names.

Referenced by TOPPViewBase::changeLabel(), and TOPPViewBase::TOPPViewBase().

Param param

Layer parameters.

Referenced by TOPPViewBase::loadFiles(), TOPPViewBase::setIntensityMode(), and TOPPViewBase::updateLayerBar().

ExperimentSharedPtrType peaks [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().