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

#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>

Inheritance diagram for SpectraIdentificationViewWidget:

Collaboration 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...

void	clear ()
	clears all visible data from table widget and void the layer More...

bool	hasData () const
	do we have data to show? 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_

bool	has_data_ = false
	do we have data to show? More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

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	Arg-C/P, Trypsin, Arg-C, Asp-N/B, Asp-N, Asp-N_ambic, Chymotrypsin, Chymotrypsin/P, CNBr, Formic_acid, Lys-C, Lys-N, Lys-C/P, PepsinA, TrypChymo, V8-DE, Trypsin/P, V8-E, leukocyte elastase, proline endopeptidase, Alpha-lytic protease, glutamyl endopeptidase, 2-iodobenzoate, iodosobenzoate, staphylococcal protease/D, proline-endopeptidase/HKR, Glu-C+P, PepsinA + P, cyanogen-bromide, Clostripain/P, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage	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.

◆ clear()

void clear ( )

clears all visible data from table widget and void the layer

◆ exportEntries_

void exportEntries_ ( )

privateslot

Export table entries as csv.

◆ getLayer()

LayerData* getLayer ( )

◆ getTableWidget()

QTableWidget* getTableWidget ( )

Access the table widget.

◆ hasData()

bool hasData ( ) const

inline

do we have data to show?

References SpectraIdentificationViewWidget::has_data_.

◆ 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

◆ 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

◆ has_data_

bool has_data_ = false

private

do we have data to show?

Referenced by SpectraIdentificationViewWidget::hasData().

◆ 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_

◆ clear()

◆ exportEntries_

◆ getLayer()

◆ getTableWidget()

◆ hasData()

◆ headerContextMenu_

◆ requestVisibleArea1D

◆ saveIDs_

◆ setLayer()

◆ showSpectrumAs1D

◆ showSpectrumMetaData

◆ spectrumDeselected

◆ spectrumDoubleClicked

◆ spectrumSelected

◆ spectrumSelectionChange_

◆ updateData_

◆ updateEntries

Member Data Documentation

◆ create_rows_for_commmon_metavalue_

◆ fragment_window_

◆ has_data_

◆ hide_no_identification_

◆ ignore_update

◆ is_ms1_shown_

◆ layer_

◆ table_widget_