| OpenMS 2.5.0

Public Slots | Public Member Functions | Static Public Member Functions | Protected Types | Protected Slots | Protected Member Functions | Protected Attributes | Static Private Attributes | Friends | List of all members
TOPPViewBase Class Reference
Visual » TOPPView

Main window of TOPPView tool. More...

`#include <OpenMS/VISUAL/APPLICATIONS/TOPPViewBase.h>`

Inheritance diagram for TOPPViewBase:

## Public Types

Type definitions
typedef LayerData::FeatureMapType | FeatureMapType
typedef LayerData::FeatureMapSharedPtrType | FeatureMapSharedPtrType
typedef LayerData::ConsensusMapType | ConsensusMapType
typedef LayerData::ConsensusMapSharedPtrType | ConsensusMapSharedPtrType
typedef LayerData::ExperimentType | ExperimentType
typedef LayerData::ExperimentSharedPtrType | ExperimentSharedPtrType
typedef LayerData::ODExperimentSharedPtrType | ODExperimentSharedPtrType
typedef ExperimentType::SpectrumType | SpectrumType
| Peak spectrum type. More...

## Public Slots

void | updateCurrentPath ()
| changes the current path according to the currently active window/layer More...
void | showURL ()
| shows the URL stored in the data of the sender QAction More...
void | openFileDialog ()
| shows the file dialog for opening files More...
void | openExampleDialog ()
| shows the file dialog for opening example files More...
void | showGoToDialog ()
| shows the DB dialog for opening files More...
void | preferencesDialog ()
| shows the preferences dialog More...
void | layerStatistics ()
| Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data. More...
void | editMetadata ()
| lets the user edit the meta data of a layer More...
void | layerActivated ()
| gets called if a layer got activated More...
void | layerZoomChanged ()
| gets called when a layer changes in zoom More...
void | linkZoom ()
| link the zoom of individual windows More...
void | layerDeactivated ()
| gets called if a layer got deactivated More...
void | closeFile ()
| closes the active window More...
void | updateToolBar ()
| updates the toolbar More...
void | updateLayerBar ()
| adapts the layer bar to the active window More...
void | updateViewBar ()
| adapts view bar to the active window More...
void | viewChanged (int)
| changes the behavior according to the selected view in the spectra view bar and calls updateSpectraViewBar() More...
void | viewTabwidgetDoubleClicked (int)
| adds empty ID structure to allow manual annotations More...
void | updateFilterBar ()
| adapts the filter bar to the active window More...
void | updateMenu ()
| enabled/disabled menu entries depending on the current state More...
void | updateTabBar (QMdiSubWindow *w)
| brings the tab corresponding to the active window in front More...
void | tileVertical ()
| tile the open windows vertically More...
void | tileHorizontal ()
| tile the open windows horizontally More...
void | showStatusMessage (std::string msg, OpenMS::UInt time)
| Shows a status message in the status bar. More...
void | showCursorStatus (double mz, double rt)
| shows m/z and rt in the status bar More...
void | showCursorStatusInvert (double mz, double rt)
| shows m/z and rt in the status bar (inverting RT and m/z) More...
void | showTOPPDialog ()
| Apply TOPP tool. More...
void | annotateWithID ()
| Annotates current layer with ID data. More...
void | showSpectrumGenerationDialog ()
| Shows the theoretical spectrum generation dialog. More...
void | showSpectrumAlignmentDialog ()
| Shows the spectrum alignment dialog. More...
void | showSpectrumAs1D (int index)
| Shows the spectrum with index `index` of the active layer in 1D. More...
void | showSpectrumAs1D (std::vector< int, std::allocator< int > > indices)
void | showCurrentPeaksAs2D ()
| Shows the current peak data of the active layer in 2D. More...
void | showCurrentPeaksAs3D ()
| Shows the current peak data of the active layer in 3D. More...
void | showCurrentPeaksAsIonMobility ()
| Shows the current peak data of the active layer as ion mobility. More...
void | showCurrentPeaksAsDIA ()
| Shows the current peak data of the active layer as DIA data. More...
void | showAboutDialog ()
| Shows the 'About' dialog. More...
void | saveLayerAll ()
| Saves the whole current layer data. More...
void | saveLayerVisible ()
| Saves the visible layer data. More...
void | toggleGridLines ()
| Toggles the grid lines. More...
void | toggleAxisLegends ()
| Toggles the axis legends. More...
void | toggleInterestingMZs ()
| Toggles drawing of interesting MZs. More...
void | showPreferences ()
| Shows current layer preferences. More...
void | metadataFileDialog ()
| dialog for inspecting database meta data More...
void | loadFile (QString)
| Loads a file given by the passed string. More...
Toolbar slots
void | setDrawMode1D (int)
void | setIntensityMode (int)
void | changeLayerFlag (bool)
void | changeLabel (QAction *)
void | changeUnassigned (QAction *)
void | resetZoom ()
void | toggleProjections ()

## Public Member Functions

| TOPPViewBase (QWidget *parent=nullptr)
| Constructor. More...
| ~TOPPViewBase () override
| Destructor. More...
void | addDataFile (const String &filename, bool show_options, bool add_to_recent, String caption="", UInt window_id=0, Size spectrum_id=0)
| Opens and displays data from a file. More...
void | addData (FeatureMapSharedPtrType feature_map, ConsensusMapSharedPtrType consensus_map, std::vector< PeptideIdentification > &peptides, ExperimentSharedPtrType peak_map, ODExperimentSharedPtrType on_disc_peak_map, LayerData::DataType data_type, bool show_as_1d, bool show_options, bool as_new_window=true, const String &filename="", const String &caption="", UInt window_id=0, Size spectrum_id=0)
| Adds a peak or feature map to the viewer. More...
void | loadFiles (const StringList &list, QSplashScreen *splash_screen)
| Opens all the files in the string list. More...
void | loadPreferences (String filename="")
| Loads the preferences from the filename given. More...
void | savePreferences ()
| Stores the preferences (used when this window is closed) More...
Param | getSpectrumParameters (UInt dim)
| Returns the parameters for a SpectrumCanvas of dimension `dim`. More...
const LayerData * | getCurrentLayer () const
| Returns the active Layer data (0 if no layer is active) More...
SpectrumCanvas * | getActiveCanvas () const
| returns a pointer to the active SpectrumCanvas (0 if none is active) More...
SpectraIdentificationViewWidget * | getSpectraIdentificationViewWidget ()
| returns a pointer to the SpectraIdentificationViewWidget More...
void | showSpectrumWidgetInWindow (SpectrumWidget *sw, const String &caption)
| Opens the provided spectrum widget in a new window. More...
float | estimateNoiseFromRandomMS1Scans (const ExperimentType &exp, UInt n_scans=10)
| Estimates the noise by evaluating n_scans random scans of MS level 1. Assumes that 4/5 of intensities is noise. More...
EnhancedWorkspace * | getWorkspace () const
| returns a pointer to the EnhancedWorkspace containing SpectrumWidgets More...
SpectrumWidget * | getActiveSpectrumWidget () const
| returns a pointer to the active SpectrumWidget (0 if none is active) More...
Spectrum1DWidget * | getActive1DWidget () const
| returns a pointer to the active Spectrum1DWidget (0 the active window is no Spectrum1DWidget or there is no active window) More...
Spectrum2DWidget * | getActive2DWidget () const
| returns a pointer to the active Spectrum2DWidget (0 the active window is no Spectrum2DWidget or there is no active window) More...
Spectrum3DWidget * | getActive3DWidget () const
| returns a pointer to the active Spectrum3DWidget (0 the active window is no Spectrum2DWidget or there is no active window) 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...

## Static Public Member Functions

static bool | containsMS1Scans (const ExperimentType &exp)
| Returns true if `contains` at least one MS1 spectrum. More...
static bool | containsIMData (const MSSpectrum &s)
| Returns true if `contains` ion mobility data. More...
static bool | hasMS1Zeros (const ExperimentType &exp)
| Returns true of experiment has at least one exact zero valued peak in any of its MS1 spectra. More...
static bool | hasPeptideIdentifications (const ExperimentType &map)
| Returns true if the experiment map contains peptide identifications. More...

## Protected Types

enum | LogState { LS_NOTICE, LS_WARNING, LS_ERROR }
| Log message states. More...

## Protected Slots

void | finishTOPPToolExecution (int exitCode, QProcess::ExitStatus exitStatus)
| slot for the finished signal of the TOPP tools execution More...
void | abortTOPPTool ()
| aborts the execution of a TOPP tool More...
void | rerunTOPPTool ()
| returns the last invoked TOPP tool with the same parameters More...
void | showSpectrumBrowser ()
| shows the spectrum browser and updates it More...
void | showSpectrumMetaData (int spectrum_index)
| shows the spectrum metadata More...
void | updateProcessLog ()
| Appends process output to log window. More...
void | fileChanged_ (const String &)
| Called if a data file has been externally changed. More...
Layer manager and filter manager slots
void | layerSelectionChange (int)
| slot for layer manager selection change More...
void | layerFilterVisibilityChange (bool)
| Enables/disables the data filters for the current layer. More...
void | layerContextMenu (const QPoint &pos)
| slot for layer manager context menu More...
void | logContextMenu (const QPoint &pos)
| slot for log window context menu More...
void | layerVisibilityChange (QListWidgetItem *item)
| slot for layer manager visibility change (check box) More...
void | filterContextMenu (const QPoint &pos)
| slot for filter manager context menu More...
void | filterEdit (QListWidgetItem *item)
| slot for editing a filter More...
void | layerEdit (QListWidgetItem *)
| slot for editing the preferences of the current layer More...
Tabbar slots
void | closeByTab (int id)
| Closes the window corresponding to the data of the tab with identifier `id`. More...
void | enhancedWorkspaceWindowChanged (int id)
| Raises the window corresponding to the data of the tab with identifier `id`. More...
void | openRecentFile ()
| Opens a file from the recent files menu. More...
void | copyLayer (const QMimeData *data, QWidget *source, int id=-1)
| Slot for drag-and-drop of layer manager to tabbar. More...

## Protected Member Functions

void | initializeDefaultParameters_ ()
| Initializes the default parameters on TOPPView construction. More...
bool | annotateMS1FromMassFingerprinting_ (const FeatureMap &identifications)
std::set< String > | getFilenamesOfOpenFiles_ ()
| unique list of files referenced by all layers More...
QStringList | getFileList_ (const String &path_overwrite="")
| Shows a dialog where the user can select files. More...
EnhancedTabBarWidgetInterface * | window_ (int id) const
| Returns the enhanced tabbar widget with id `id`. More...
void | checkPreferences_ ()
| check if all available preferences get set by the .ini file. If there are some missing entries fill them with default values. More...
void | showLogMessage_ (LogState state, const String &heading, const String &body)
| Shows a log message in the log_ window. More...
void | showTOPPDialog_ (bool visible)
| Apply TOPP tool. If `visible` is true, only the visible data is used, otherwise the whole layer is used. More...
reimplemented Qt events
void | closeEvent (QCloseEvent *event) override
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

QListWidget * | layers_view_
| Layer management widget. More...
FileWatcher * | watcher_
| Watcher that tracks file changes (in order to update the data in the different views) More...
bool | watcher_msgbox_
| Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again, if file changes again before the messagebox is closed) More...
bool | zoom_together_
| Stores whether the individual windows should zoom together (be linked) or not. More...
QAction * | linkZoom_action_
QTextEdit * | log_
| Log output window. More...
EnhancedWorkspace * | ws_
| Main workspace. More...
EnhancedTabBar * | tab_bar_
| Tab bar. The address of the corresponding window to a tab is stored as an int in tabData() More...
QMenu * | add_2d_context_
| Additional context menu for 2D layers. More...
String | current_path_
QTabWidget * | views_tabwidget_
| Tabwidget that hold the different views on the loaded data. More...
TOPPViewIdentificationViewBehavior * | identificationview_behavior_
| TOPPView behavior for the identification view. More...
TOPPViewSpectraViewBehavior * | spectraview_behavior_
| TOPPView behavior for the spectra view. More...
dock widgets
QDockWidget * | layer_dock_widget_
QDockWidget * | views_dockwidget_
QDockWidget * | filter_dock_widget_
Spectrum selection widgets
SpectraViewWidget * | spectra_view_widget_
SpectraIdentificationViewWidget * | spectra_identification_view_widget_
Filter widgets
QListWidget * | filters_
QCheckBox * | filters_check_box_
Toolbar
QToolBar * | tool_bar_
QButtonGroup * | intensity_button_group_
QToolBar * | tool_bar_1d_
QButtonGroup * | draw_group_1d_
QToolBar * | tool_bar_2d_peak_
QToolBar * | tool_bar_2d_feat_
QToolBar * | tool_bar_2d_cons_
QToolBar * | tool_bar_2d_ident_
QAction * | dm_precursors_2d_
QAction * | dm_hull_2d_
QAction * | dm_hulls_2d_
QToolButton * | dm_label_2d_
QActionGroup * | group_label_2d_
QToolButton * | dm_unassigned_2d_
QActionGroup * | group_unassigned_2d_
QAction * | dm_elements_2d_
QAction * | projections_2d_
QAction * | dm_ident_2d_
Status bar
QLabel * | message_label_
| Label for messages in the status bar. More...
QLabel * | mz_label_
| m/z label for messages in the status bar More...
QLabel * | rt_label_
| RT label for messages in the status bar. 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...

## Static Private Attributes

static const String | CAPTION_3D_SUFFIX_ = " (3D)"
| Suffix appended to caption of tabs when layer is shown in 3D. More...

## Friends

class | TestTOPPView

## Recent files

QStringList | recent_files_
| list of the recently opened files More...
std::vector< QAction * > | recent_actions_
| list of the recently opened files actions (menu entries) More...
void | addRecentFile_ (const String &filename)
| adds a Filename to the recent files More...
void | updateRecentMenu_ ()
| update the recent files menu More...

## TOPP tool execution

struct {
Param | param
String | tool
String | in
String | out
String | file_name
String | layer_name
UInt | window_id
Size | spectrum_id
QProcess * | process
QTime | timer
bool | visible
} | topp_
| Information needed for execution of TOPP tools. More...
void | runTOPPTool_ ()
| Runs the TOPP tool according to the information in topp_. More...

## Detailed Description

Main window of TOPPView tool.

Uses the default QMainWindow layout (see Qt documentation) with a central widget in the middle (consistent of a EnhancedTabBar and an EnhancedWorkspace) and multiple docked widgets around it (to the right and below) and multiple tool bars. On top and bottom are a menu bar and a status bar.

The main layout is using

- Central Widget:
  - EnhancedTabBar: tab_bar_
  - EnhancedWorkspace: ws_
- Docked to the right:
  - layer_dock_widget_
  - views_dockwidget_
  - filter_dock_widget_
- Docked to the bottom:
  - log_bar (only connected through slots)

The views_dockwidget_ internally holds a tab widget views_tabwidget_ which holds the two different views on the data (spectra and identification view) which are implemented using identificationview_behavior_ and spectraview_behavior_.

Improvement:
  Use DataRepository singleton to share data between TOPPView and the canvas classes (Hiwi)

Improvement:
  For painting single mass traces with no width we currently paint each line twice (once going down, and then coming back up). This could be more efficient...

Improvement:
  Keep spectrum browser widgets of all layers in memory in order to avoid rebuilding the entire tree view every time the active layer changes (Hiwi, Johannes)

## Member Typedef Documentation

## ◆ ConsensusMapSharedPtrType

typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

## ◆ ConsensusMapType

typedef LayerData::ConsensusMapType ConsensusMapType

## ◆ ExperimentSharedPtrType

typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType

## ◆ ExperimentType

typedef LayerData::ExperimentType ExperimentType

## ◆ FeatureMapSharedPtrType

typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType

## ◆ FeatureMapType

typedef LayerData::FeatureMapType FeatureMapType

## ◆ ODExperimentSharedPtrType

typedef LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType

## ◆ SpectrumType

typedef ExperimentType::SpectrumType SpectrumType

Peak spectrum type.

## Member Enumeration Documentation

## ◆ LogState

enum LogState

protected

Log message states.

Enumerator
LS_NOTICE | Notice.
LS_WARNING | Warning.
LS_ERROR | Fatal error.

## Constructor & Destructor Documentation

## ◆ TOPPViewBase()

TOPPViewBase | ( | QWidget * | parent = `nullptr` | ) |

Constructor.

References EnhancedTabBar::addTab(), TOPPViewBase::annotateWithID(), TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::closeByTab(), TOPPViewBase::closeFile(), TOPPViewBase::copyLayer(), TOPPViewBase::current_path_, DefaultParamHandler::defaultsToParam_(), Spectrum1DCanvas::DM_CONNECTEDLINES, TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_label_2d_, Spectrum1DCanvas::DM_PEAKS, TOPPViewBase::dm_precursors_2d_, TOPPViewBase::dm_unassigned_2d_, TOPPViewBase::draw_group_1d_, TOPPViewBase::editMetadata(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::filters_, TOPPViewBase::filters_check_box_, Param::getValue(), TOPPViewBase::group_label_2d_, TOPPViewBase::group_unassigned_2d_, TOPPViewBase::identificationview_behavior_, SpectrumCanvas::IM_LOG, SpectrumCanvas::IM_NONE, SpectrumCanvas::IM_PERCENTAGE, SpectrumCanvas::IM_SNAP, TOPPViewBase::initializeDefaultParameters_(), TOPPViewBase::intensity_button_group_, TOPPViewBase::layer_dock_widget_, TOPPViewBase::layerContextMenu(), TOPPViewBase::layerEdit(), TOPPViewBase::layerFilterVisibilityChange(), TOPPViewBase::layers_view_, TOPPViewBase::layerSelectionChange(), TOPPViewBase::layerStatistics(), TOPPViewBase::layerVisibilityChange(), TOPPViewBase::linkZoom(), TOPPViewBase::linkZoom_action_, TOPPViewBase::loadPreferences(), TOPPViewBase::log_, TOPPViewBase::logContextMenu(), TOPPViewBase::message_label_, TOPPViewBase::metadataFileDialog(), TOPPViewBase::mz_label_, LayerData::NamesOfLabelType, TOPPViewBase::openExampleDialog(), TOPPViewBase::openFileDialog(), TOPPViewBase::openRecentFile(), DefaultParamHandler::param_, TOPPViewBase::preferencesDialog(), TOPPViewBase::projections_2d_, TOPPViewBase::recent_actions_, EnhancedTabBar::removeId(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::resetZoom(), TOPPViewBase::rt_label_, TOPPViewBase::saveLayerAll(), TOPPViewBase::saveLayerVisible(), TOPPViewBase::setDrawMode1D(), TOPPViewBase::setIntensityMode(), TOPPViewBase::showAboutDialog(), TOPPViewBase::showGoToDialog(), TOPPViewBase::showPreferences(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::showSpectrumGenerationDialog(), TOPPViewBase::showSpectrumMetaData(), TOPPViewBase::showTOPPDialog(), TOPPViewBase::showURL(), LayerData::SIZE_OF_LABEL_TYPE, TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, TOPPViewBase::spectraview_behavior_, TOPPViewBase::tab_bar_, TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::toggleAxisLegends(), TOPPViewBase::toggleGridLines(), TOPPViewBase::toggleInterestingMZs(), TOPPViewBase::toggleProjections(), TOPPViewBase::tool_bar_, TOPPViewBase::tool_bar_1d_, TOPPViewBase::tool_bar_2d_cons_, TOPPViewBase::tool_bar_2d_feat_, TOPPViewBase::tool_bar_2d_ident_, TOPPViewBase::tool_bar_2d_peak_, TOPPViewBase::topp_, TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateTabBar(), TOPPViewBase::updateToolBar(), TOPPViewBase::updateViewBar(), TOPPViewBase::viewChanged(), TOPPViewBase::views_dockwidget_, TOPPViewBase::views_tabwidget_, TOPPViewBase::viewTabwidgetDoubleClicked(), TOPPViewBase::watcher_, TOPPViewBase::ws_, and TOPPViewBase::zoom_together_.

## ◆ ~TOPPViewBase()

~TOPPViewBase | ( |  | ) |

override

Destructor.

References TOPPViewBase::abortTOPPTool(), TOPPViewBase::identificationview_behavior_, TOPPViewBase::savePreferences(), and TOPPViewBase::spectraview_behavior_.

## Member Function Documentation

## ◆ abortTOPPTool

void abortTOPPTool | ( |  | ) |

protected slot

aborts the execution of a TOPP tool

References TOPPViewBase::log_, TOPPViewBase::topp_, and TOPPViewBase::updateMenu().

Referenced by TOPPViewBase::~TOPPViewBase().

## ◆ addData()

void addData | ( | FeatureMapSharedPtrType | feature_map,
|  | ConsensusMapSharedPtrType | consensus_map,
|  | std::vector< PeptideIdentification > & | peptides,
|  | ExperimentSharedPtrType | peak_map,
|  | ODExperimentSharedPtrType | on_disc_peak_map,
|  | LayerData::DataType | data_type,
|  | bool | show_as_1d,
|  | bool | show_options,
|  | bool | as_new_window = `true`,
|  | const String & | filename = `""`,
|  | const String & | caption = `""`,
|  | UInt | window_id = `0`,
|  | Size | spectrum_id = `0`
| ) |  |

Adds a peak or feature map to the viewer.

Parameters

  feature_map | The feature data (empty if not feature data)
  consensus_map | The consensus feature data (empty if not consensus feature data)
  peptides | The peptide identifications (empty if not ID data)
  peak_map | The peak data (empty if not peak data)
  on_disc_peak_map | The peak data managed on disc (empty if not peak data)
  data_type | Type of the data
  show_as_1d | Force dataset to be opened in 1D mode (even if it contains several spectra)
  show_options | If the options dialog should be shown (otherwise the defaults are used)
  filename | source file name (if the data came from a file)
  caption | Sets the layer name and window caption of the data. If unset the file name is used. If set, the file is not monitored for changes.
  window_id | in which window the file is opened if opened as a new layer (0 or default equals current
  spectrum_id | determines the spectrum to show in 1D view.

add filter

References Spectrum1DCanvas::activateSpectrum(), DataFilters::add(), SpectrumCanvas::addLayer(), Spectrum1DWidget::canvas(), SpectrumWidget::canvas(), TOPPViewOpenDialog::disableCutoff(), TOPPViewOpenDialog::disableDimension(), TOPPViewOpenDialog::disableLocation(), LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_IDENT, TOPPViewBase::estimateNoiseFromRandomMS1Scans(), DataFilters::DataFilter::field, TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), TOPPViewOpenDialog::getMergeLayer(), LayerData::getPeakData(), TOPPViewBase::getSpectrumParameters(), Param::getValue(), DataFilters::GREATER_EQUAL, TOPPViewBase::hasMS1Zeros(), DataFilters::INTENSITY, TOPPViewOpenDialog::isCutoffEnabled(), TOPPViewOpenDialog::isDataDIA(), Spectrum2DCanvas::mergeIntoLayer(), LayerData::name, DataFilters::DataFilter::op, TOPPViewOpenDialog::openAsNewWindow(), DefaultParamHandler::param_, SpectrumCanvas::setFilters(), TOPPViewOpenDialog::setMergeLayers(), TOPPViewBase::showSpectrumWidgetInWindow(), LayerData::type, TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), DataFilters::DataFilter::value, TOPPViewOpenDialog::viewMapAs1D(), TOPPViewOpenDialog::viewMapAs2D(), TOPPViewBase::views_tabwidget_, TOPPViewBase::window_(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::copyLayer(), and TOPPViewBase::showSpectrumGenerationDialog().

## ◆ addDataFile()

void addDataFile | ( | const String & | filename,
|  | bool | show_options,
|  | bool | add_to_recent,
|  | String | caption = `""`,
|  | UInt | window_id = `0`,
|  | Size | spectrum_id = `0`
| ) |  |

Opens and displays data from a file.

Loads the data and adds it to the application by calling addData_()

Parameters

  filename | The file to open
  show_options | If the options dialog should be shown (otherwise the defaults are used)
  caption | Sets the layer name and window caption of the data. If unset the file name is used.
  add_to_recent | If the file should be added to the recent files after opening
  window_id | in which window the file is opened if opened as a new layer (0 or default equals current window).
  spectrum_id | determines the spectrum to show in 1D view.

References File::absolutePath(), TOPPViewBase::addData(), FileWatcher::addFile(), TOPPViewBase::addRecentFile_(), File::basename(), FileTypes::CONSENSUSXML, TOPPViewBase::containsMS1Scans(), LayerData::DT_CHROMATOGRAM, LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_IDENT, LayerData::DT_PEAK, File::exists(), FileTypes::FEATUREXML, IndexedMzMLHandler::getNrChromatograms(), IndexedMzMLHandler::getNrSpectra(), IndexedMzMLHandler::getParsingSuccess(), FileHandler::getType(), Param::getValue(), ProgressLogger::GUI, FileTypes::IDXML, FileTypes::INI, OpenMS::Constants::k, ConsensusXMLFile::load(), MzIdentMLFile::load(), IdXMLFile::load(), FeatureXMLFile::load(), FileHandler::loadExperiment(), TOPPViewBase::LS_ERROR, TOPPViewBase::LS_WARNING, FileTypes::MZIDENTML, FileTypes::MZML, IndexedMzMLHandler::openFile(), OPENMS_LOG_INFO, DefaultParamHandler::param_, File::removeExtension(), TOPPViewBase::showLogMessage_(), FileTypes::typeToName(), FileTypes::UNKNOWN, TOPPViewBase::watcher_, and BaseException::what().

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::loadFile(), TOPPViewBase::loadFiles(), TOPPViewBase::openExampleDialog(), TOPPViewBase::openFileDialog(), and TOPPViewBase::openRecentFile().

## ◆ addRecentFile_()

void addRecentFile_ | ( | const String & | filename | ) |

protected

adds a Filename to the recent files

References File::absolutePath(), Param::getValue(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, String::toQString(), and TOPPViewBase::updateRecentMenu_().

Referenced by TOPPViewBase::addDataFile().

## ◆ annotateMS1FromMassFingerprinting_()

bool annotateMS1FromMassFingerprinting_ | ( | const FeatureMap & | identifications | ) |

protected

add annotations from an AccurateMassSearch to an MS1 spectrum

Returns
  true on success, otherwise false

References IDMapper::annotate(), LayerData::DT_PEAK, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), DefaultParamHandler::getParameters(), LayerData::getPeakDataMuteable(), TOPPViewBase::LS_NOTICE, DefaultParamHandler::setParameters(), Param::setValue(), TOPPViewBase::showLogMessage_(), and LayerData::type.

Referenced by TOPPViewBase::annotateWithID().

## ◆ annotateWithID

void annotateWithID | ( |  | ) |

slot

Annotates current layer with ID data.

References IDMapper::annotate(), TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::current_path_, LayerData::DT_FEATURE, LayerData::DT_PEAK, FileTypes::FEATUREXML, TOPPViewBase::getActiveCanvas(), LayerData::getConsensusMap(), SpectrumCanvas::getCurrentLayer(), DefaultParamHandler::getDefaults(), LayerData::getFeatureMap(), LayerData::getPeakDataMuteable(), FeatureMap::getProteinIdentifications(), FileHandler::getType(), FileTypes::IDXML, MzIdentMLFile::load(), IdXMLFile::load(), FeatureXMLFile::load(), TOPPViewBase::LS_NOTICE, FileTypes::MZIDENTML, DefaultParamHandler::setParameters(), Param::setValue(), TOPPViewBase::showLogMessage_(), String::toQString(), LayerData::type, TOPPViewBase::updateViewBar(), TOPPViewBase::views_tabwidget_, LayerData::visible, and BaseException::what().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ changeLabel

void changeLabel | ( | QAction * | action | ) |

slot

References Spectrum2DWidget::canvas(), TOPPViewBase::dm_label_2d_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::getCurrentLayer(), LayerData::L_INDEX, LayerData::L_NONE, LayerData::NamesOfLabelType, SpectrumCanvas::setLabel(), LayerData::SIZE_OF_LABEL_TYPE, and TOPPViewBase::updateToolBar().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ changeLayerFlag

void changeLayerFlag | ( | bool | on | ) |

slot

References LayerData::C_ELEMENTS, TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_precursors_2d_, LayerData::F_HULL, LayerData::F_HULLS, TOPPViewBase::getActive2DWidget(), LayerData::I_PEPTIDEMZ, and LayerData::P_PRECURSORS.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ changeUnassigned

void changeUnassigned | ( | QAction * | action | ) |

slot

References Spectrum2DWidget::canvas(), TOPPViewBase::dm_unassigned_2d_, LayerData::F_UNASSIGNED, TOPPViewBase::getActive2DWidget(), SpectrumCanvas::getLayerFlag(), LayerData::I_LABELS, LayerData::I_PEPTIDEMZ, SpectrumCanvas::setLayerFlag(), and TOPPViewBase::updateToolBar().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ checkPreferences_()

void checkPreferences_ | ( |  | ) |

protected

check if all available preferences get set by the .ini file. If there are some missing entries fill them with default values.

## ◆ closeByTab

void closeByTab | ( | int | id | ) |

protected slot

Closes the window corresponding to the data of the tab with identifier `id`.

References TOPPViewBase::updateMenu(), and TOPPViewBase::window_().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ closeEvent()

void closeEvent | ( | QCloseEvent * | event | ) |

override protected

References TOPPViewBase::ws_.

## ◆ closeFile

void closeFile | ( |  | ) |

slot

closes the active window

References TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ containsIMData()

bool containsIMData | ( | const MSSpectrum & | s | ) |

static

Returns true if `contains` ion mobility data.

References MSSpectrum::getFloatDataArrays().

Referenced by TOPPViewBase::showCurrentPeaksAsIonMobility().

## ◆ containsMS1Scans()

bool containsMS1Scans | ( | const ExperimentType & | exp | ) |

static

Returns true if `contains` at least one MS1 spectrum.

References MSExperiment::size().

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), and TOPPViewBase::hasMS1Zeros().

## ◆ copyLayer

void copyLayer | ( | const QMimeData * | data,
|  | QWidget * | source,
|  | int | id = `-1`
| ) |  |

protected slot

Slot for drag-and-drop of layer manager to tabbar.

References TOPPViewBase::addData(), TOPPViewBase::addDataFile(), MSExperiment::addSpectrum(), LayerData::DT_CHROMATOGRAM, LayerData::filename, TOPPViewBase::getActiveCanvas(), LayerData::getConsensusMap(), SpectrumCanvas::getCurrentLayer(), LayerData::getFeatureMap(), LayerData::getOnDiscPeakData(), LayerData::getPeakData(), LayerData::getPeakDataMuteable(), SpectraViewWidget::getTreeWidget(), TOPPViewBase::layers_view_, TOPPViewBase::LS_ERROR, LayerData::name, LayerData::peptides, TOPPViewBase::showLogMessage_(), TOPPViewBase::spectra_view_widget_, LayerData::type, and BaseException::what().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow(), and TOPPViewBase::TOPPViewBase().

## ◆ editMetadata

void editMetadata | ( |  | ) |

slot

lets the user edit the meta data of a layer

References TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), TOPPViewBase::LS_NOTICE, TOPPViewBase::showLogMessage_(), SpectrumCanvas::showMetaData(), and LayerData::visible.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ enhancedWorkspaceWindowChanged

void enhancedWorkspaceWindowChanged | ( | int | id | ) |

protected slot

Raises the window corresponding to the data of the tab with identifier `id`.

References SpectrumWidget::canvas(), SpectrumCanvas::getCurrentLayer(), SpectrumCanvas::getLayerCount(), LayerData::getPeakData(), TOPPViewBase::hasPeptideIdentifications(), TOPPViewBase::views_tabwidget_, and TOPPViewBase::window_().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow(), and TOPPViewBase::TOPPViewBase().

## ◆ estimateNoiseFromRandomMS1Scans()

float estimateNoiseFromRandomMS1Scans | ( | const ExperimentType & | exp,
|  | UInt | n_scans = `10`
| ) |  |

Estimates the noise by evaluating n_scans random scans of MS level 1. Assumes that 4/5 of intensities is noise.

References TOPPViewBase::containsMS1Scans(), MSExperiment::end(), and MSExperiment::size().

Referenced by TOPPViewBase::addData().

## ◆ fileChanged_

void fileChanged_ | ( | const String & | filename | ) |

protected slot

Called if a data file has been externally changed.

References FileWatcher::addFile(), SpectrumWidget::canvas(), LayerData::DT_CHROMATOGRAM, LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_PEAK, LayerData::filename, LayerData::getConsensusMap(), LayerData::getFeatureMap(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), LayerData::getPeakDataMuteable(), Param::getValue(), ConsensusXMLFile::load(), FileHandler::loadExperiment(), FileHandler::loadFeatures(), DefaultParamHandler::param_, FileWatcher::removeFile(), String::toQString(), LayerData::type, TOPPViewBase::updateFilterBar(), SpectrumCanvas::updateLayer(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), TOPPViewBase::watcher_, TOPPViewBase::watcher_msgbox_, BaseException::what(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ filterContextMenu

void filterContextMenu | ( | const QPoint & | pos | ) |

protected slot

slot for filter manager context menu

References DataFilters::add(), TOPPViewBase::filterEdit(), LayerData::filters, TOPPViewBase::filters_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), SpectrumCanvas::getCurrentLayer(), LayerData::name, DataFilters::remove(), SpectrumCanvas::setFilters(), String::toQString(), and TOPPViewBase::updateFilterBar().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ filterEdit

void filterEdit | ( | QListWidgetItem * | item | ) |

protected slot

slot for editing a filter

References LayerData::filters, TOPPViewBase::filters_, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), DataFilters::replace(), SpectrumCanvas::setFilters(), and TOPPViewBase::updateFilterBar().

Referenced by TOPPViewBase::filterContextMenu(), and TOPPViewBase::TOPPViewBase().

## ◆ finishTOPPToolExecution

void finishTOPPToolExecution | ( | int | exitCode,
|  | QProcess::ExitStatus | exitStatus
| ) |  |

protected slot

slot for the finished signal of the TOPP tools execution

References TOPPViewBase::addDataFile(), Param::getValue(), TOPPViewBase::log_, TOPPViewBase::LS_ERROR, TOPPViewBase::LS_NOTICE, DefaultParamHandler::param_, File::readable(), File::remove(), TOPPViewBase::showLogMessage_(), TOPPViewBase::topp_, String::toQString(), DataValue::toString(), and TOPPViewBase::updateMenu().

Referenced by TOPPViewBase::runTOPPTool_().

## ◆ getActive1DWidget()

Spectrum1DWidget * getActive1DWidget | ( |  | ) | const

returns a pointer to the active Spectrum1DWidget (0 the active window is no Spectrum1DWidget or there is no active window)

References TOPPViewBase::getActiveSpectrumWidget().

Referenced by TOPPViewBase::layerContextMenu(), TOPPViewBase::setDrawMode1D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::toggleInterestingMZs(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateToolBar().

## ◆ getActive2DWidget()

Spectrum2DWidget * getActive2DWidget | ( |  | ) | const

returns a pointer to the active Spectrum2DWidget (0 the active window is no Spectrum2DWidget or there is no active window)

References TOPPViewBase::getActiveSpectrumWidget().

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::loadFiles(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::toggleProjections(), TOPPViewBase::updateToolBar(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

## ◆ getActive3DWidget()

Spectrum3DWidget * getActive3DWidget | ( |  | ) | const

returns a pointer to the active Spectrum3DWidget (0 the active window is no Spectrum2DWidget or there is no active window)

References TOPPViewBase::getActiveSpectrumWidget().

Referenced by TOPPViewBase::loadFiles(), and TOPPViewBase::updateToolBar().

## ◆ getActiveCanvas()

SpectrumCanvas * getActiveCanvas | ( |  | ) | const

returns a pointer to the active SpectrumCanvas (0 if none is active)

References SpectrumWidget::canvas(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::getCurrentLayer(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerEdit(), TOPPViewBase::layerFilterVisibilityChange(), TOPPViewBase::layerSelectionChange(), TOPPViewBase::layerVisibilityChange(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::loadFiles(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::saveLayerAll(), TOPPViewBase::saveLayerVisible(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showPreferences(), TOPPViewBase::showSpectrumMetaData(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::toggleGridLines(), TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateViewBar().

## ◆ getActiveSpectrumWidget()

SpectrumWidget * getActiveSpectrumWidget | ( |  | ) | const

returns a pointer to the active SpectrumWidget (0 if none is active)

References TOPPViewBase::ws_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerStatistics(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::loadFiles(), TOPPViewBase::resetZoom(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::setIntensityMode(), TOPPViewBase::showGoToDialog(), TOPPViewBase::toggleAxisLegends(), TOPPViewBase::updateToolBar(), and TOPPViewBase::viewTabwidgetDoubleClicked().

## ◆ getCurrentLayer()

const LayerData * getCurrentLayer | ( |  | ) | const

Returns the active Layer data (0 if no layer is active)

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::getCurrentLayer().

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::filterContextMenu(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::updateCurrentPath(), and TOPPViewBase::updateFilterBar().

## ◆ getFileList_()

QStringList getFileList_ | ( | const String & | path_overwrite = `""` | ) |

protected

Shows a dialog where the user can select files.

References TOPPViewBase::current_path_, String::toQString(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::metadataFileDialog(), TOPPViewBase::openExampleDialog(), and TOPPViewBase::openFileDialog().

## ◆ getFilenamesOfOpenFiles_()

std::set< String > getFilenamesOfOpenFiles_ | ( |  | ) |

protected

unique list of files referenced by all layers

References SpectrumWidget::canvas(), LayerData::filename, SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), and TOPPViewBase::ws_.

## ◆ getSpectraIdentificationViewWidget()

SpectraIdentificationViewWidget * getSpectraIdentificationViewWidget | ( |  | ) |

returns a pointer to the SpectraIdentificationViewWidget

References TOPPViewBase::spectra_identification_view_widget_.

## ◆ getSpectrumParameters()

Param getSpectrumParameters | ( | UInt | dim | ) |

Returns the parameters for a SpectrumCanvas of dimension `dim`.

References Param::copy(), Param::getValue(), DefaultParamHandler::param_, Param::setValue(), and DataValue::toString().

Referenced by TOPPViewBase::addData(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

## ◆ getWorkspace()

EnhancedWorkspace * getWorkspace | ( |  | ) | const

returns a pointer to the EnhancedWorkspace containing SpectrumWidgets

References TOPPViewBase::ws_.

## ◆ hasMS1Zeros()

bool hasMS1Zeros | ( | const ExperimentType & | exp | ) |

static

Returns true of experiment has at least one exact zero valued peak in any of its MS1 spectra.

References TOPPViewBase::containsMS1Scans(), and MSExperiment::size().

Referenced by TOPPViewBase::addData().

## ◆ hasPeptideIdentifications()

bool hasPeptideIdentifications | ( | const ExperimentType & | map | ) |

static

Returns true if the experiment map contains peptide identifications.

References MSExperiment::empty(), and MSExperiment::size().

Referenced by TOPPViewBase::enhancedWorkspaceWindowChanged().

## ◆ initializeDefaultParameters_()

void initializeDefaultParameters_ | ( |  | ) |

protected

Initializes the default parameters on TOPPView construction.

References DefaultParamHandler::defaults_, DefaultParamHandler::getDefaults(), Param::insert(), Param::setMaxInt(), Param::setMinInt(), Param::setSectionDescription(), Param::setValidStrings(), Param::setValue(), and DefaultParamHandler::subsections_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ layerActivated

void layerActivated | ( |  | ) |

slot

gets called if a layer got activated

References TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateToolBar(), and TOPPViewBase::updateViewBar().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ layerContextMenu

void layerContextMenu | ( | const QPoint & | pos | ) |

protected slot

slot for layer manager context menu

References Spectrum1DWidget::canvas(), Spectrum1DCanvas::flipLayer(), Spectrum1DCanvas::flippedLayersExist(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getLayer(), TOPPViewBase::layers_view_, LayerData::name, SpectrumCanvas::removeLayer(), SpectrumCanvas::setLayerName(), Spectrum1DCanvas::setMirrorModeActive(), SpectrumCanvas::showCurrentLayerPreferences(), TOPPViewBase::tab_bar_, String::toQString(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateViewBar().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ layerDeactivated

void layerDeactivated | ( |  | ) |

slot

gets called if a layer got deactivated

## ◆ layerEdit

void layerEdit | ( | QListWidgetItem * |  | ) |

protected slot

slot for editing the preferences of the current layer

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showCurrentLayerPreferences().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ layerFilterVisibilityChange

void layerFilterVisibilityChange | ( | bool | on | ) |

protected slot

Enables/disables the data filters for the current layer.

References SpectrumCanvas::changeLayerFilterState(), and TOPPViewBase::getActiveCanvas().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ layerSelectionChange

void layerSelectionChange | ( | int | i | ) |

protected slot

slot for layer manager selection change

References SpectrumCanvas::activateLayer(), TOPPViewBase::getActiveCanvas(), and TOPPViewBase::updateFilterBar().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ layerStatistics

void layerStatistics | ( |  | ) |

slot

Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data.

References TOPPViewBase::getActiveSpectrumWidget(), SpectrumWidget::showStatistics(), and TOPPViewBase::updateFilterBar().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ layerVisibilityChange

void layerVisibilityChange | ( | QListWidgetItem * | item | ) |

protected slot

slot for layer manager visibility change (check box)

References SpectrumCanvas::changeVisibility(), TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getLayer(), TOPPViewBase::layers_view_, and LayerData::visible.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ layerZoomChanged

void layerZoomChanged | ( |  | ) |

slot

gets called when a layer changes in zoom

References Spectrum1DWidget::canvas(), SpectrumWidget::canvas(), LayerData::DT_CHROMATOGRAM, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), LayerData::getPeakData(), SpectrumCanvas::getVisibleArea(), DIntervalBase< D >::maxX(), DIntervalBase< D >::minX(), DIntervalBase< D >::setMaxX(), DIntervalBase< D >::setMinX(), SpectrumCanvas::setVisibleArea(), LayerData::type, TOPPViewBase::ws_, and TOPPViewBase::zoom_together_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ linkZoom

void linkZoom | ( |  | ) |

slot

link the zoom of individual windows

References TOPPViewBase::linkZoom_action_, and TOPPViewBase::zoom_together_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ loadFile

void loadFile | ( | QString | filename | ) |

slot

Loads a file given by the passed string.

References TOPPViewBase::addDataFile().

## ◆ loadFiles()

void loadFiles | ( | const StringList & | list,
|  | QSplashScreen * | splash_screen
| ) |  |

Opens all the files in the string list.

References TOPPViewBase::addDataFile(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), LayerData::param, SpectrumCanvas::setCurrentLayerParameters(), and Param::setValue().

Referenced by main().

## ◆ loadPreferences()

void loadPreferences | ( | String | filename = `""` | ) |

Loads the preferences from the filename given.

If the filename is empty, the application name + ".ini" is used as filename

References Param::begin(), Param::copy(), Param::end(), File::exists(), Param::exists(), Param::getValue(), VersionInfo::getVersion(), ParamXMLFile::load(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, DefaultParamHandler::setParameters(), Param::setValue(), Param::size(), String::toQString(), DataValue::toString(), and TOPPViewBase::updateRecentMenu_().

Referenced by main(), and TOPPViewBase::TOPPViewBase().

## ◆ logContextMenu

void logContextMenu | ( | const QPoint & | pos | ) |

protected slot

slot for log window context menu

References TOPPViewBase::log_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ metadataFileDialog

void metadataFileDialog | ( |  | ) |

slot

dialog for inspecting database meta data

References MetaDataBrowser::add(), TOPPViewBase::getFileList_(), FileHandler::getOptions(), FileHandler::loadExperiment(), PeakFileOptions::setMetadataOnly(), and BaseException::what().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ openExampleDialog

void openExampleDialog | ( |  | ) |

slot

shows the file dialog for opening example files

References TOPPViewBase::addDataFile(), TOPPViewBase::getFileList_(), and File::getOpenMSDataPath().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ openFileDialog

void openFileDialog | ( |  | ) |

slot

shows the file dialog for opening files

References TOPPViewBase::addDataFile(), and TOPPViewBase::getFileList_().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ openRecentFile

void openRecentFile | ( |  | ) |

protected slot

Opens a file from the recent files menu.

References TOPPViewBase::addDataFile().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ preferencesDialog

void preferencesDialog | ( |  | ) |

slot

shows the preferences dialog

References Param::getValue(), TOPPViewBase::LS_ERROR, DefaultParamHandler::param_, TOPPViewBase::savePreferences(), Param::setValue(), TOPPViewBase::showLogMessage_(), DataValue::toBool(), and DataValue::toQString().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ rerunTOPPTool

void rerunTOPPTool | ( |  | ) |

protected slot

returns the last invoked TOPP tool with the same parameters

References TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), TOPPViewBase::LS_NOTICE, File::remove(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showLogMessage_(), TOPPViewBase::topp_, and LayerData::visible.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ resetZoom

void resetZoom | ( |  | ) |

slot

References SpectrumWidget::canvas(), TOPPViewBase::getActiveSpectrumWidget(), and SpectrumCanvas::resetZoom().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ runTOPPTool_()

void runTOPPTool_ | ( |  | ) |

protected

Runs the TOPP tool according to the information in topp_.

References LayerData::chromatogram_flag_set(), LayerData::DT_CHROMATOGRAM, LayerData::DT_FEATURE, LayerData::DT_PEAK, File::findSiblingTOPPExecutable(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), LayerData::getConsensusMap(), SpectrumCanvas::getCurrentLayer(), LayerData::getCurrentSpectrumIndex(), LayerData::getFeatureMap(), LayerData::getPeakData(), SpectrumCanvas::getVisibleConsensusData(), SpectrumCanvas::getVisibleFeatureData(), SpectrumCanvas::getVisiblePeakData(), SpectrumWidget::getWindowId(), ProgressLogger::GUI, TOPPViewBase::LS_ERROR, TOPPViewBase::LS_NOTICE, LayerData::name, LayerData::remove_chromatogram_flag(), ProgressLogger::setLogType(), TOPPViewBase::showLogMessage_(), ConsensusXMLFile::store(), FeatureXMLFile::store(), MzMLFile::store(), TOPPViewBase::topp_, String::toQString(), LayerData::type, TOPPViewBase::updateMenu(), TOPPViewBase::updateProcessLog(), and File::writable().

Referenced by TOPPViewBase::rerunTOPPTool(), and TOPPViewBase::showTOPPDialog_().

## ◆ saveLayerAll

void saveLayerAll | ( |  | ) |

slot

Saves the whole current layer data.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::saveCurrentLayer().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ saveLayerVisible

void saveLayerVisible | ( |  | ) |

slot

Saves the visible layer data.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::saveCurrentLayer().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ savePreferences()

void savePreferences | ( |  | ) |

Stores the preferences (used when this window is closed)

References Param::copy(), Param::getValue(), VersionInfo::getVersion(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, Param::removeAll(), Param::setValue(), and ParamXMLFile::store().

Referenced by TOPPViewBase::preferencesDialog(), and TOPPViewBase::~TOPPViewBase().

## ◆ setDrawMode1D

void setDrawMode1D | ( | int | index | ) |

slot

References Spectrum1DWidget::canvas(), TOPPViewBase::getActive1DWidget(), and Spectrum1DCanvas::setDrawMode().

Referenced by TOPPViewBase::showSpectrumGenerationDialog(), and TOPPViewBase::TOPPViewBase().

## ◆ setIntensityMode

void setIntensityMode | ( | int | index | ) |

slot

References TOPPViewBase::getActiveSpectrumWidget(), TOPPViewBase::intensity_button_group_, and SpectrumWidget::setIntensityMode().

Referenced by TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::TOPPViewBase().

## ◆ showAboutDialog

void showAboutDialog | ( |  | ) |

slot

Shows the 'About' dialog.

References QApplicationTOPP::showAboutDialog().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ showCurrentPeaksAs2D

void showCurrentPeaksAs2D | ( |  | ) |

slot

Shows the current peak data of the active layer in 2D.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum2DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, LayerData::filename, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), LayerData::getOnDiscPeakData(), LayerData::getPeakDataMuteable(), TOPPViewBase::getSpectrumParameters(), String::hasSuffix(), LayerData::name, String::prefix(), SpectrumCanvas::setLayerName(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ showCurrentPeaksAs3D

void showCurrentPeaksAs3D | ( |  | ) |

slot

Shows the current peak data of the active layer in 3D.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum3DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, LayerData::DT_PEAK, LayerData::filename, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayerIndex(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), LayerData::getPeakDataMuteable(), TOPPViewBase::getSpectrumParameters(), SpectrumCanvas::IM_SNAP, LayerData::isIonMobilityData(), TOPPViewBase::LS_NOTICE, LayerData::name, Spectrum3DCanvas::openglwidget(), TOPPViewBase::setIntensityMode(), SpectrumCanvas::setLayerName(), SpectrumCanvas::setVisibleArea(), Spectrum3DOpenGLCanvas::setYLabel(), TOPPViewBase::showLogMessage_(), TOPPViewBase::showSpectrumWidgetInWindow(), LayerData::type, TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ showCurrentPeaksAsDIA

void showCurrentPeaksAsDIA | ( |  | ) |

slot

Shows the current peak data of the active layer as DIA data.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum2DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, LayerData::filename, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), LayerData::getCurrentSpectrum(), LayerData::getOnDiscPeakData(), LayerData::getPeakData(), SpectrumSettings::getPrecursors(), TOPPViewBase::getSpectrumParameters(), String::hasSuffix(), LayerData::isDIAData(), OpenMS::Constants::k, LayerData::name, String::prefix(), SpectrumCanvas::setLayerName(), MSSpectrum::setMSLevel(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ showCurrentPeaksAsIonMobility

void showCurrentPeaksAsIonMobility | ( |  | ) |

slot

Shows the current peak data of the active layer as ion mobility.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum2DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, TOPPViewBase::containsIMData(), LayerData::filename, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), LayerData::getCurrentSpectrum(), LayerData::getCurrentSpectrumIndex(), MSSpectrum::getFloatDataArrays(), TOPPViewBase::getSpectrumParameters(), String::hasSuffix(), SpectrumWidget::IM_MS_AXIS_TITLE, SpectrumWidget::IM_ONEKZERO_AXIS_TITLE, OpenMS::Constants::k, LayerData::name, String::prefix(), SpectrumCanvas::setLayerName(), AxisWidget::setLegend(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), TOPPViewBase::ws_, and SpectrumWidget::xAxis().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ showCursorStatus

void showCursorStatus | ( | double | mz,
|  | double | rt
| ) |  |

slot

shows m/z and rt in the status bar

References TOPPViewBase::message_label_, TOPPViewBase::mz_label_, String::number(), and TOPPViewBase::rt_label_.

Referenced by TOPPViewBase::showCursorStatusInvert(), and TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ showCursorStatusInvert

void showCursorStatusInvert | ( | double | mz,
|  | double | rt
| ) |  |

slot

shows m/z and rt in the status bar (inverting RT and m/z)

References TOPPViewBase::showCursorStatus().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ showGoToDialog

void showGoToDialog | ( |  | ) |

slot

shows the DB dialog for opening files

References TOPPViewBase::getActiveSpectrumWidget(), and SpectrumWidget::showGoToDialog().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ showLogMessage_()

void showLogMessage_ | ( | TOPPViewBase::LogState | state,
|  | const String & | heading,
|  | const String & | body
| ) |  |

protected

Shows a log message in the log_ window.

References DateTime::getTime(), TOPPViewBase::log_, TOPPViewBase::LS_ERROR, TOPPViewBase::LS_NOTICE, TOPPViewBase::LS_WARNING, DateTime::now(), and String::toQString().

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::preferencesDialog(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showTOPPDialog_(), and TOPPViewBase::updateToolBar().

## ◆ showPreferences

void showPreferences | ( |  | ) |

slot

Shows current layer preferences.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showCurrentLayerPreferences().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ showSpectrumAlignmentDialog

void showSpectrumAlignmentDialog | ( |  | ) |

slot

Shows the spectrum alignment dialog.

References Spectrum1DWidget::canvas(), SpectrumAlignmentDialog::get1stLayerIndex(), SpectrumAlignmentDialog::get2ndLayerIndex(), TOPPViewBase::getActive1DWidget(), Spectrum1DCanvas::getAlignmentScore(), Spectrum1DCanvas::getAlignmentSize(), SpectrumAlignmentDialog::getTolerance(), SpectrumAlignmentDialog::isPPM(), Spectrum1DCanvas::mirrorModeActive(), Spectrum1DWidget::performAlignment(), and Param::setValue().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ showSpectrumAs1D [1/2]

void showSpectrumAs1D | ( | int | index | ) |

slot

Shows the spectrum with index `index` of the active layer in 1D.

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::identificationview_behavior_, TOPPViewSpectraViewBehavior::showSpectrumAs1D(), TOPPViewIdentificationViewBehavior::showSpectrumAs1D(), TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, and TOPPViewBase::spectraview_behavior_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

## ◆ showSpectrumAs1D [2/2]

void showSpectrumAs1D | ( | std::vector< int, std::allocator< int > > | indices | ) |

slot

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewSpectraViewBehavior::showSpectrumAs1D(), TOPPViewBase::spectra_view_widget_, and TOPPViewBase::spectraview_behavior_.

## ◆ showSpectrumBrowser

void showSpectrumBrowser | ( |  | ) |

protected slot

shows the spectrum browser and updates it

References TOPPViewBase::updateViewBar(), and TOPPViewBase::views_dockwidget_.

## ◆ showSpectrumGenerationDialog

void showSpectrumGenerationDialog | ( |  | ) |

slot

Shows the theoretical spectrum generation dialog.

References TOPPViewBase::addData(), MSExperiment::addSpectrum(), Spectrum1DCanvas::DM_PEAKS, TOPPViewBase::draw_group_1d_, LayerData::DT_CHROMATOGRAM, AASequence::fromString(), AASequence::getMonoWeight(), TheoreticalSpectrumGenerationDialog::getParam(), TheoreticalSpectrumGenerationDialog::getSequence(), TheoreticalSpectrumGenerator::getSpectrum(), Param::getValue(), Precursor::setCharge(), TOPPViewBase::setDrawMode1D(), MSSpectrum::setMSLevel(), Peak1D::setMZ(), DefaultParamHandler::setParameters(), SpectrumSettings::setPrecursors(), Param::setValue(), DataValue::toBool(), and BaseException::what().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ showSpectrumMetaData

void showSpectrumMetaData | ( | int | spectrum_index | ) |

protected slot

shows the spectrum metadata

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showMetaData().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ showSpectrumWidgetInWindow()

void showSpectrumWidgetInWindow | ( | SpectrumWidget * | sw,
|  | const String & | caption
| ) |  |

Opens the provided spectrum widget in a new window.

References EnhancedTabBar::addTab(), SpectrumWidget::canvas(), TOPPViewBase::copyLayer(), TOPPViewBase::enhancedWorkspaceWindowChanged(), Spectrum2DWidget::getHorizontalProjection(), Spectrum2DWidget::getVerticalProjection(), SpectrumWidget::getWindowId(), TOPPViewBase::layerActivated(), TOPPViewBase::layerZoomChanged(), EnhancedTabBar::setCurrentId(), SpectrumWidget::setWindowId(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showCursorStatus(), TOPPViewBase::showCursorStatusInvert(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::showStatusMessage(), TOPPViewBase::tab_bar_, String::toQString(), TOPPViewBase::updateLayerBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

## ◆ showStatusMessage

void showStatusMessage | ( | std::string | msg,
|  | OpenMS::UInt | time
| ) |  |

slot

Shows a status message in the status bar.

If `time` is 0 the status message is displayed until showStatusMessage is called with an empty message or a new message. Otherwise the message is displayed for `time` ms.

References TOPPViewBase::message_label_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

## ◆ showTOPPDialog

void showTOPPDialog | ( |  | ) |

slot

Apply TOPP tool.

References TOPPViewBase::showTOPPDialog_().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ showTOPPDialog_()

void showTOPPDialog_ | ( | bool | visible | ) |

protected

Apply TOPP tool. If `visible` is true, only the visible data is used, otherwise the whole layer is used.

References TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), SpectrumCanvas::getCurrentLayer(), ToolsDialog::getInput(), ToolsDialog::getOutput(), ToolsDialog::getTool(), File::getUniqueName(), Param::getValue(), TOPPViewBase::LS_ERROR, TOPPViewBase::LS_NOTICE, DefaultParamHandler::param_, TOPPViewBase::runTOPPTool_(), TOPPViewBase::showLogMessage_(), TOPPViewBase::topp_, DataValue::toString(), LayerData::visible, and File::writable().

Referenced by TOPPViewBase::showTOPPDialog().

## ◆ showURL

void showURL | ( |  | ) |

slot

shows the URL stored in the data of the sender QAction

References GUIHelpers::openURL().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ tileHorizontal

void tileHorizontal | ( |  | ) |

slot

tile the open windows horizontally

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ tileVertical

void tileVertical | ( |  | ) |

slot

tile the open windows vertically

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ toggleAxisLegends

void toggleAxisLegends | ( |  | ) |

slot

Toggles the axis legends.

References TOPPViewBase::getActiveSpectrumWidget(), and SpectrumWidget::showLegend().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ toggleGridLines

void toggleGridLines | ( |  | ) |

slot

Toggles the grid lines.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showGridLines().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ toggleInterestingMZs

void toggleInterestingMZs | ( |  | ) |

slot

Toggles drawing of interesting MZs.

References TOPPViewBase::getActive1DWidget().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ toggleProjections

void toggleProjections | ( |  | ) |

slot

References TOPPViewBase::getActive2DWidget(), Spectrum2DWidget::projectionsVisible(), and Spectrum2DWidget::toggleProjections().

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ updateCurrentPath

void updateCurrentPath | ( |  | ) |

slot

changes the current path according to the currently active window/layer

References TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), Param::getValue(), DefaultParamHandler::param_, and File::path().

Referenced by TOPPViewBase::layerActivated(), and TOPPViewBase::TOPPViewBase().

## ◆ updateFilterBar

void updateFilterBar | ( |  | ) |

slot

adapts the filter bar to the active window

References LayerData::filters, TOPPViewBase::filters_, TOPPViewBase::filters_check_box_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), SpectrumCanvas::getCurrentLayer(), SpectrumCanvas::getLayerCount(), DataFilters::isActive(), DataFilters::size(), and OpenMS::StringConversions::toString().

Referenced by TOPPViewBase::addData(), TOPPViewBase::fileChanged_(), TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerSelectionChange(), TOPPViewBase::layerStatistics(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), and TOPPViewBase::TOPPViewBase().

## ◆ updateLayerBar

void updateLayerBar | ( |  | ) |

slot

adapts the layer bar to the active window

References SpectrumCanvas::activeLayerIndex(), LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_PEAK, LayerData::filename, LayerData::flipped, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), Param::getValue(), TOPPViewBase::layers_view_, LayerData::modified, LayerData::name, LayerData::param, String::toQString(), DataValue::toQString(), LayerData::type, and LayerData::visible.

Referenced by TOPPViewBase::addData(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerContextMenu(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showSpectrumWidgetInWindow(), and TOPPViewBase::TOPPViewBase().

## ◆ updateMenu

void updateMenu | ( |  | ) |

slot

enabled/disabled menu entries depending on the current state

References Spectrum1DWidget::canvas(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActiveCanvas(), Spectrum1DCanvas::mirrorModeActive(), and TOPPViewBase::topp_.

Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::addData(), TOPPViewBase::closeByTab(), TOPPViewBase::closeFile(), TOPPViewBase::fileChanged_(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::layerContextMenu(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), and TOPPViewBase::TOPPViewBase().

## ◆ updateProcessLog

void updateProcessLog | ( |  | ) |

protected slot

Appends process output to log window.

References TOPPViewBase::log_, and TOPPViewBase::topp_.

Referenced by TOPPViewBase::runTOPPTool_().

## ◆ updateRecentMenu_()

void updateRecentMenu_ | ( |  | ) |

protected

update the recent files menu

References Param::getValue(), DefaultParamHandler::param_, TOPPViewBase::recent_actions_, TOPPViewBase::recent_files_, and Param::setValue().

Referenced by TOPPViewBase::addRecentFile_(), and TOPPViewBase::loadPreferences().

## ◆ updateTabBar

void updateTabBar | ( | QMdiSubWindow * | w | ) |

slot

brings the tab corresponding to the active window in front

References EnhancedTabBarWidgetInterface::getWindowId(), EnhancedTabBar::setCurrentId(), and TOPPViewBase::tab_bar_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ updateToolBar

void updateToolBar | ( |  | ) |

slot

updates the toolbar

References LayerData::C_ELEMENTS, Spectrum1DWidget::canvas(), Spectrum2DWidget::canvas(), SpectrumWidget::canvas(), TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_label_2d_, TOPPViewBase::dm_precursors_2d_, TOPPViewBase::dm_unassigned_2d_, TOPPViewBase::draw_group_1d_, LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_IDENT, LayerData::DT_PEAK, LayerData::F_HULL, LayerData::F_HULLS, LayerData::F_UNASSIGNED, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), Spectrum1DCanvas::getDrawMode(), SpectrumCanvas::getIntensityMode(), SpectrumCanvas::getLayerCount(), SpectrumCanvas::getLayerFlag(), LayerData::I_PEPTIDEMZ, TOPPViewBase::intensity_button_group_, LayerData::L_NONE, LayerData::label, TOPPViewBase::LS_ERROR, LayerData::P_PRECURSORS, TOPPViewBase::showLogMessage_(), TOPPViewBase::tool_bar_1d_, TOPPViewBase::tool_bar_2d_cons_, TOPPViewBase::tool_bar_2d_feat_, TOPPViewBase::tool_bar_2d_ident_, TOPPViewBase::tool_bar_2d_peak_, and LayerData::type.

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::changeUnassigned(), TOPPViewBase::layerActivated(), and TOPPViewBase::TOPPViewBase().

## ◆ updateViewBar

void updateViewBar | ( |  | ) |

slot

adapts view bar to the active window

References TOPPViewBase::getActiveCanvas(), SpectraViewWidget::getComboBox(), SpectrumCanvas::getCurrentLayer(), SpectraIdentificationViewWidget::getLayer(), SpectraIdentificationViewWidget::getTableWidget(), SpectraViewWidget::getTreeWidget(), TOPPViewBase::layers_view_, SpectraIdentificationViewWidget::setLayer(), TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, SpectraViewWidget::updateEntries(), and TOPPViewBase::views_tabwidget_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateWithID(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerActivated(), TOPPViewBase::layerContextMenu(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showSpectrumBrowser(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

## ◆ viewChanged

void viewChanged | ( | int | tab_index | ) |

slot

changes the behavior according to the selected view in the spectra view bar and calls updateSpectraViewBar()

References TOPPViewSpectraViewBehavior::activateBehavior(), TOPPViewIdentificationViewBehavior::activateBehavior(), TOPPViewSpectraViewBehavior::deactivateBehavior(), TOPPViewIdentificationViewBehavior::deactivateBehavior(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::identificationview_behavior_, TOPPViewBase::layer_dock_widget_, TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, TOPPViewBase::spectraview_behavior_, TOPPViewBase::updateViewBar(), and TOPPViewBase::views_tabwidget_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ viewTabwidgetDoubleClicked

void viewTabwidgetDoubleClicked | ( | int | tab_index | ) |

slot

adds empty ID structure to allow manual annotations

References TOPPViewIdentificationViewBehavior::activateBehavior(), TOPPViewSpectraViewBehavior::deactivateBehavior(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActiveSpectrumWidget(), TOPPViewBase::identificationview_behavior_, TOPPViewBase::layer_dock_widget_, TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::spectraview_behavior_, TOPPViewBase::updateViewBar(), and TOPPViewBase::views_tabwidget_.

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ window_()

EnhancedTabBarWidgetInterface * window_ | ( | int | id | ) | const

protected

Returns the enhanced tabbar widget with id `id`.

References EnhancedTabBarWidgetInterface::getWindowId(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::closeByTab(), and TOPPViewBase::enhancedWorkspaceWindowChanged().

## Friends And Related Function Documentation

## ◆ TestTOPPView

friend class TestTOPPView

friend

## Member Data Documentation

## ◆ add_2d_context_

QMenu* add_2d_context_

protected

Additional context menu for 2D layers.

## ◆ CAPTION_3D_SUFFIX_

const String CAPTION_3D_SUFFIX_ = " (3D)"

static private

Suffix appended to caption of tabs when layer is shown in 3D.

Referenced by TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

## ◆ current_path_

String current_path_

protected

The current path (used for loading and storing). Depending on the preferences this is static or changes with the current window/layer.

Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::getFileList_(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateCurrentPath().

## ◆ dm_elements_2d_

QAction* dm_elements_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ dm_hull_2d_

QAction* dm_hull_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ dm_hulls_2d_

QAction* dm_hulls_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ dm_ident_2d_

QAction* dm_ident_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ dm_label_2d_

QToolButton* dm_label_2d_

protected

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ dm_precursors_2d_

QAction* dm_precursors_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ dm_unassigned_2d_

QToolButton* dm_unassigned_2d_

protected

Referenced by TOPPViewBase::changeUnassigned(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ draw_group_1d_

QButtonGroup* draw_group_1d_

protected

Referenced by TOPPViewBase::showSpectrumGenerationDialog(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ filter_dock_widget_

QDockWidget* filter_dock_widget_

protected

Referenced by TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

## ◆ filters_

QListWidget* filters_

protected

Referenced by TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateFilterBar().

## ◆ filters_check_box_

QCheckBox* filters_check_box_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateFilterBar().

## ◆ group_label_2d_

QActionGroup* group_label_2d_

protected

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ group_unassigned_2d_

QActionGroup* group_unassigned_2d_

protected

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ identificationview_behavior_

TOPPViewIdentificationViewBehavior* identificationview_behavior_

protected

TOPPView behavior for the identification view.

Referenced by TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), TOPPViewBase::viewTabwidgetDoubleClicked(), and TOPPViewBase::~TOPPViewBase().

## ◆ intensity_button_group_

QButtonGroup* intensity_button_group_

protected

Referenced by TOPPViewBase::setIntensityMode(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ layer_dock_widget_

QDockWidget* layer_dock_widget_

protected

Referenced by TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

## ◆ layers_view_

QListWidget* layers_view_

protected

Layer management widget.

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerVisibilityChange(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateLayerBar(), and TOPPViewBase::updateViewBar().

## ◆ linkZoom_action_

QAction* linkZoom_action_

protected

Referenced by TOPPViewBase::linkZoom(), and TOPPViewBase::TOPPViewBase().

## ◆ log_

QTextEdit* log_

protected

Log output window.

Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::logContextMenu(), TOPPViewBase::showLogMessage_(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateProcessLog().

## ◆ message_label_

QLabel* message_label_

protected

Label for messages in the status bar.

Referenced by TOPPViewBase::showCursorStatus(), TOPPViewBase::showStatusMessage(), and TOPPViewBase::TOPPViewBase().

## ◆ mz_label_

QLabel* mz_label_

protected

m/z label for messages in the status bar

Referenced by TOPPViewBase::showCursorStatus(), and TOPPViewBase::TOPPViewBase().

## ◆ projections_2d_

QAction* projections_2d_

protected

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ recent_actions_

std::vector<QAction*> recent_actions_

protected

list of the recently opened files actions (menu entries)

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateRecentMenu_().

## ◆ recent_files_

QStringList recent_files_

protected

list of the recently opened files

Referenced by TOPPViewBase::addRecentFile_(), TOPPViewBase::loadPreferences(), TOPPViewBase::savePreferences(), and TOPPViewBase::updateRecentMenu_().

## ◆ rt_label_

QLabel* rt_label_

protected

RT label for messages in the status bar.

Referenced by TOPPViewBase::showCursorStatus(), and TOPPViewBase::TOPPViewBase().

## ◆ spectra_identification_view_widget_

SpectraIdentificationViewWidget* spectra_identification_view_widget_

protected

Referenced by TOPPViewBase::getSpectraIdentificationViewWidget(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateViewBar(), and TOPPViewBase::viewChanged().

## ◆ spectra_view_widget_

SpectraViewWidget* spectra_view_widget_

protected

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateViewBar(), and TOPPViewBase::viewChanged().

## ◆ spectraview_behavior_

TOPPViewSpectraViewBehavior* spectraview_behavior_

protected

TOPPView behavior for the spectra view.

Referenced by TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), TOPPViewBase::viewTabwidgetDoubleClicked(), and TOPPViewBase::~TOPPViewBase().

## ◆ tab_bar_

EnhancedTabBar* tab_bar_

protected

Tab bar. The address of the corresponding window to a tab is stored as an int in tabData()

Referenced by TOPPViewBase::layerContextMenu(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateTabBar().

## ◆ tool_bar_

QToolBar* tool_bar_

protected

Referenced by TOPPViewBase::TOPPViewBase().

## ◆ tool_bar_1d_

QToolBar* tool_bar_1d_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ tool_bar_2d_cons_

QToolBar* tool_bar_2d_cons_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ tool_bar_2d_feat_

QToolBar* tool_bar_2d_feat_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ tool_bar_2d_ident_

QToolBar* tool_bar_2d_ident_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ tool_bar_2d_peak_

QToolBar* tool_bar_2d_peak_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

## ◆ topp_

struct { ... } topp_

Information needed for execution of TOPP tools.

Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateProcessLog().

## ◆ views_dockwidget_

QDockWidget* views_dockwidget_

protected

Referenced by TOPPViewBase::showSpectrumBrowser(), and TOPPViewBase::TOPPViewBase().

## ◆ views_tabwidget_

QTabWidget* views_tabwidget_

protected

Tabwidget that hold the different views on the loaded data.

Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateWithID(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateViewBar(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

## ◆ watcher_

FileWatcher* watcher_

protected

Watcher that tracks file changes (in order to update the data in the different views)

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), and TOPPViewBase::TOPPViewBase().

## ◆ watcher_msgbox_

bool watcher_msgbox_

protected

Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again, if file changes again before the messagebox is closed)

Referenced by TOPPViewBase::fileChanged_().

## ◆ ws_

EnhancedWorkspace* ws_

protected

Main workspace.

Referenced by TOPPViewBase::addData(), TOPPViewBase::closeEvent(), TOPPViewBase::closeFile(), TOPPViewBase::fileChanged_(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), TOPPViewBase::getFileList_(), TOPPViewBase::getFilenamesOfOpenFiles_(), TOPPViewBase::getWorkspace(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::window_().

## ◆ zoom_together_

bool zoom_together_

protected

Stores whether the individual windows should zoom together (be linked) or not.

Referenced by TOPPViewBase::layerZoomChanged(), TOPPViewBase::linkZoom(), and TOPPViewBase::TOPPViewBase().