Tabular visualization / selection of identified spectra. More...
#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>
Inheritance diagram for SpectraIdentificationViewWidget:
Public Slots | |
| void | updateEntries () |
| Rebuild table entries. More... | |
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=0) | |
| Constructor. More... | |
| virtual | ~SpectraIdentificationViewWidget () |
| Destructor. More... | |
| void | attachLayer (LayerData *model) |
| Attach model. More... | |
| 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 ¶m) |
| 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... | |
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_ |
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 | Asp-N, no cleavage, unspecific cleavage, CNBr, Asp-N/B, Trypsin, PepsinA, Chymotrypsin/P, Arg-C, Asp-N_ambic, Chymotrypsin, Lys-C, Lys-N, Alpha-lytic protease, glutamyl endopeptidase, 2-iodobenzoate, TrypChymo, Arg-C/P, Lys-C/P, Formic_acid, leukocyte elastase, proline endopeptidase, Trypsin/P, V8-DE, V8-E | 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 max: 4 | 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 = 0 |
||
| ) |
Constructor.
◆ ~SpectraIdentificationViewWidget()
|
virtual |
Destructor.
Member Function Documentation
◆ addCheckboxItemToBottomRow_()
|
private |
◆ addDoubleItemToBottomRow_()
◆ addIntItemToBottomRow_()
◆ addTextItemToBottomRow_()
|
private |
◆ attachLayer()
| void attachLayer | ( | LayerData * | model | ) |
Attach model.
Referenced by TOPPViewBase::updateViewBar().
◆ cellClicked_
|
privateslot |
Cell clicked in table_widget.
◆ exportEntries_
|
privateslot |
Export table entries as csv.
◆ getTableWidget()
| QTableWidget* getTableWidget | ( | ) |
Access the table widget.
Referenced by TOPPViewBase::updateViewBar().
◆ headerContextMenu_
|
privateslot |
Display header context menu.
◆ requestVisibleArea1D
◆ saveIDs_
|
privateslot |
Saves the (potentially filtered) IDs as an idXML or mzIdentML file.
◆ showSpectrumAs1D
|
signal |
◆ showSpectrumMetaData
|
signal |
◆ spectrumDeselected
|
signal |
◆ spectrumDoubleClicked
|
signal |
◆ spectrumSelected
|
signal |
◆ spectrumSelectionChange_
|
privateslot |
Emits spectrumSelected with the current spectrum index.
◆ updateData_
|
privateslot |
update PeptideIdentification / PeptideHits, when data in the table changes (status of checkboxes)
◆ updateEntries
|
slot |
Rebuild table entries.
Referenced by TOPPViewBase::updateViewBar().
Member Data Documentation
◆ create_rows_for_commmon_metavalue_
|
private |
◆ hide_no_identification_
|
private |
◆ ignore_update
| bool ignore_update |
Helper function to block outgoing signals.
◆ is_ms1_shown_
|
private |
◆ layer_
|
private |
◆ table_widget_
|
private |