Class that stores the data for one layer of type PeptideIdentifications. More...

#include <OpenMS/VISUAL/LayerDataIdent.h>

Inheritance diagram for LayerDataIdent:

Collaboration diagram for LayerDataIdent:

Public Member Functions
	LayerDataIdent ()
	Default constructor. More...

	LayerDataIdent (const LayerDataIdent &ld)=delete
	no Copy-ctor (should not be needed) More...

LayerDataIdent &	operator= (const LayerDataIdent &ld)=delete
	no assignment operator (should not be needed) More...

std::unique_ptr< Painter2DBase >	getPainter2D () const override
	Obtain a painter which can draw the layer on a 2D canvas. More...

std::unique_ptr< LayerData1DBase >	to1DLayer () const override
	Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer, and make it 1D (i.e. support showing a single spec/chrom etc) More...

std::unique_ptr< LayerStoreData >	storeVisibleData (const RangeAllType &visible_range, const DataFilters &layer_filters) const override
	Returns a visitor which contains the current visible data and can write the data to disk. More...

std::unique_ptr< LayerStoreData >	storeFullData () const override
	Returns a visitor which contains the the full data of the layer and can write the data to disk in the appropriate format (e.g. mzML) More...

ProjectionData	getProjection (const DIM_UNIT unit_x, const DIM_UNIT unit_y, const RangeAllType &area) const override

PeakIndex	findHighestDataPoint (const RangeAllType &) const override
	Find the datapoint with the highest intensity within the given range and return a proxy to that datapoint. More...

PointXYType	peakIndexToXY (const PeakIndex &peak, const DimMapper< 2 > &mapper) const override
	Convert a PeakIndex to a XY coordinate (via `mapper`). More...

void	updateRanges () override
	Update ranges of the underlying data. More...

RangeAllType	getRange () const override

std::unique_ptr< LayerStatistics >	getStats () const override
	Compute layer statistics (via visitor) More...

virtual const PepIds &	getPeptideIds () const override
	get the peptide IDs for this layer More...

virtual PepIds &	getPeptideIds () override

virtual void	setPeptideIds (const PepIds &ids) override
	overwrite the peptide IDs for this layer More...

virtual void	setPeptideIds (PepIds &&ids) override

Public Member Functions inherited from LayerDataBase
	LayerDataBase ()=delete
	Default constructor (for virtual inheritance) More...

	LayerDataBase (const DataType type)
	C'tor for child classes. More...

	LayerDataBase (const LayerDataBase &ld)=default
	Copy-C'tor. More...

LayerDataBase &	operator= (const LayerDataBase &ld)=delete
	Assignment operator. More...

	LayerDataBase (LayerDataBase &&ld)=delete

LayerDataBase &	operator= (LayerDataBase &&ld)=delete
	Move assignment – deleted, by same argument as for move c'tor. More...

virtual	~LayerDataBase ()=default
	D'tor. More...

virtual PeakIndex	findClosestDataPoint (const RangeAllType &area) const
	Find the closest datapoint within the given range and return a proxy to that datapoint. More...

virtual String	getDataArrayDescription (const PeakIndex &peak_index)
	Get name and value of all data-arrays corresponding to the given datapoint. More...

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

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...

const String &	getName () const
	The name of the layer, usually the basename of the file. More...

void	setName (const String &new_name)
	Set the name of the layer, usually the basename of the file. More...

const String &	getNameSuffix () const
	get the extra annotation to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D More...

void	setNameSuffix (const String &decorator)
	set an extra annotation as suffix to the layers name, e.g. '[39]' for which chromatogram index is currently shown in 1D More...

virtual String	getDecoratedName () const
	get name augmented with attributes, e.g. '*' if modified More...

Private Attributes
std::vector< PeptideIdentification >	peptides_
	peptide identifications More...

Additional Inherited Members
Public Types inherited from LayerDataBase
using	RangeAllType = RangeManager< RangeRT, RangeMZ, RangeIntensity, RangeMobility >

Public Types inherited from LayerDataDefs
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...

Public Types inherited from IPeptideIds
using	PepIds = std::vector< PeptideIdentification >

Public Attributes inherited from LayerDataBase
std::bitset< SIZE_OF_FLAGS >	flags
	Actual state of each flag. More...

bool	visible = true
	if this layer is visible More...

DataType	type = DT_UNKNOWN
	data type (peak or feature data, etc) More...

String	filename
	file name of the file the data comes from (if available) More...

Param	param
	Layer parameters. More...

MultiGradient	gradient
	Gradient for 2D and 3D views. More...

DataFilters	filters
	Filters to apply before painting. More...

bool	modifiable = false
	Flag that indicates if the layer data can be modified (so far used for features only) More...

bool	modified = false
	Flag that indicates that the layer data was modified since loading it. More...

LabelType	label = L_NONE
	Label type. More...

int	peptide_id_index = -1
	Selected peptide id and hit index (-1 if none is selected) More...

int	peptide_hit_index = -1

Static Public Attributes inherited from LayerDataDefs
static const std::string	NamesOfLabelType [SIZE_OF_LABEL_TYPE]
	Label names. More...

Detailed Description

Class that stores the data for one layer of type PeptideIdentifications.

Constructor & Destructor Documentation

◆ LayerDataIdent() [1/2]

LayerDataIdent ( )

inline

Default constructor.

◆ LayerDataIdent() [2/2]

LayerDataIdent ( const LayerDataIdent & ld )

delete

no Copy-ctor (should not be needed)

Member Function Documentation

◆ findHighestDataPoint()

PeakIndex findHighestDataPoint ( const RangeAllType & area ) const

inlineoverridevirtual

Find the datapoint with the highest intensity within the given range and return a proxy to that datapoint.

Parameters

area	Range to search in. Only dimensions used in the canvas are populated.

Returns: A proxy (e.g. scan + peak index in an MSExperiment) which points to the data

Reimplemented from LayerDataBase.

◆ getPainter2D()

std::unique_ptr<Painter2DBase> getPainter2D ( ) const

overridevirtual

Obtain a painter which can draw the layer on a 2D canvas.

Returns: A painter

Implements LayerDataBase.

◆ getPeptideIds() [1/2]

virtual const PepIds& getPeptideIds ( ) const

inlineoverridevirtual

get the peptide IDs for this layer

Implements IPeptideIds.

◆ getPeptideIds() [2/2]

virtual PepIds& getPeptideIds ( )

inlineoverridevirtual

Implements IPeptideIds.

◆ getProjection()

ProjectionData getProjection	(	const DIM_UNIT	unit_x,
		const DIM_UNIT	unit_y,
		const RangeAllType &	area
	)		const

overridevirtual

Calculate a projection of the current layer for the given unit and the given area. E.g. the area might be restricted in RT and m/z, and then requested projection should return the XIC (unit == RT) It is up to the implementation to decide on binning.

Implements LayerDataBase.

◆ getRange()

RangeAllType getRange ( ) const

inlineoverridevirtual

Returns the data range of the whole layer (i.e. all scans/chroms/etc) in all known dimensions. If a layer does not support the dimension (or the layer is empty) the dimension will be empty If you need the data range for a 1D view (i.e. only a single spec/chrom/etc), call 'LayerDataBase1D::getRange1D()'

Implements LayerDataBase.

◆ getStats()

std::unique_ptr<LayerStatistics> getStats ( ) const

overridevirtual

Compute layer statistics (via visitor)

Implements LayerDataBase.

◆ operator=()

LayerDataIdent& operator= ( const LayerDataIdent & ld )

delete

no assignment operator (should not be needed)

◆ peakIndexToXY()

PointXYType peakIndexToXY	(	const PeakIndex &	peak,
		const DimMapper< 2 > &	mapper
	)		const

overridevirtual

Convert a PeakIndex to a XY coordinate (via mapper).

Parameters

peak	The Peak to convert
mapper	Converts the internal representation (e.g. Peak1D) to an XY coordinate

Returns: XY coordinate in data units (e.g. X=m/z, Y=intensity)

Implements LayerDataBase.

◆ setPeptideIds() [1/2]

virtual void setPeptideIds ( const PepIds & ids )

inlineoverridevirtual

overwrite the peptide IDs for this layer

Implements IPeptideIds.

◆ setPeptideIds() [2/2]

virtual void setPeptideIds ( PepIds && ids )

inlineoverridevirtual

Implements IPeptideIds.

◆ storeFullData()

std::unique_ptr<LayerStoreData> storeFullData ( ) const

overridevirtual

Returns a visitor which contains the the full data of the layer and can write the data to disk in the appropriate format (e.g. mzML)

Reimplemented from LayerDataBase.

◆ storeVisibleData()

std::unique_ptr<LayerStoreData> storeVisibleData	(	const RangeAllType &	,
		const DataFilters &
	)		const

overridevirtual

Returns a visitor which contains the current visible data and can write the data to disk.

Reimplemented from LayerDataBase.

◆ to1DLayer()

std::unique_ptr<LayerData1DBase> to1DLayer ( ) const

inlineoverridevirtual

Create a shallow copy (i.e. shared experimental data using shared_ptr) of the current layer, and make it 1D (i.e. support showing a single spec/chrom etc)

Returns: A new layer for 1D

Implements LayerDataBase.

◆ updateRanges()

void updateRanges ( )

inlineoverridevirtual

Update ranges of the underlying data.

Implements LayerDataBase.

Member Data Documentation

◆ peptides_

std::vector<PeptideIdentification> peptides_

private

peptide identifications

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ LayerDataIdent() [1/2]

◆ LayerDataIdent() [2/2]

Member Function Documentation

◆ findHighestDataPoint()

◆ getPainter2D()

◆ getPeptideIds() [1/2]

◆ getPeptideIds() [2/2]

◆ getProjection()

◆ getRange()

◆ getStats()

◆ operator=()

◆ peakIndexToXY()

◆ setPeptideIds() [1/2]

◆ setPeptideIds() [2/2]

◆ storeFullData()

◆ storeVisibleData()

◆ to1DLayer()

◆ updateRanges()

Member Data Documentation

◆ peptides_