LayerDataIdent Class Reference

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...
	LayerDataIdent (LayerDataIdent &&ld)=default
	move Ctor More...
LayerDataIdent &	operator= (LayerDataIdent &&ld)=default
	move assignment More...
std::unique_ptr< Painter1DBase >	getPainter1D () const override
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. More...
	LayerDataBase (const DataType type)
	C'tor for child classes. More...
	LayerDataBase (const LayerDataBase &ld)=delete
	no Copy-ctor (should not be needed) More...
LayerDataBase &	operator= (const LayerDataBase &ld)=delete
	no assignment operator (should not be needed) More...
	LayerDataBase (LayerDataBase &&ld)=default
	move C'tor More...
LayerDataBase &	operator= (LayerDataBase &&ld)=default
	move assignment More...
virtual	~LayerDataBase ()=default
	D'tor. 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...
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...

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

Additional Inherited Members
Public Types inherited from LayerDataBase
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...
using	RangeAllType = RangeManager< RangeRT, RangeMZ, RangeIntensity, RangeMobility >
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...
bool	flipped = false
	if this layer is flipped (1d mirror view) More...
DataType	type = DT_UNKNOWN
	data type (peak or feature data) 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...
std::vector< Annotations1DContainer >	annotations_1d = std::vector<Annotations1DContainer>(1)
	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 = 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 LayerDataBase
static const std::string	NamesOfLabelType [SIZE_OF_LABEL_TYPE]
	Label names. More...
Protected Member Functions inherited from LayerDataBase
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...
Protected Attributes inherited from LayerDataBase
FeatureMapSharedPtrType	features_ = FeatureMapSharedPtrType(new FeatureMapType())
	feature data More...
ConsensusMapSharedPtrType	consensus_map_ = ConsensusMapSharedPtrType(new ConsensusMapType())
	consensus feature data More...
ExperimentSharedPtrType	peak_map_ = ExperimentSharedPtrType(new ExperimentType())
	peak data More...
ODExperimentSharedPtrType	on_disc_peaks = ODExperimentSharedPtrType(new OnDiscMSExperiment())
	on disc peak data More...
ExperimentSharedPtrType	chromatogram_map_ = ExperimentSharedPtrType(new ExperimentType())
	chromatogram data More...
OSWDataSharedPtrType	chrom_annotation_
	Chromatogram annotation data. More...
Size	current_spectrum_idx_ = 0
	Index of the current spectrum. More...
ExperimentType::SpectrumType	cached_spectrum_
	Current cached spectrum. More...

Detailed Description

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

Constructor & Destructor Documentation

LayerDataIdent() [1/3]

LayerDataIdent ( )

inline

Default constructor.

LayerDataIdent() [2/3]

LayerDataIdent ( const LayerDataIdent &  ld )

delete

no Copy-ctor (should not be needed)

LayerDataIdent() [3/3]

LayerDataIdent ( LayerDataIdent &&  ld )

default

move Ctor

Member Function Documentation

getPainter1D()

std::unique_ptr<Painter1DBase> getPainter1D ( ) const

overridevirtual

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.

getRange()

RangeAllType getRange ( ) const

inlineoverridevirtual

Returns the data range in all known dimensions. If a layer does not support the dimension (or the layer is empty) the dimension will be empty

Implements LayerDataBase.

getStats()

std::unique_ptr<LayerStatistics> getStats ( ) const

overridevirtual

compute layer statistics (via visitor)

Implements LayerDataBase.

operator=() [1/2]

LayerDataIdent& operator= ( const LayerDataIdent &  ld )

delete

no assignment operator (should not be needed)

operator=() [2/2]

LayerDataIdent& operator= ( LayerDataIdent &&  ld )

default

move assignment

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.

updateRanges()

void updateRanges ( )

inlineoverridevirtual

Update ranges of the underlying data.

Implements LayerDataBase.

Member Data Documentation

peptides_

std::vector<PeptideIdentification> peptides_

private

peptide identifications