#include <OpenMS/VISUAL/LayerData1DPeak.h>

Inheritance diagram for LayerData1DPeak:

Collaboration diagram for LayerData1DPeak:

Public Member Functions
	LayerData1DPeak ()

	LayerData1DPeak (const LayerDataPeak &base)

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...

std::unique_ptr< Painter1DBase >	getPainter1D () const override
	Obtain a painter which can draw the layer on a canvas. More...

bool	hasIndex (Size index) const override
	Does the layer have at least `index` items (e.g. spectra, chroms, etc), so a call to setCurrentIndex() is valid? More...

RangeAllType	getRangeForArea (const RangeAllType partial_range) const override
	Given a `partial_range` for the current 1D layer (e.g. an m/z range), fill in the other dimensions (usually intensity) from all data points which are within the input range. More...

const ExperimentType::SpectrumType &	getCurrentSpectrum () const

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

RangeAllType	getRange1D () const override

QMenu *	getContextMenuAnnotation (Annotation1DItem *annot_item, bool &need_repaint) override
	Get a context menu (with lambda actions included) for this 1D layer, when a Annotation1DItem was right-clicked. More...

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

Annotation1DItem *	addPeakAnnotation (const PeakIndex &peak_index, const QString &text, const QColor &color) override
	Add a Annotation1DPeakItem to getCurrentAnnotations(). The specific type is determined by the derived class (e.g. Peak1D, ChromatogramPeak1D, etc) More...

void	synchronizePeakAnnotations ()

void	removePeakAnnotationsFromPeptideHit (const std::vector< Annotation1DItem * > &selected_annotations)
	remove peak annotations in the given list from the currently active PeptideHit More...

void	updatePeptideHitAnnotations_ (PeptideHit &hit)
	updates the PeakAnnotations in the current PeptideHit with manually changed annotations More...

Public Member Functions inherited from LayerDataPeak
	LayerDataPeak ()
	Default constructor. More...

	LayerDataPeak (const LayerDataPeak &ld)=default
	Copy-ctor. More...

LayerDataPeak &	operator= (const LayerDataPeak &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 &area) const override
	Find the datapoint with the highest intensity within the given range and return a proxy to that datapoint. More...

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

RangeAllType	getRange () const override

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

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

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

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

const ExperimentType::SpectrumType &	getSpectrum (Size spectrum_idx) const

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...

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...

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...

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...

Public Member Functions inherited from LayerData1DBase
String	getDecoratedName () const override
	get name augmented with attributes, e.g. '*' if modified 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 `spectrum_index's` spectrum (1D view) More...

Annotations1DContainer &	getAnnotations (Size spectrum_index)
	Returns a mutable reference to the annotations of the `spectrum_index's` spectrum (1D view) More...

Size	getCurrentIndex () const
	Get the index of the current spectrum (1D view) More...

void	setCurrentIndex (Size index)
	Set the index of the current spectrum (1D view) – and prepares annotations. More...

Additional Inherited Members
Public Types inherited from LayerDataPeak
using	SpectrumType = ExperimentType::SpectrumType

using	PeakType = SpectrumType::PeakType

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 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

Public Attributes inherited from LayerData1DBase
bool	flipped = false
	if this layer is flipped (1d mirror view) More...

std::vector< QColor >	peak_colors_1d
	Peak colors of the currently shown spectrum. More...

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

Protected Attributes inherited from LayerDataPeak
ExperimentSharedPtrType	peak_map_ = ExperimentSharedPtrType(new ExperimentType())
	peak data More...

ODExperimentSharedPtrType	on_disc_peaks_ = ODExperimentSharedPtrType(new OnDiscMSExperiment())
	on disc peak data More...

Protected Attributes inherited from LayerData1DBase
Size	current_idx_ = 0
	Index of the current spectrum/chromatogram etc (by default, show the first one) More...

std::vector< Annotations1DContainer >	annotations_1d_ = std::vector<Annotations1DContainer>(1)
	Annotations of all spectra of the experiment (1D view) More...

Constructor & Destructor Documentation

◆ LayerData1DPeak() [1/2]

LayerData1DPeak ( )

inline

◆ LayerData1DPeak() [2/2]

LayerData1DPeak ( const LayerDataPeak & base )

inline

Member Function Documentation

◆ addPeakAnnotation()

Annotation1DItem* addPeakAnnotation	(	const PeakIndex &	peak_index,
		const QString &	text,
		const QColor &	color
	)

overridevirtual

Add a Annotation1DPeakItem to getCurrentAnnotations(). The specific type is determined by the derived class (e.g. Peak1D, ChromatogramPeak1D, etc)

Parameters

peak_index	Which peak should be annotated?
text	Text to annotate with
color	Color of the text

Returns: The item that was created

Implements LayerData1DBase.

◆ findClosestDataPoint()

PeakIndex findClosestDataPoint ( const RangeAllType & ) const

overridevirtual

Find the closest datapoint 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.

◆ getContextMenuAnnotation()

QMenu* getContextMenuAnnotation	(	Annotation1DItem *	annot_item,
		bool &	need_repaint
	)

overridevirtual

Get a context menu (with lambda actions included) for this 1D layer, when a Annotation1DItem was right-clicked.

Parameters

annot_item	The annotation item clicked on
need_repaint	Reference of bool in calling function, which must know if the action requires repainting the canvas

Returns: A context menu to embed into the generic menu

Implements LayerData1DBase.

◆ getCurrentSpectrum()

const ExperimentType::SpectrumType& getCurrentSpectrum ( ) const

inline

References LayerDataPeak::getSpectrum().

◆ getPainter1D()

std::unique_ptr<Painter1DBase> getPainter1D ( ) const

overridevirtual

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

Returns: A painter

Implements LayerData1DBase.

◆ getRange1D()

RangeAllType getRange1D ( ) const

inlineoverridevirtual

Returns the data range in all known dimensions for the data of the currently active index (i.e. only a single spec/chrom/etc). 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 the whole layer (i.e. all specs/chroms/etc), call 'LayerDataBase::getRange()'

Implements LayerData1DBase.

References RangeManager< RangeBases >::assign().

◆ getRangeForArea()

RangeAllType getRangeForArea ( const RangeAllType partial_range ) const

inlineoverridevirtual

Given a partial_range for the current 1D layer (e.g. an m/z range), fill in the other dimensions (usually intensity) from all data points which are within the input range.

Parameters

partial_range Range with at least one dimension populated (which is used to filter the current spectrum/chrom/...)

Returns: Range of the data points within the input range (e.g. for spectra: m/z and intensity; or chroms: RT and intensity, etc)

Implements LayerData1DBase.

References RangeManager< RangeBases >::assign().

◆ hasIndex()

bool hasIndex ( Size index ) const

inlineoverridevirtual

Does the layer have at least index items (e.g. spectra, chroms, etc), so a call to setCurrentIndex() is valid?

Implements LayerData1DBase.

◆ removePeakAnnotationsFromPeptideHit()

void removePeakAnnotationsFromPeptideHit ( const std::vector< Annotation1DItem * > & selected_annotations )

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

◆ 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.

◆ 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

◆ updatePeptideHitAnnotations_()

void updatePeptideHitAnnotations_ ( PeptideHit & hit )

updates the PeakAnnotations in the current PeptideHit with manually changed annotations

◆ updateRanges()

void updateRanges ( )

inlineoverridevirtual

Update ranges of the underlying data.

Implements LayerDataBase.

References LayerDataPeak::updateRanges().

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ LayerData1DPeak() [1/2]

◆ LayerData1DPeak() [2/2]

Member Function Documentation

◆ addPeakAnnotation()

◆ findClosestDataPoint()

◆ getContextMenuAnnotation()

◆ getCurrentSpectrum()

◆ getPainter1D()

◆ getRange1D()

◆ getRangeForArea()

◆ hasIndex()

◆ removePeakAnnotationsFromPeptideHit()

◆ storeFullData()

◆ storeVisibleData()

◆ synchronizePeakAnnotations()

◆ updatePeptideHitAnnotations_()

◆ updateRanges()