| OpenMS 2.5.0

Signals | Public Member Functions | Public Attributes | Protected Slots | Private Slots | Private Member Functions | Private Attributes | List of all members
SpectraIdentificationViewWidget Class Reference

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

`#include <OpenMS/VISUAL/SpectraIdentificationViewWidget.h>`

Inheritance diagram for SpectraIdentificationViewWidget:

## 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=nullptr)
| Constructor. More...
| ~SpectraIdentificationViewWidget () override
| Destructor. More...
void | setLayer (LayerData *model)
| set / get layer data More...
LayerData * | getLayer ()
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 &param)
| 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...

## Protected Slots

void | updateEntries ()
| Rebuild table entries. 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_
QTableWidget * | fragment_window_

## 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 | PepsinA, Alpha-lytic protease, 2-iodobenzoate, Asp-N, Chymotrypsin, iodosobenzoate, Lys-C, staphylococcal protease/D, proline-endopeptidase/HKR, Lys-N, TrypChymo, Formic_acid, Trypsin/P, V8-DE, V8-E, Trypsin, CNBr, Lys-C/P, Asp-N_ambic, Asp-N/B, leukocyte elastase, Chymotrypsin/P, proline endopeptidase, Arg-C, Arg-C/P, glutamyl endopeptidase, PepsinA + P, Glu-C+P, Clostripain/P, cyanogen-bromide, elastase-trypsin-chymotrypsin, no cleavage, unspecific cleavage | 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: -2.0 max: 4.0 | 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 = `nullptr`
| ) |  |

Constructor.

## ◆ ~SpectraIdentificationViewWidget()

~SpectraIdentificationViewWidget | ( |  | ) |

override

Destructor.

## Member Function Documentation

## ◆ addCheckboxItemToBottomRow_()

void addCheckboxItemToBottomRow_ | ( | bool | selected,
|  | Size | column_index,
|  | const QColor & | c
| ) |  |

private

## ◆ addDoubleItemToBottomRow_()

void addDoubleItemToBottomRow_ | ( | const double | d,
|  | Size | column_index,
|  | const QColor & | c
| ) |  |

private

## ◆ addIntItemToBottomRow_()

void addIntItemToBottomRow_ | ( | const Int | i,
|  | Size | column_index,
|  | const QColor & | c
| ) |  |

private

## ◆ addTextItemToBottomRow_()

void addTextItemToBottomRow_ | ( | const QString & | text,
|  | Size | column_index,
|  | const QColor & | c
| ) |  |

private

## ◆ cellClicked_

void cellClicked_ | ( | int | row,
|  | int | column
| ) |  |

private slot

Cell clicked in table_widget.

## ◆ exportEntries_

void exportEntries_ | ( |  | ) |

private slot

Export table entries as csv.

## ◆ getLayer()

LayerData* getLayer | ( |  | ) |

Referenced by TOPPViewBase::updateViewBar().

## ◆ getTableWidget()

QTableWidget* getTableWidget | ( |  | ) |

Access the table widget.

Referenced by TOPPViewBase::updateViewBar().

## ◆ headerContextMenu_

void headerContextMenu_ | ( | const QPoint & |  | ) |

private slot

Display header context menu.

## ◆ requestVisibleArea1D

void requestVisibleArea1D | ( | double | ,
|  | double |
| ) |  |

signal

## ◆ saveIDs_

void saveIDs_ | ( |  | ) |

private slot

Saves the (potentially filtered) IDs as an idXML or mzIdentML file.

## ◆ setLayer()

void setLayer | ( | LayerData * | model | ) |

set / get layer data

Referenced by TOPPViewBase::updateViewBar().

## ◆ showSpectrumAs1D

void showSpectrumAs1D | ( | int |  | ) |

signal

## ◆ showSpectrumMetaData

void showSpectrumMetaData | ( | int |  | ) |

signal

## ◆ spectrumDeselected

void spectrumDeselected | ( | int |  | ) |

signal

## ◆ spectrumDoubleClicked

void spectrumDoubleClicked | ( | int |  | ) |

signal

## ◆ spectrumSelected

void spectrumSelected | ( | int | ,
|  | int | ,
|  | int |
| ) |  |

signal

## ◆ spectrumSelectionChange_

void spectrumSelectionChange_ | ( | QTableWidgetItem * | ,
|  | QTableWidgetItem * |
| ) |  |

private slot

Emits spectrumSelected with the current spectrum index.

## ◆ updateData_

void updateData_ | ( | QTableWidgetItem * | item | ) |

private slot

update PeptideIdentification / PeptideHits, when data in the table changes (status of checkboxes)

## ◆ updateEntries

void updateEntries | ( |  | ) |

protected slot

Rebuild table entries.

## Member Data Documentation

## ◆ create_rows_for_commmon_metavalue_

QCheckBox* create_rows_for_commmon_metavalue_

private

## ◆ fragment_window_

QTableWidget* fragment_window_

private

## ◆ hide_no_identification_

QCheckBox* hide_no_identification_

private

## ◆ ignore_update

bool ignore_update

Helper function to block outgoing signals.

## ◆ is_ms1_shown_

bool is_ms1_shown_

private

## ◆ layer_

LayerData* layer_

private

## ◆ table_widget_

QTableWidget* table_widget_

private