OpenMS  2.8.0
Classes | Signals | Public Member Functions | Public Attributes | Protected Slots | Private Slots | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
SpectraIDViewTab Class Reference

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

#include <OpenMS/VISUAL/SpectraIDViewTab.h>

Inheritance diagram for SpectraIDViewTab:
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Collaboration diagram for SpectraIDViewTab:
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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, behaves as clear() More...
 
LayerDataBasegetLayer ()
 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...
 
virtual DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 *item)
 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

LayerDataBaselayer_ = nullptr
 
QCheckBox * hide_no_identification_ = nullptr
 
QCheckBox * create_rows_for_commmon_metavalue_ = nullptr
 
TableViewtable_widget_ = nullptr
 
TableViewprotein_table_widget_ = nullptr
 
QTableWidgetfragment_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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
enzyme stringTrypsin Trypsin, Asp-N/B, 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, Arg-C/P, Asp-N, Clostripain/P, Arg-C, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavageEnzyme to use for digestion (select 'no cleavage' to skip digestion)
model stringnaive trained, naiveThe cleavage model to use for digestion. 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u).
min_peptide_length int3 min: 1Minimum peptide length after digestion (shorter ones will be discarded)
model_trained:threshold float0.5 min: -2.0 max: 4.0Model 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 int1 min: 0Maximum number of missed cleavages considered. All possible resulting peptides will be created.

Note:

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 *  item)
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, 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_

LayerDataBase* 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