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SpectraIdentificationViewWidget Class Reference

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

#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>

Inheritance diagram for SpectraIdentificationViewWidget:
QWidget DefaultParamHandler

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 (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 ()
 
- 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
 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

LayerDatalayer_
 
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< 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, noneEnzyme to use for digestion (select 'none' 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 max: 4Model 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

SpectraIdentificationViewWidget ( const Param preferences,
QWidget parent = 0 
)

Constructor.

virtual ~SpectraIdentificationViewWidget ( )
virtual

Destructor.

Member Function Documentation

void attachLayer ( LayerData model)

Attach model.

Referenced by TOPPViewBase::updateViewBar().

void cellClicked_ ( int  row,
int  column 
)
privateslot

Cell clicked in table_widget.

void exportEntries_ ( )
privateslot

Export table entries as csv.

QTableWidget* getTableWidget ( )
void headerContextMenu_ ( const QPoint &  )
privateslot

Display header context menu.

void requestVisibleArea1D ( double  ,
double   
)
signal
void saveIdXML_ ( )
privateslot

Saves the (potentially filtered) idXML.

void showSpectrumAs1D ( int  )
signal
void showSpectrumMetaData ( int  )
signal
void spectrumDeselected ( int  )
signal
void spectrumDoubleClicked ( int  )
signal
void spectrumSelected ( int  )
signal
void spectrumSelectionChange_ ( QTableWidgetItem *  ,
QTableWidgetItem *   
)
privateslot

Emits spectrumSelected with the current spectrum index.

void updateEntries ( )
slot

Rebuild table entries.

Referenced by TOPPViewBase::updateViewBar().

Member Data Documentation

QCheckBox* create_rows_for_commmon_metavalue_
private
QCheckBox* hide_no_identification_
private
bool ignore_update

Helper function to block outgoing signals.

bool is_ms1_shown_
private
LayerData* layer_
private
QTableWidget* table_widget_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:44 using doxygen 1.8.9.1