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

#include <OpenMS/VISUAL/SpectraIDViewTab.h>

Inheritance diagram for SpectraIDViewTab:

Collaboration diagram for SpectraIDViewTab:

Classes
class	SelfResizingTableView_

Signals
void	spectrumSelected (int spectrum_index, int pep_id_index, int pep_hit_index)
	request to show a specific spectrum, and (if available) a specific pepId + pepHit in there (otherwise -1, -1) More...

void	spectrumDeselected (int spectrum_index)
	request to unshow a spectrum More...

void	requestVisibleArea1D (double lower_mz, double upper_mz)
	request to zoom into a 1D spec More...

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

	~SpectraIDViewTab () override=default
	Destructor. More...

bool	hasData (const LayerDataBase *layer) override

void	updateEntries (LayerDataBase *model) override
	set layer data and create table anew; if given a nullptr or the layer is not LayerDataPeak, behaves as clear() More...

LayerDataBase *	getLayer ()
	get layer data More...

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

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 = false
	Helper member to block outgoing signals. More...

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

void	updateProteinEntries_ (int spec_cell_row_idx)
	Rebuild protein table entries. More...

void	switchOrientation_ ()
	Switch horizontal or vertical layout of the PSM and Proteintable. More...

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

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

void	currentCellChanged_ (int row, int column, int old_row, int old_column)
	Cell clicked in table_widget; emits which spectrum (row) was clicked, and may show additional data. More...

void	createProteinToPeptideIDMap_ ()
	Create 'protein accession to peptide identification' map using C++ STL unordered_map. More...

void	currentSpectraSelectionChanged_ ()
	Cell selected or deselected: this is only used to check for deselection, rest happens in currentCellChanged_. More...

void	updatedSingleProteinCell_ (QTableWidgetItem *)
	update ProteinHits, when data in the table changes (status of checkboxes) More...

void	proteinCellClicked_ (int row, int column)
	Protein Cell clicked in protein_table_widget; emits which protein (row) was clicked, and may show additional data. More...

Private Member Functions
void	fillRow_ (const MSSpectrum &spectrum, const int spec_index, const QColor &background_color)
	partially fill the bottom-most row More...

void	openUniProtSiteWithAccession_ (const QString &accession)
	open browser to navigate to uniport site with accession More...

Static Private Member Functions
static QString	extractNumFromAccession_ (const QString &listItem)
	extract the required part of the accession More...

Private Attributes
LayerDataPeak *	layer_ = nullptr

QCheckBox *	hide_no_identification_ = nullptr

QCheckBox *	create_rows_for_commmon_metavalue_ = nullptr

TableView *	table_widget_ = nullptr

TableView *	protein_table_widget_ = nullptr

QTableWidget *	fragment_window_ = nullptr

QSplitter *	tables_splitter_ = nullptr

bool	is_first_time_loading_ = true

std::unordered_map< String, std::vector< const PeptideIdentification * > >	protein_to_peptide_id_map

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_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, Asp-N/B, Asp-N_ambic, Chymotrypsin, Chymotrypsin/P, CNBr, Formic_acid, Lys-C, Lys-N, Lys-C/P, PepsinA, TrypChymo, Trypsin/P, V8-DE, V8-E, Alpha-lytic protease, leukocyte elastase, proline endopeptidase, glutamyl endopeptidase, 2-iodobenzoate, iodosobenzoate, staphylococcal protease/D, proline-endopeptidase/HKR, Glu-C+P, PepsinA + P, cyanogen-bromide, Clostripain/P, elastase-trypsin-chymotrypsin, Asp-N, Arg-C/P, Trypsin, unspecific cleavage, no 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

◆ SpectraIDViewTab()

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

Constructor.

◆ ~SpectraIDViewTab()

~SpectraIDViewTab ( )

overridedefault

Destructor.

Member Function Documentation

◆ clear()

void clear ( )

overridevirtual

clears all visible data from table widget and voids the layer

Implements DataTabBase.

◆ createProteinToPeptideIDMap_

void createProteinToPeptideIDMap_ ( )

privateslot

Create 'protein accession to peptide identification' map using C++ STL unordered_map.

◆ currentCellChanged_

void currentCellChanged_	(	int	row,
		int	column,
		int	old_row,
		int	old_column
	)

privateslot

Cell clicked in table_widget; emits which spectrum (row) was clicked, and may show additional data.

◆ currentSpectraSelectionChanged_

void currentSpectraSelectionChanged_ ( )

privateslot

Cell selected or deselected: this is only used to check for deselection, rest happens in currentCellChanged_.

◆ extractNumFromAccession_()

static QString extractNumFromAccession_ ( const QString & listItem )

staticprivate

extract the required part of the accession

◆ fillRow_()

void fillRow_	(	const MSSpectrum &	spectrum,
		const int	spec_index,
		const QColor &	background_color
	)

private

partially fill the bottom-most row

◆ getLayer()

LayerDataBase* getLayer ( )

get layer data

◆ hasData()

bool hasData ( const LayerDataBase * layer )

overridevirtual

given a layer, determine if the tab could use it to show data (useful to decide if the tab should be enabled/disabled) If a nullptr is given, it HAS to return false!

Implements DataTabBase.

◆ openUniProtSiteWithAccession_()

void openUniProtSiteWithAccession_ ( const QString & accession )

private

open browser to navigate to uniport site with accession

◆ proteinCellClicked_

void proteinCellClicked_	(	int	row,
		int	column
	)

privateslot

Protein Cell clicked in protein_table_widget; emits which protein (row) was clicked, and may show additional data.

◆ requestVisibleArea1D

void requestVisibleArea1D	(	double	lower_mz,
		double	upper_mz
	)

signal

request to zoom into a 1D spec

◆ saveIDs_

void saveIDs_ ( )

privateslot

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

◆ spectrumDeselected

void spectrumDeselected ( int spectrum_index )

signal

request to unshow a spectrum

◆ spectrumSelected

void spectrumSelected	(	int	spectrum_index,
		int	pep_id_index,
		int	pep_hit_index
	)

signal

request to show a specific spectrum, and (if available) a specific pepId + pepHit in there (otherwise -1, -1)

◆ switchOrientation_

void switchOrientation_ ( )

protectedslot

Switch horizontal or vertical layout of the PSM and Proteintable.

◆ updatedSingleCell_

void updatedSingleCell_ ( QTableWidgetItem * item )

privateslot

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

◆ updatedSingleProteinCell_

void updatedSingleProteinCell_ ( QTableWidgetItem * )

privateslot

update ProteinHits, when data in the table changes (status of checkboxes)

◆ updateEntries()

void updateEntries ( LayerDataBase * model )

overridevirtual

set layer data and create table anew; if given a nullptr or the layer is not LayerDataPeak, behaves as clear()

Implements DataTabBase.

◆ updateEntries_

void updateEntries_ ( )

protectedslot

Rebuild table entries.

◆ updateProteinEntries_

void updateProteinEntries_ ( int spec_cell_row_idx )

protectedslot

Rebuild protein table entries.

Member Data Documentation

◆ create_rows_for_commmon_metavalue_

QCheckBox* create_rows_for_commmon_metavalue_ = nullptr

private

◆ fragment_window_

QTableWidget* fragment_window_ = nullptr

private

◆ hide_no_identification_

QCheckBox* hide_no_identification_ = nullptr

private

◆ ignore_update

bool ignore_update = false

Helper member to block outgoing signals.

◆ is_first_time_loading_

bool is_first_time_loading_ = true

private

◆ layer_

LayerDataPeak* layer_ = nullptr

private

◆ protein_table_widget_

TableView* protein_table_widget_ = nullptr

private

◆ protein_to_peptide_id_map

std::unordered_map<String, std::vector<const PeptideIdentification*> > protein_to_peptide_id_map

private

◆ table_widget_

TableView* table_widget_ = nullptr

private

◆ tables_splitter_

QSplitter* tables_splitter_ = nullptr

private

Classes

Signals

Public Member Functions

Public Attributes

Protected Slots

Private Slots

Private Member Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SpectraIDViewTab()

◆ ~SpectraIDViewTab()

Member Function Documentation

◆ clear()

◆ createProteinToPeptideIDMap_

◆ currentCellChanged_

◆ currentSpectraSelectionChanged_

◆ extractNumFromAccession_()

◆ fillRow_()

◆ getLayer()

◆ hasData()

◆ openUniProtSiteWithAccession_()

◆ proteinCellClicked_

◆ requestVisibleArea1D

◆ saveIDs_

◆ spectrumDeselected

◆ spectrumSelected

◆ switchOrientation_

◆ updatedSingleCell_

◆ updatedSingleProteinCell_

◆ updateEntries()

◆ updateEntries_

◆ updateProteinEntries_

Member Data Documentation

◆ create_rows_for_commmon_metavalue_

◆ fragment_window_

◆ hide_no_identification_

◆ ignore_update

◆ is_first_time_loading_

◆ layer_

◆ protein_table_widget_

◆ protein_to_peptide_id_map

◆ table_widget_

◆ tables_splitter_