Tabular visualization / selection of identified spectra. More...

#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>

Inheritance diagram for SpectraIdentificationViewWidget:

Signals
void	spectrumSelected (int, int, int)

void	spectrumDeselected (int)

void	spectrumDoubleClicked (int)

void	showSpectrumAs1D (int)

void	showSpectrumMetaData (int)

void	requestVisibleArea1D (double, double)

Public Member Functions
	SpectraIdentificationViewWidget (const Param &preferences, QWidget *parent=nullptr)
	Constructor. More...

	~SpectraIdentificationViewWidget () override
	Destructor. More...

void	setLayer (LayerData *model)
	set / get layer data More...

LayerData *	getLayer ()

QTableWidget *	getTableWidget ()
	Access the table widget. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Public Attributes
bool	ignore_update
	Helper function to block outgoing signals. More...

Protected Slots
void	updateEntries ()
	Rebuild table entries. More...

Private Slots
void	spectrumSelectionChange_ (QTableWidgetItem , QTableWidgetItem )
	Emits spectrumSelected with the current spectrum index. More...

void	exportEntries_ ()
	Export table entries as csv. More...

void	saveIDs_ ()
	Saves the (potentially filtered) IDs as an idXML or mzIdentML file. More...

void	updateData_ (QTableWidgetItem *item)
	update PeptideIdentification / PeptideHits, when data in the table changes (status of checkboxes) More...

void	headerContextMenu_ (const QPoint &)
	Display header context menu. More...

void	cellClicked_ (int row, int column)
	Cell clicked in table_widget. More...

Private Member Functions
void	addTextItemToBottomRow_ (const QString &text, Size column_index, const QColor &c)

void	addIntItemToBottomRow_ (const Int i, Size column_index, const QColor &c)

void	addDoubleItemToBottomRow_ (const double d, Size column_index, const QColor &c)

void	addCheckboxItemToBottomRow_ (bool selected, Size column_index, const QColor &c)

Private Attributes
LayerData *	layer_

QCheckBox *	hide_no_identification_

QCheckBox *	create_rows_for_commmon_metavalue_

QTableWidget *	table_widget_

bool	is_ms1_shown_

QTableWidget *	fragment_window_

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

Tabular visualization / selection of identified spectra.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
enzyme	string	Trypsin	CNBr, Trypsin/P, V8-DE, V8-E, PepsinA + P, cyanogen-bromide, Clostripain/P, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage, Trypsin, Chymotrypsin, Chymotrypsin/P, glutamyl endopeptidase, Alpha-lytic protease, 2-iodobenzoate, iodosobenzoate, staphylococcal protease/D, proline-endopeptidase/HKR, Glu-C+P, Asp-N, Asp-N/B, PepsinA, TrypChymo, Formic_acid, Lys-C, Lys-N, Lys-C/P, leukocyte elastase, proline endopeptidase, Arg-C, Asp-N_ambic, Arg-C/P	Enzyme to use for digestion (select 'no cleavage' to skip digestion)
model	string	naive	trained, naive	The cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).
min_peptide_length	int	3	min: 1	Minimum peptide length after digestion (shorter ones will be discarded)
model_trained:threshold	float	0.5	min: -2.0 max: 4.0	Model threshold for calling a cleavage. Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage.
model_naive:missed_cleavages	int	1	min: 0	Maximum number of missed cleavages considered. All possible resulting peptides will be created.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ SpectraIdentificationViewWidget()

SpectraIdentificationViewWidget	(	const Param &	preferences,
		QWidget *	parent = `nullptr`
	)

Constructor.

◆ ~SpectraIdentificationViewWidget()

~SpectraIdentificationViewWidget ( )

override

Destructor.

Member Function Documentation

◆ addCheckboxItemToBottomRow_()

void addCheckboxItemToBottomRow_	(	bool	selected,
		Size	column_index,
		const QColor &	c
	)

private

◆ addDoubleItemToBottomRow_()

void addDoubleItemToBottomRow_	(	const double	d,
		Size	column_index,
		const QColor &	c
	)

private

◆ addIntItemToBottomRow_()

void addIntItemToBottomRow_	(	const Int	i,
		Size	column_index,
		const QColor &	c
	)

private

◆ addTextItemToBottomRow_()

void addTextItemToBottomRow_	(	const QString &	text,
		Size	column_index,
		const QColor &	c
	)

private

◆ cellClicked_

void cellClicked_	(	int	row,
		int	column
	)

privateslot

Cell clicked in table_widget.

◆ exportEntries_

void exportEntries_ ( )

privateslot

Export table entries as csv.

◆ getLayer()

LayerData* getLayer ( )

Referenced by TOPPViewBase::updateViewBar().

◆ getTableWidget()

QTableWidget* getTableWidget ( )

Access the table widget.

Referenced by TOPPViewBase::updateViewBar().

◆ headerContextMenu_

void headerContextMenu_ ( const QPoint & )

privateslot

Display header context menu.

◆ requestVisibleArea1D

void requestVisibleArea1D	(	double	,
		double
	)

signal

◆ saveIDs_

void saveIDs_ ( )

privateslot

Saves the (potentially filtered) IDs as an idXML or mzIdentML file.

◆ setLayer()

void setLayer ( LayerData * model )

set / get layer data

Referenced by TOPPViewBase::updateViewBar().

◆ showSpectrumAs1D

void showSpectrumAs1D ( int )

signal

◆ showSpectrumMetaData

void showSpectrumMetaData ( int )

signal

◆ spectrumDeselected

void spectrumDeselected ( int )

signal

◆ spectrumDoubleClicked

void spectrumDoubleClicked ( int )

signal

◆ spectrumSelected

void spectrumSelected	(	int	,
		int	,
		int
	)

signal

◆ spectrumSelectionChange_

void spectrumSelectionChange_	(	QTableWidgetItem *	,
		QTableWidgetItem *
	)

privateslot

Emits spectrumSelected with the current spectrum index.

◆ updateData_

void updateData_ ( QTableWidgetItem * item )

privateslot

update PeptideIdentification / PeptideHits, when data in the table changes (status of checkboxes)

◆ updateEntries

void updateEntries ( )

protectedslot

Rebuild table entries.

Member Data Documentation

◆ create_rows_for_commmon_metavalue_

QCheckBox* create_rows_for_commmon_metavalue_

private

◆ fragment_window_

QTableWidget* fragment_window_

private

◆ hide_no_identification_

QCheckBox* hide_no_identification_

private

◆ ignore_update

bool ignore_update

Helper function to block outgoing signals.

◆ is_ms1_shown_

bool is_ms1_shown_

private

◆ layer_

LayerData* layer_

private

◆ table_widget_

QTableWidget* table_widget_

private

Signals

Public Member Functions

Public Attributes

Protected Slots

Private Slots

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SpectraIdentificationViewWidget()

◆ ~SpectraIdentificationViewWidget()

Member Function Documentation

◆ addCheckboxItemToBottomRow_()

◆ addDoubleItemToBottomRow_()

◆ addIntItemToBottomRow_()

◆ addTextItemToBottomRow_()

◆ cellClicked_

◆ exportEntries_

◆ getLayer()

◆ getTableWidget()

◆ headerContextMenu_

◆ requestVisibleArea1D

◆ saveIDs_

◆ setLayer()

◆ showSpectrumAs1D

◆ showSpectrumMetaData

◆ spectrumDeselected

◆ spectrumDoubleClicked

◆ spectrumSelected

◆ spectrumSelectionChange_

◆ updateData_

◆ updateEntries

Member Data Documentation

◆ create_rows_for_commmon_metavalue_

◆ fragment_window_

◆ hide_no_identification_

◆ ignore_update

◆ is_ms1_shown_

◆ layer_

◆ table_widget_