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 |
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| ) |
Constructor.
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virtual |
Destructor.
| void attachLayer | ( | LayerData * | model | ) |
Attach model.
Referenced by TOPPViewBase::updateViewBar().
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privateslot |
Cell clicked in table_widget.
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privateslot |
Export table entries as csv.
| QTableWidget* getTableWidget | ( | ) |
Referenced by TOPPViewBase::updateViewBar().
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privateslot |
Display header context menu.
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signal |
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privateslot |
Saves the (potentially filtered) idXML.
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signal |
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signal |
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signal |
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signal |
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signal |
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privateslot |
Emits spectrumSelected with the current spectrum index.
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slot |
Rebuild table entries.
Referenced by TOPPViewBase::updateViewBar().
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private |
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private |
| bool ignore_update |
Helper function to block outgoing signals.
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private |
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private |
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private |
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5 |