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
tsg:isotope_model	string	none	none, coarse, fine	Model to use for isotopic peaks ('none' means no isotopic peaks are added, 'coarse' adds isotopic peaks in unit mass distance, 'fine' uses the hyperfine isotopic generator to add accurate isotopic peaks. Note that adding isotopic peaks is very slow.
tsg:max_isotope	int	2		Defines the maximal isotopic peak which is added if 'isotope_model' is 'coarse'
tsg:max_isotope_probability	float	0.05		Defines the maximal isotopic probability to cover if 'isotope_model' is 'fine'
tsg:add_metainfo	string	false	true, false	Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++
tsg:add_losses	string	false	true, false	Adds common losses to those ion expect to have them, only water and ammonia loss is considered
tsg:sort_by_position	string	true	true, false	Sort output by position
tsg:add_precursor_peaks	string	false	true, false	Adds peaks of the unfragmented precursor ion to the spectrum
tsg:add_all_precursor_charges	string	false	true, false	Adds precursor peaks with all charges in the given range
tsg:add_abundant_immonium_ions	string	false	true, false	Add most abundant immonium ions (for Proline, Cystein, Iso/Leucine, Histidin, Phenylalanin, Tyrosine, Tryptophan)
tsg:add_first_prefix_ion	string	false	true, false	If set to true e.g. b1 ions are added
tsg:add_y_ions	string	true	true, false	Add peaks of y-ions to the spectrum
tsg:add_b_ions	string	true	true, false	Add peaks of b-ions to the spectrum
tsg:add_a_ions	string	false	true, false	Add peaks of a-ions to the spectrum
tsg:add_c_ions	string	false	true, false	Add peaks of c-ions to the spectrum
tsg:add_x_ions	string	false	true, false	Add peaks of x-ions to the spectrum
tsg:add_z_ions	string	false	true, false	Add peaks of z-ions to the spectrum (sometimes observed in CID and for some AAs in ExD due to H abstraction)
tsg:add_zp1_ions	string	false	true, false	Add peaks of z+1-radical cations (also [z+H]^{+} or simply z) to the spectrum (often observed in ExD)
tsg:add_zp2_ions	string	false	true, false	Add peaks of z+2-radical cations (also [z+2H]*^{2+} or simply z') to the spectrum (often observed in ExD esp. with higher precursor charges >3 and smaller z-ions.)
tsg:y_intensity	float	1.0	min: 0.0	Intensity of the y-ions
tsg:b_intensity	float	1.0	min: 0.0	Intensity of the b-ions
tsg:a_intensity	float	1.0	min: 0.0	Intensity of the a-ions
tsg:c_intensity	float	1.0	min: 0.0	Intensity of the c-ions
tsg:x_intensity	float	1.0	min: 0.0	Intensity of the x-ions
tsg:z_intensity	float	1.0	min: 0.0	Intensity of the z-ions
tsg:relative_loss_intensity	float	0.1	min: 0.0 max: 1.0	Intensity of loss ions, in relation to the intact ion intensity
tsg:precursor_intensity	float	1.0	min: 0.0	Intensity of the precursor peak
tsg:precursor_H2O_intensity	float	1.0	min: 0.0	Intensity of the H2O loss peak of the precursor
tsg:precursor_NH3_intensity	float	1.0	min: 0.0	Intensity of the NH3 loss peak of the precursor
align:tolerance	float	0.3		Defines the absolute (in Da) or relative (in ppm) tolerance
align:is_relative_tolerance	string	false	true, false	If true, the 'tolerance' is interpreted as ppm-value

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_