Tabular visualization / selection of identified specra. More...
#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>
 
  
 | Public Slots | |
| void | updateEntries () | 
| Rebuild table entries.  More... | |
| Signals | |
| void | spectrumSelected (int) | 
| void | spectrumDeselected (int) | 
| void | spectrumDoubleClicked (int) | 
| void | showSpectrumAs1D (int) | 
| void | showSpectrumMetaData (int) | 
| void | requestVisibleArea1D (DoubleReal, DoubleReal) | 
| 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 () | 
|  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 | saveIdXML_ () | 
| Saves the (potentially filtered) idXML.  More... | |
| void | headerContextMenu_ (const QPoint &) | 
| Display header context menu.  More... | |
| void | cellClicked_ (int row, int column) | 
| Cell clicked in table_widget.  More... | |
| 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... | |
Tabular visualization / selection of identified specra.
Parameters of this class are:| Name | Type | Default | Restrictions | Description | 
|---|---|---|---|---|
| enzyme | string | Trypsin | Trypsin, none | Enzyme to use for digestion (select 'none' 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. | 
| SpectraIdentificationViewWidget | ( | const Param & | preferences, | 
| QWidget * | parent = 0 | ||
| ) | 
Constructor.
| 
 | virtual | 
Destructor.
| void attachLayer | ( | LayerData * | model | ) | 
Attach model.
Referenced by TOPPViewBase::updateViewBar().
| 
 | privateslot | 
Cell clicked in table_widget.
| 
 | privateslot | 
Export table entries as csv.
| QTableWidget* getTableWidget | ( | ) | 
Referenced by TOPPViewBase::updateViewBar().
| 
 | privateslot | 
Display header context menu.
| 
 | signal | 
| 
 | privateslot | 
Saves the (potentially filtered) idXML.
| 
 | signal | 
| 
 | signal | 
| 
 | signal | 
| 
 | signal | 
| 
 | signal | 
| 
 | privateslot | 
Emits spectrumSelected with the current spectrum index.
| 
 | slot | 
Rebuild table entries.
Referenced by TOPPViewBase::updateViewBar().
| 
 | private | 
| 
 | private | 
| bool ignore_update | 
Helper function to block outgoing signals.
| 
 | private | 
| 
 | private | 
| 
 | private | 
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5 |