LayerData Class Reference

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

#include <OpenMS/VISUAL/LayerData.h>

Collaboration diagram for LayerData:

Type definitions
enum	DataType {   DT_PEAK , DT_CHROMATOGRAM , DT_FEATURE , DT_CONSENSUS ,   DT_IDENT , DT_UNKNOWN }
enum	Flags {   F_HULL , F_HULLS , F_UNASSIGNED , P_PRECURSORS ,   P_PROJECTIONS , C_ELEMENTS , I_PEPTIDEMZ , I_LABELS ,   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. More...
typedef boost::shared_ptr< FeatureMap >	FeatureMapSharedPtrType
	SharedPtr on feature map. More...
typedef ConsensusMap	ConsensusMapType
	consensus features More...
typedef boost::shared_ptr< ConsensusMap >	ConsensusMapSharedPtrType
	SharedPtr on consensus features. More...
typedef PeakMap	ExperimentType
	Main data type (experiment) More...
typedef boost::shared_ptr< ExperimentType >	ExperimentSharedPtrType
	SharedPtr on MSExperiment. More...
typedef boost::shared_ptr< const ExperimentType >	ConstExperimentSharedPtrType
typedef boost::shared_ptr< OnDiscMSExperiment >	ODExperimentSharedPtrType
	SharedPtr on On-Disc MSExperiment. More...
typedef boost::shared_ptr< OSWData >	OSWDataSharedPtrType
	SharedPtr on OSWData. More...
std::bitset< SIZE_OF_FLAGS >	flags
	Actual state of each flag. More...
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	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...
std::vector< QColor >	peak_colors_1d
	Peak colors of the currently shown spectrum. 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...
int	peptide_id_index
	Selected peptide id and hit index (-1 if none is selected) More...
int	peptide_hit_index
static const std::string	NamesOfLabelType [SIZE_OF_LABEL_TYPE]
	Label names. More...
String	name_
	layer name More...
FeatureMapSharedPtrType	features_
	feature data More...
ConsensusMapSharedPtrType	consensus_map_
	consensus feature data More...
ExperimentSharedPtrType	peak_map_
	peak data More...
ODExperimentSharedPtrType	on_disc_peaks
	on disc peak data More...
ExperimentSharedPtrType	chromatogram_map_
	chromatogram data More...
OSWDataSharedPtrType	chrom_annotation_
	Chromatogram annotation data. More...
Size	current_spectrum_idx_
	Index of the current spectrum. More...
ExperimentType::SpectrumType	cached_spectrum_
	Current cached spectrum. More...
	LayerData ()
	Default constructor. More...
	LayerData (const LayerData &ld)=delete
	no Copy-ctor (should not be needed) More...
LayerData &	operator= (const LayerData &ld)=delete
	no assignment operator (should not be needed) More...
	LayerData (LayerData &&ld)=default
	move Ctor More...
LayerData &	operator= (LayerData &&ld)=default
	move assignment 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 ConstExperimentSharedPtrType	getPeakData () const
	Returns a const reference to the current in-memory peak data. More...
const ExperimentSharedPtrType &	getPeakDataMuteable ()
	Returns a mutable reference to the current in-memory peak data. More...
void	setPeakData (ExperimentSharedPtrType p)
	Set the current in-memory peak data. More...
void	setOnDiscPeakData (ODExperimentSharedPtrType p)
	Set the current on-disc data. More...
const ODExperimentSharedPtrType &	getOnDiscPeakData () const
	Returns a mutable reference to the on-disc data. More...
const ExperimentSharedPtrType &	getChromatogramData () const
	Returns a mutable reference to the current chromatogram data. More...
ExperimentSharedPtrType &	getChromatogramData ()
	Returns a mutable reference to the current chromatogram data. More...
OSWDataSharedPtrType &	getChromatogramAnnotation ()
const OSWDataSharedPtrType &	getChromatogramAnnotation () const
void	setChromatogramAnnotation (OSWData &&data)
	add annotation from an OSW sqlite file. More...
bool	annotate (const std::vector< PeptideIdentification > &identifications, const std::vector< ProteinIdentification > &protein_identifications)
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...
const ExperimentType::SpectrumType &	getCurrentSpectrum () const
	Returns a const reference to the current spectrum (1D view) More...
void	sortCurrentSpectrumByPosition ()
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. More...
Size	getCurrentSpectrumIndex () const
	Get the index of the current spectrum (1D view) More...
void	setCurrentSpectrumIndex (Size index)
	Set the index of the current spectrum (1D view) More...
ExperimentSharedPtrType	getFullChromData ()
bool	isIonMobilityData () const
	Check whether the current layer should be represented as ion mobility. More...
void	labelAsIonMobilityData () const
bool	isDIAData () const
	Check whether the current layer contains DIA (SWATH-MS) data. More...
void	labelAsDIAData ()
	Label the current layer as DIA (SWATH-MS) data. More...
bool	chromatogram_flag_set () const
	Check whether the current layer is a chromatogram. More...
void	set_chromatogram_flag ()
	set the chromatogram flag More...
void	remove_chromatogram_flag ()
	remove the chromatogram flag More...
void	updateRanges ()
	Update ranges of all data structures. More...
float	getMinIntensity () const
	Returns the minimum intensity of the internal data, depending on type. More...
float	getMaxIntensity () const
	Returns the maximum intensity of the internal data, depending on type. More...
void	synchronizePeakAnnotations ()
void	removePeakAnnotationsFromPeptideHit (const std::vector< Annotation1DItem * > &selected_annotations)
	remove peak annotations in the given list from the currently active PeptideHit More...
const String &	getName () const
void	setName (const String &new_name)
String	getDecoratedName () const
	get name augmented with attributes, e.g. [flipped], or '*' if modified More...
void	updateCache_ ()
	Update current cached spectrum for easy retrieval. More...
void	updatePeptideHitAnnotations_ (PeptideHit &hit)
	updates the PeakAnnotations in the current PeptideHit with manually changed annotations More...

Detailed Description

Class that stores the data for one layer.

The data for a layer can be peak data, feature data (feature, consensus), chromatogram or peptide identification data.

For 2D and 3D data, the data is generally accessible through getPeakData() while features are accessible through getFeatureMap() and getConsensusMap(). For 1D data, the current spectrum must be accessed through getCurrentSpectrum().

Peak data is stored using a shared pointer to an MSExperiment data structure as well as a shared pointer to a OnDiscMSExperiment data structure. Note that the actual data may not be in memory as this is not efficient for large files and therefore may have to be retrieved from disk on-demand.

Note

The spectrum for 1D viewing retrieved through getCurrentSpectrum() is a copy of the actual raw data and *different* from the one retrieved through getPeakData()[index]. Any changes to applied to getCurrentSpectrum() are non-persistent and will be gone the next time the cache is updated. Persistent changes can be applied to getPeakDataMuteable() and will be available on the next cache update.

Layer is mainly used as a member variable of PlotCanvas which holds a vector of LayerData objects.

Member Typedef Documentation

ConsensusMapSharedPtrType

typedef boost::shared_ptr<ConsensusMap> ConsensusMapSharedPtrType

SharedPtr on consensus features.

ConsensusMapType

typedef ConsensusMap ConsensusMapType

consensus features

ConstExperimentSharedPtrType

typedef boost::shared_ptr<const ExperimentType> ConstExperimentSharedPtrType

ExperimentSharedPtrType

typedef boost::shared_ptr<ExperimentType> ExperimentSharedPtrType

SharedPtr on MSExperiment.

ExperimentType

typedef PeakMap ExperimentType

Main data type (experiment)

FeatureMapSharedPtrType

typedef boost::shared_ptr<FeatureMap > FeatureMapSharedPtrType

SharedPtr on feature map.

FeatureMapType

typedef FeatureMap FeatureMapType

Features.

ODExperimentSharedPtrType

typedef boost::shared_ptr<OnDiscMSExperiment> ODExperimentSharedPtrType

SharedPtr on On-Disc MSExperiment.

OSWDataSharedPtrType

typedef boost::shared_ptr<OSWData> OSWDataSharedPtrType

SharedPtr on OSWData.

Member Enumeration Documentation

DataType

enum DataType

Dataset types. Order in the enum determines the order in which layer types are drawn.

Enumerator
DT_PEAK	Spectrum profile or centroided data.
DT_CHROMATOGRAM	Chromatogram data.
DT_FEATURE	Feature data.
DT_CONSENSUS	Consensus feature data.
DT_IDENT	Peptide identification data.
DT_UNKNOWN	Undefined data type indicating an error.

Flags

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.
I_LABELS	Identifications: Show labels (not sequences)
SIZE_OF_FLAGS

LabelType

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() [1/3]

LayerData

(

)

Default constructor.

LayerData() [2/3]

LayerData ( const LayerData &  ld )

delete

no Copy-ctor (should not be needed)

LayerData() [3/3]

LayerData ( LayerData &&  ld )

default

move Ctor

Member Function Documentation

annotate()

bool annotate	(	const std::vector< PeptideIdentification > &	identifications,
		const std::vector< ProteinIdentification > &	protein_identifications
	)

add peptide identifications to the layer Only supported for DT_PEAK, DT_FEATURE and DT_CONSENSUS. Will return false otherwise.

chromatogram_flag_set()

bool chromatogram_flag_set ( ) const

inline

Check whether the current layer is a chromatogram.

This is needed because type will *not* distinguish properly between chromatogram and spectra data. This is due to the fact that we store chromatograms for display in 1D in a data layer using MSSpectrum and so the layer looks like PEAK data to tools.

Referenced by TOPPViewBase::layerZoomChanged(), and TOPPViewBase::runTOPPTool_().

getAnnotations() [1/2]

Annotations1DContainer& getAnnotations ( Size  spectrum_index )

inline

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

getAnnotations() [2/2]

const Annotations1DContainer& getAnnotations ( Size  spectrum_index ) const

inline

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

getChromatogramAnnotation() [1/2]

OSWDataSharedPtrType& getChromatogramAnnotation

(

)

get annotation (e.g. to build a hierachical ID View) Not const, because we might have incomplete data, which needs to be loaded from sql source

getChromatogramAnnotation() [2/2]

const OSWDataSharedPtrType& getChromatogramAnnotation

(

)

const

get annotation (e.g. to build a hierachical ID View) Not actually const (only the pointer, not the data), because we might have incomplete data, which needs to be loaded from sql source

getChromatogramData() [1/2]

ExperimentSharedPtrType& getChromatogramData ( )

inline

Returns a mutable reference to the current chromatogram data.

getChromatogramData() [2/2]

const ExperimentSharedPtrType& getChromatogramData ( ) const

inline

Returns a mutable reference to the current chromatogram data.

Referenced by TOPPViewBase::updateMenu().

getConsensusMap() [1/2]

ConsensusMapSharedPtrType& getConsensusMap ( )

inline

Returns current consensus map (mutable)

getConsensusMap() [2/2]

const ConsensusMapSharedPtrType& getConsensusMap ( ) const

inline

Returns a const reference to the consensus feature data.

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

getCurrentAnnotations() [1/2]

Annotations1DContainer& getCurrentAnnotations ( )

inline

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

getCurrentAnnotations() [2/2]

const Annotations1DContainer& getCurrentAnnotations ( ) const

inline

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

getCurrentSpectrum()

const ExperimentType::SpectrumType& getCurrentSpectrum

(

)

const

Returns a const reference to the current spectrum (1D view)

Note

Only use this function to access the current spectrum for the 1D view

Referenced by TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

getCurrentSpectrumIndex()

Size getCurrentSpectrumIndex ( ) const

inline

Get the index of the current spectrum (1D view)

Referenced by TOPPViewBase::runTOPPTool_(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

getDecoratedName()

String getDecoratedName

(

)

const

get name augmented with attributes, e.g. [flipped], or '*' if modified

getFeatureMap() [1/2]

FeatureMapSharedPtrType& getFeatureMap ( )

inline

Returns a const reference to the current feature data.

getFeatureMap() [2/2]

const FeatureMapSharedPtrType& getFeatureMap ( ) const

inline

Returns a const reference to the current feature data.

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

getFullChromData()

ExperimentSharedPtrType getFullChromData ( )

inline

get the full chromExperiment Could be backed up in layer.getChromatogramData() (if layer.getPeakDataMuteable() shows converted chroms already) ... or layer.getChromatogramData() is empty and thus layer.getPeakDataMuteable() is the original chrom data

getMaxIntensity()

float getMaxIntensity

(

)

const

Returns the maximum intensity of the internal data, depending on type.

getMinIntensity()

float getMinIntensity

(

)

const

Returns the minimum intensity of the internal data, depending on type.

getName()

const String& getName ( ) const

inline

Referenced by TOPPViewBase::addData(), TOPPViewBase::copyLayer(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), and TOPPViewBase::showTOPPDialog_().

getOnDiscPeakData()

const ODExperimentSharedPtrType& getOnDiscPeakData ( ) const

inline

Returns a mutable reference to the on-disc data.

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::showCurrentPeaksAs2D(), and TOPPViewBase::showCurrentPeaksAsDIA().

getPeakData()

const ConstExperimentSharedPtrType getPeakData

(

)

const

Returns a const reference to the current in-memory peak data.

Note

Depending on the caching strategy (on-disk or in-memory), all or some spectra may have zero size and contain only meta data since peak data is cached on disk.

Do *not* use this function to access the current spectrum for the 1D view, use getCurrentSpectrum() instead.

Referenced by TOPPViewBase::addData(), TOPPViewBase::runTOPPTool_(), and TOPPViewBase::showCurrentPeaksAsDIA().

getPeakDataMuteable()

const ExperimentSharedPtrType& getPeakDataMuteable ( )

inline

Returns a mutable reference to the current in-memory peak data.

Note

Depending on the caching strategy (on-disk or in-memory), all or some spectra may have zero size and contain only meta data since peak data is cached on disk.

Do *not* use this function to access the current spectrum for the 1D view, use getCurrentSpectrum() instead.

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), TOPPViewBase::showCurrentPeaksAs2D(), and TOPPViewBase::showCurrentPeaksAs3D().

getSpectrum()

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.

isDIAData()

bool isDIAData ( ) const

inline

Check whether the current layer contains DIA (SWATH-MS) data.

Referenced by TOPPViewBase::showCurrentPeaksAsDIA().

isIonMobilityData()

bool isIonMobilityData ( ) const

inline

Check whether the current layer should be represented as ion mobility.

Referenced by TOPPViewBase::showCurrentPeaksAs3D().

labelAsDIAData()

void labelAsDIAData ( )

inline

Label the current layer as DIA (SWATH-MS) data.

labelAsIonMobilityData()

void labelAsIonMobilityData ( ) const

inline

operator=() [1/2]

LayerData& operator= ( const LayerData &  ld )

delete

no assignment operator (should not be needed)

operator=() [2/2]

LayerData& operator= ( LayerData &&  ld )

default

move assignment

remove_chromatogram_flag()

void remove_chromatogram_flag ( )

inline

remove the chromatogram flag

Referenced by TOPPViewBase::runTOPPTool_().

removePeakAnnotationsFromPeptideHit()

void removePeakAnnotationsFromPeptideHit

(

const std::vector< Annotation1DItem * > &

selected_annotations

)

remove peak annotations in the given list from the currently active PeptideHit

set_chromatogram_flag()

void set_chromatogram_flag ( )

inline

set the chromatogram flag

setChromatogramAnnotation()

void setChromatogramAnnotation

(

OSWData &&

data

)

add annotation from an OSW sqlite file.

setCurrentSpectrumIndex()

void setCurrentSpectrumIndex ( Size  index )

inline

Set the index of the current spectrum (1D view)

setName()

void setName ( const String &  new_name )

inline

setOnDiscPeakData()

void setOnDiscPeakData ( ODExperimentSharedPtrType  p )

inline

Set the current on-disc data.

setPeakData()

void setPeakData ( ExperimentSharedPtrType  p )

inline

Set the current in-memory peak data.

sortCurrentSpectrumByPosition()

void sortCurrentSpectrumByPosition ( )

inline

synchronizePeakAnnotations()

void synchronizePeakAnnotations

(

)

updates the PeakAnnotations in the current PeptideHit with manually changed annotations if no PeptideIdentification or PeptideHit for the spectrum exist, it is generated

updateCache_()

void updateCache_ ( )

private

Update current cached spectrum for easy retrieval.

updatePeptideHitAnnotations_()

void updatePeptideHitAnnotations_ ( PeptideHit &  hit )

private

updates the PeakAnnotations in the current PeptideHit with manually changed annotations

updateRanges()

void updateRanges

(

)

Update ranges of all data structures.

Updates ranges of all tracked data structures (spectra, chromatograms, features etc).

Member Data Documentation

annotations_1d

std::vector<Annotations1DContainer> annotations_1d

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

cached_spectrum_

ExperimentType::SpectrumType cached_spectrum_

private

Current cached spectrum.

chrom_annotation_

OSWDataSharedPtrType chrom_annotation_

private

Chromatogram annotation data.

chromatogram_map_

ExperimentSharedPtrType chromatogram_map_

private

chromatogram data

consensus_map_

ConsensusMapSharedPtrType consensus_map_

private

consensus feature data

current_spectrum_idx_

Size current_spectrum_idx_

private

Index of the current spectrum.

features_

FeatureMapSharedPtrType features_

private

feature data

filename

String filename

file name of the file the data comes from (if available)

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

filters

DataFilters filters

Filters to apply before painting.

flags

std::bitset<SIZE_OF_FLAGS> flags

Actual state of each flag.

flipped

bool flipped

if this layer is flipped (1d mirror view)

gradient

MultiGradient gradient

Gradient for 2D and 3D views.

label

LabelType label

Label type.

Referenced by TOPPViewBase::updateToolBar().

modifiable

bool modifiable

Flag that indicates if the layer data can be modified (so far used for features only)

modified

bool modified

Flag that indicates that the layer data was modified since loading it.

name_

String name_

private

layer name

NamesOfLabelType

const std::string NamesOfLabelType[SIZE_OF_LABEL_TYPE]

static

Label names.

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

on_disc_peaks

ODExperimentSharedPtrType on_disc_peaks

private

on disc peak data

param

Param param

Layer parameters.

Referenced by TOPPViewBase::loadFiles().

peak_colors_1d

std::vector<QColor> peak_colors_1d

Peak colors of the currently shown spectrum.

peak_map_

ExperimentSharedPtrType peak_map_

private

peak data

peptide_hit_index

int peptide_hit_index

peptide_id_index

int peptide_id_index

Selected peptide id and hit index (-1 if none is selected)

peptides

std::vector<PeptideIdentification> peptides

peptide identifications

Referenced by TOPPViewBase::copyLayer().

type

DataType type

data type (peak or feature data)

Referenced by TOPPViewBase::addData(), TOPPViewBase::copyLayer(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateToolBar().

visible

bool visible

if this layer is visible

Referenced by TOPPViewBase::editMetadata(), TOPPViewBase::rerunTOPPTool(), and TOPPViewBase::showTOPPDialog_().