Main window of TOPPView tool. More...

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

Inheritance diagram for TOPPViewBase:

Collaboration diagram for TOPPViewBase:

Protected Member Functions
Recent files
void	addRecentFile_ (const String &filename)
	adds a Filename to the recent files More...

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
dock widgets
QDockWidget *	layer_dock_widget_

QDockWidget *	views_dockwidget_

QDockWidget *	filter_dock_widget_

LayerListView *	layers_view_
	Layer management widget. More...

DataSelectionTabs *	selection_view_

Filter widget
FilterList *	filter_list_

FileWatcher *	watcher_ = nullptr
	Watcher that tracks file changes (in order to update the data in the different views) More...

bool	watcher_msgbox_ = false
	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_ = false
	Stores whether the individual windows should zoom together (be linked) or not. More...

LogWindow *	log_
	Log output window. More...

TOOL_SCAN	scan_mode_
	Determines TVToolDiscovery scans for tools and generates new params. More...

TVToolDiscovery	tool_scanner_
	Scans for tools and generates a param for each. More...

VERBOSITY	verbosity_
	Verbosity of TV. More...

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_

EnhancedWorkspace	ws_
	Main workspace. More...

QMdiSubWindow *	lastActiveSubwindow_ = nullptr

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

RecentFilesMenu	recent_files_
	manages recent list of filenames and the menu that goes with it More...

TOPPViewMenu	menu_
	manages the menu items (active/inactive) and recent files etc More...

Status bar
QLabel *	message_label_
	Label for messages in the status bar. More...

QLabel *	x_label_
	x-axis label for messages in the status bar More...

QLabel *	y_label_
	y-axis 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...

Friends
class	TestTOPPView

Type definitions
enum class	TOOL_SCAN { SKIP_SCAN , SCAN_IF_NEWER_VERSION , FORCE_SCAN }
	Used for deciding whether new tool/util params should be generated or reused from TOPPView's ini file. More...

enum class	VERBOSITY { DEFAULT , VERBOSE }

enum class	LOAD_RESULT { OK , FILE_NOT_FOUND , FILETYPE_UNKNOWN , FILETYPE_UNSUPPORTED , LOAD_ERROR }

typedef LayerDataBase::FeatureMapType	FeatureMapType

typedef LayerDataBase::FeatureMapSharedPtrType	FeatureMapSharedPtrType

typedef LayerDataBase::ConsensusMapType	ConsensusMapType

typedef LayerDataBase::ConsensusMapSharedPtrType	ConsensusMapSharedPtrType

typedef LayerDataBase::ExperimentType	ExperimentType

typedef LayerDataBase::ExperimentSharedPtrType	ExperimentSharedPtrType

typedef LayerDataBase::ODExperimentSharedPtrType	ODExperimentSharedPtrType

typedef ExperimentType::SpectrumType	SpectrumType
	Peak spectrum type. More...

	TOPPViewBase (TOOL_SCAN scan_mode=TOOL_SCAN::SCAN_IF_NEWER_VERSION, VERBOSITY verbosity=VERBOSITY::DEFAULT, QWidget *parent=nullptr)
	Constructor. More...

	~TOPPViewBase () override
	Destructor. More...

LOAD_RESULT	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 (const FeatureMapSharedPtrType &feature_map, const ConsensusMapSharedPtrType &consensus_map, std::vector< PeptideIdentification > &peptides, const ExperimentSharedPtrType &peak_map, const ODExperimentSharedPtrType &on_disc_peak_map, LayerDataBase::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	getCanvasParameters (UInt dim) const
	Returns the parameters for a PlotCanvas of dimension `dim`. More...

const LayerDataBase *	getCurrentLayer () const
	Returns the active Layer data (0 if no layer is active) More...

LayerDataBase *	getCurrentLayer ()
	Returns the active Layer data (0 if no layer is active) More...

EnhancedWorkspace *	getWorkspace ()
	returns a pointer to the EnhancedWorkspace containing PlotWidgets More...

PlotWidget *	getActivePlotWidget () const
	returns a pointer to the active PlotWidget (0 if none is active) More...

Plot1DWidget *	getActive1DWidget () const
	returns a pointer to the active Plot1DWidget (0 the active window is no Plot1DWidget or there is no active window) More...

Plot2DWidget *	getActive2DWidget () const
	returns a pointer to the active Plot2DWidget (0 the active window is no Plot2DWidget or there is no active window) More...

Plot3DWidget *	getActive3DWidget () const
	returns a pointer to the active Plot3DWidget (0 the active window is no Plot2DWidget or there is no active window) More...

PlotCanvas *	getActiveCanvas () const
	returns a pointer to the active PlotCanvas (0 if none is active) More...

void	showPlotWidgetInWindow (PlotWidget *sw)
	Opens the provided spectrum widget in a new window. More...

void	updateCurrentPath ()
	changes the current path according to the currently active window/layer More...

void	openFilesByDialog (const String &initial_directory="")
	shows the file dialog for opening files (a starting directory, e.g. for the example files can be provided; otherwise, uses the current_path_) More...

void	showGoToDialog () const
	shows the DB dialog for opening files More...

void	preferencesDialog ()
	shows the preferences dialog More...

void	layerStatistics () const
	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	zoomOtherWindows () const
	gets called when a layer changes in zoom; will apply the same zoom to other windows (if linked) More...

void	linkZoom ()
	link the zoom of individual windows More...

void	layerDeactivated ()
	gets called if a layer got deactivated More...

void	closeTab ()
	closes the active window More...

void	rerunTOPPTool ()
	returns the last invoked TOPP tool with the same parameters More...

void	updateBarsAndMenus ()
	calls update*Bar and updateMenu_() to make sure the interface matches the current data 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	updateMenu ()
	activates/deactivates menu entries More...

void	updateFilterBar ()
	adapts the filter bar to the active window More...

void	showStatusMessage (const std::string &msg, OpenMS::UInt time)
	Shows a status message in the status bar. More...

void	showCursorStatus (const String &x, const String &y)
	shows X/Y axis mouse values in the status bar More...

void	showTOPPDialog ()
	Apply TOPP tool. More...

void	annotateWithAMS ()
	Annotates current layer with ID data from AccurateMassSearch. More...

void	annotateWithID ()
	Annotates current layer with ID data. More...

void	annotateWithOSW ()
	Annotates current chromatogram layer with ID data. More...

void	showSpectrumGenerationDialog ()
	Shows the theoretical spectrum generation dialog. More...

void	showSpectrumAlignmentDialog ()
	Shows the spectrum alignment dialog. More...

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 (const MSSpectrum &spec)
	Shows the current peak data of the active layer as ion mobility. More...

void	showCurrentPeaksAsDIA (const Precursor &pc, const MSExperiment &exp)
	Shows the current peak data of the active layer as DIA data. More...

void	saveLayerAll () const
	Saves the whole current layer data. More...

void	saveLayerVisible () const
	Saves the visible layer data. More...

void	toggleGridLines () const
	Toggles the grid lines. More...

void	toggleAxisLegends () const
	Toggles the axis legends. More...

void	toggleInterestingMZs () const
	Toggles drawing of interesting MZs. More...

void	showPreferences () const
	Shows current layer preferences. More...

void	metadataFileDialog ()
	dialog for inspecting database meta data 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 = nullptr

QElapsedTimer	timer

bool	visible_area_only

}	topp_
	Information needed for execution of TOPP tools. More...

void	runTOPPTool_ ()
	Runs the TOPP tool according to the information in topp_. 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...

reimplemented Qt events
QMenu *	add_2d_context_
	Additional context menu for 2D layers. More...

String	current_path_

static const String	CAPTION_3D_SUFFIX_
	Suffix appended to caption of tabs when layer is shown in 3D. More...

TheoreticalSpectrumGenerationDialog	spec_gen_dialog_
	This dialog is a member so that its settings can be perserved upon closing. More...

void	closeEvent (QCloseEvent *event) override

void	showTOPPDialog_ (bool visible)
	Apply TOPP tool. If `visible` is true, only the visible data is used, otherwise the whole layer is used. More...

Toolbar slots
void	setDrawMode1D (int) const

void	setIntensityMode (int)

void	changeLayerFlag (bool)

void	changeLabel (QAction *)

void	changeUnassigned (QAction *)

void	resetZoom () const

void	toggleProjections ()

void	openFile (const String &filename)

void	layerFilterVisibilityChange (bool) const
	Enables/disables the data filters for the current layer. More...

void	showSpectrumMetaData (int spectrum_index) const
	shows a spectrum's metadata with index `spectrum_index` from the currently active canvas More...

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	showSpectrumBrowser ()
	shows the spectrum browser and updates it More...

Tabbar slots
void	closeByTab (int id)
	Closes the window corresponding to the data of the tab with identifier `id`. More...

void	showWindow (int id)
	Raises the window corresponding to the data of the tab with identifier `id`. More...

void	copyLayer (const QMimeData data, QWidget source, int id=-1)
	Slot for drag-and-drop of layer manager to tabbar. More...

void	updateProcessLog ()
	Appends process output to log window. More...

void	fileChanged_ (const String &)
	Called if a data file has been externally changed. More...

void	initializeDefaultParameters_ ()
	Initializes the default parameters on TOPPView construction. More...

QStringList	chooseFilesDialog_ (const String &path_overwrite="")
	Shows a dialog where the user can select files. More...

Additional Inherited Members
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...

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 inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. 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 idview_behaviour_ 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 LayerDataBase::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

◆ ConsensusMapType

typedef LayerDataBase::ConsensusMapType ConsensusMapType

◆ ExperimentSharedPtrType

typedef LayerDataBase::ExperimentSharedPtrType ExperimentSharedPtrType

◆ ExperimentType

typedef LayerDataBase::ExperimentType ExperimentType

◆ FeatureMapSharedPtrType

typedef LayerDataBase::FeatureMapSharedPtrType FeatureMapSharedPtrType

◆ FeatureMapType

typedef LayerDataBase::FeatureMapType FeatureMapType

◆ ODExperimentSharedPtrType

typedef LayerDataBase::ODExperimentSharedPtrType ODExperimentSharedPtrType

◆ SpectrumType

typedef ExperimentType::SpectrumType SpectrumType

Peak spectrum type.

Member Enumeration Documentation

◆ LOAD_RESULT

enum LOAD_RESULT

strong

Enumerator
OK
FILE_NOT_FOUND	file did not exist
FILETYPE_UNKNOWN	file exists, but type could no be determined
FILETYPE_UNSUPPORTED	filetype is known, but the format not supported as layer data
LOAD_ERROR	an error occurred while loading the file

◆ TOOL_SCAN

enum TOOL_SCAN

strong

Used for deciding whether new tool/util params should be generated or reused from TOPPView's ini file.

Enumerator
SKIP_SCAN	TVToolDiscovery does not generate params for each tool/util unless they are absolutely needed and could not be extracted from TOPPView's ini file. This may be useful for testing.
SCAN_IF_NEWER_VERSION	Only generate params for each tool/util if TOPPView's last ini file has an older version. (Default behaviour)
FORCE_SCAN	Forces TVToolDiscovery to generate params and using them instead of the params in TOPPView's ini file.

◆ VERBOSITY

enum VERBOSITY

strong

Enumerator
DEFAULT
VERBOSE

Constructor & Destructor Documentation

◆ TOPPViewBase()

TOPPViewBase	(	TOOL_SCAN	scan_mode = `TOOL_SCAN::SCAN_IF_NEWER_VERSION`,
		VERBOSITY	verbosity = `VERBOSITY::DEFAULT`,
		QWidget *	parent = `nullptr`
	)

explicit

Constructor.

References EnhancedTabBar::addTab(), TOPPViewMenu::addWindowToggle(), TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::closeByTab(), EnhancedTabBar::closeRequested(), CONNECTCAST, TOPPViewBase::copyLayer(), TOPPViewBase::current_path_, EnhancedTabBar::currentIdChanged(), DefaultParamHandler::defaultsToParam_(), Plot1DCanvas::DM_CONNECTEDLINES, TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_label_2d_, Plot1DCanvas::DM_PEAKS, TOPPViewBase::dm_precursors_2d_, TOPPViewBase::dm_unassigned_2d_, TOPPViewBase::draw_group_1d_, EnhancedTabBar::dropOnTab(), EnhancedTabBar::dropOnWidget(), EnhancedWorkspace::dropReceived(), FileWatcher::fileChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::filter_list_, FilterList::filterChanged(), TOPPViewBase::getActiveCanvas(), Param::getValue(), TOPPViewBase::group_label_2d_, TOPPViewBase::group_unassigned_2d_, PlotCanvas::IM_LOG, PlotCanvas::IM_NONE, PlotCanvas::IM_PERCENTAGE, PlotCanvas::IM_SNAP, TOPPViewBase::initializeDefaultParameters_(), TOPPViewBase::intensity_button_group_, TOPPViewBase::lastActiveSubwindow_, TOPPViewBase::layer_dock_widget_, LayerListView::layerDataChanged(), TOPPViewBase::layers_view_, TOPPViewBase::loadPreferences(), TOPPViewBase::log_, TOPPViewBase::menu_, TOPPViewBase::message_label_, LayerDataDefs::NamesOfLabelType, TOPPViewBase::openFile(), DefaultParamHandler::param_, TOPPViewBase::projections_2d_, TOPPViewBase::recent_files_, RecentFilesMenu::recentFileClicked(), EnhancedTabBar::removeId(), TOPPViewBase::resetZoom(), TOPPViewBase::selection_view_, TOPPViewBase::setDrawMode1D(), PlotCanvas::setFilters(), TOPPViewBase::setIntensityMode(), TVToolDiscovery::setPluginPath(), TVToolDiscovery::setVerbose(), TOPPViewBase::showWindow(), LayerDataDefs::SIZE_OF_LABEL_TYPE, TOPPViewBase::tab_bar_, 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::tool_scanner_, ParamValue::toString(), TOPPViewBase::updateBarsAndMenus(), TOPPViewBase::updateMenu(), OpenMS::user_section, TOPPViewBase::VERBOSE, TOPPViewBase::verbosity_, TOPPViewBase::views_dockwidget_, TOPPViewBase::watcher_, TOPPViewBase::ws_, TOPPViewBase::x_label_, and TOPPViewBase::y_label_.

◆ ~TOPPViewBase()

~TOPPViewBase ( )

override

Destructor.

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

Member Function Documentation

◆ abortTOPPTool

void abortTOPPTool ( )

protectedslot

aborts the execution of a TOPP tool

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

Referenced by TOPPViewBase::~TOPPViewBase().

◆ addData()

void addData	(	const FeatureMapSharedPtrType &	feature_map,
		const ConsensusMapSharedPtrType &	consensus_map,
		std::vector< PeptideIdentification > &	peptides,
		const ExperimentSharedPtrType &	peak_map,
		const ODExperimentSharedPtrType &	on_disc_peak_map,
		LayerDataBase::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)
as_new_window	Open the layer in a new window within TOPPView
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.

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

◆ addDataFile()

TOPPViewBase::LOAD_RESULT 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_(), LogWindow::appendNewHeader(), File::basename(), FileTypes::CONSENSUSXML, FileTypeList::contains(), LayerDataDefs::DT_CHROMATOGRAM, LayerDataDefs::DT_CONSENSUS, LayerDataDefs::DT_FEATURE, LayerDataDefs::DT_IDENT, LayerDataDefs::DT_PEAK, LayerDataDefs::DT_UNKNOWN, File::exists(), FileTypes::FEATUREXML, TOPPViewBase::FILE_NOT_FOUND, TOPPViewBase::FILETYPE_UNKNOWN, TOPPViewBase::FILETYPE_UNSUPPORTED, TOPPViewBase::getCurrentLayer(), IndexedMzMLHandler::getNrChromatograms(), IndexedMzMLHandler::getNrSpectra(), IndexedMzMLHandler::getParsingSuccess(), FileHandler::getType(), Param::getValue(), ProgressLogger::GUI, FileTypes::IDXML, OpenMS::Constants::k, TOPPViewBase::LOAD_ERROR, FileHandler::loadConsensusFeatures(), FileHandler::loadExperiment(), FileHandler::loadFeatures(), FileHandler::loadIdentifications(), TOPPViewBase::log_, FileTypes::MZIDENTML, FileTypes::MZML, TOPPViewBase::OK, IndexedMzMLHandler::openFile(), OPENMS_LOG_INFO, OPENMS_LOG_WARN, DefaultParamHandler::param_, FileHandler::stripExtension(), OpenMS::supported_types, FileHandler::swapExtension(), OpenMS::StringUtils::toQString(), FileTypes::typeToName(), FileTypes::UNKNOWN, GUILock::unlock(), OpenMS::user_section, and TOPPViewBase::watcher_.

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::loadFiles(), TOPPViewBase::openFile(), and TOPPViewBase::openFilesByDialog().

◆ addRecentFile_()

void addRecentFile_ ( const String & filename )

protected

adds a Filename to the recent files

References RecentFilesMenu::add(), and TOPPViewBase::recent_files_.

Referenced by TOPPViewBase::addDataFile().

◆ annotateWithAMS

void annotateWithAMS ( )

slot

Annotates current layer with ID data from AccurateMassSearch.

References LayerAnnotatorBase::annotateWithFileDialog(), TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), and TOPPViewBase::log_.

◆ annotateWithID

void annotateWithID ( )

slot

Annotates current layer with ID data.

References LayerAnnotatorBase::annotateWithFileDialog(), TOPPViewBase::current_path_, DataSelectionTabs::currentTabChanged(), TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), DataSelectionTabs::IDENT_IDX, TOPPViewBase::log_, and TOPPViewBase::selection_view_.

◆ annotateWithOSW

void annotateWithOSW ( )

slot

Annotates current chromatogram layer with ID data.

References LayerAnnotatorBase::annotateWithFileDialog(), TOPPViewBase::current_path_, DataSelectionTabs::currentTabChanged(), DataSelectionTabs::DIAOSW_IDX, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), TOPPViewBase::log_, and TOPPViewBase::selection_view_.

◆ changeLabel

void changeLabel ( QAction * action )

slot

References Plot2DWidget::canvas(), TOPPViewBase::dm_label_2d_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::getCurrentLayer(), LayerDataDefs::L_INDEX, LayerDataDefs::L_NONE, LayerDataDefs::NamesOfLabelType, PlotCanvas::setLabel(), LayerDataDefs::SIZE_OF_LABEL_TYPE, and TOPPViewBase::updateToolBar().

Referenced by TOPPViewBase::TOPPViewBase().

◆ changeLayerFlag

void changeLayerFlag ( bool on )

slot

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

Referenced by TOPPViewBase::TOPPViewBase().

◆ changeUnassigned

void changeUnassigned ( QAction * action )

slot

References Plot2DWidget::canvas(), TOPPViewBase::dm_unassigned_2d_, LayerDataDefs::F_UNASSIGNED, TOPPViewBase::getActive2DWidget(), PlotCanvas::getLayerFlag(), LayerDataDefs::I_LABELS, LayerDataDefs::I_PEPTIDEMZ, PlotCanvas::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.

◆ chooseFilesDialog_()

QStringList chooseFilesDialog_ ( const String & path_overwrite = "" )

protected

Shows a dialog where the user can select files.

References OpenMS::BOTH, TOPPViewBase::current_path_, OpenMS::supported_types, FileTypeList::toFileDialogFilter(), and String::toQString().

Referenced by TOPPViewBase::metadataFileDialog(), and TOPPViewBase::openFilesByDialog().

◆ closeByTab

void closeByTab ( int id )

protectedslot

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

References EnhancedWorkspace::getWidget(), TOPPViewBase::updateBarsAndMenus(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

◆ closeEvent()

void closeEvent ( QCloseEvent * event )

overrideprotected

References TOPPViewBase::ws_.

◆ closeTab

void closeTab ( )

slot

closes the active window

References TOPPViewBase::ws_.

◆ copyLayer

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

protectedslot

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

References TOPPViewBase::addData(), TOPPViewBase::addDataFile(), LogWindow::appendNewHeader(), LayerDataBase::filename, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), LayerDataBase::getName(), SpectraTreeTab::getSelectedScan(), TOPPViewBase::layers_view_, TOPPViewBase::log_, and LayerDataBase::type.

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

◆ editMetadata

void editMetadata ( )

slot

lets the user edit the meta data of a layer

References LogWindow::appendNewHeader(), TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), TOPPViewBase::log_, PlotCanvas::showMetaData(), and LayerDataBase::visible.

◆ fileChanged_

void fileChanged_ ( const String & filename )

protectedslot

◆ finishTOPPToolExecution

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

protectedslot

slot for the finished signal of the TOPP tools execution

References TOPPViewBase::addDataFile(), LogWindow::addNewline(), LogWindow::appendNewHeader(), File::getTempDirectory(), Param::getValue(), TOPPViewBase::log_, DefaultParamHandler::param_, File::readable(), File::remove(), TOPPViewBase::topp_, OpenMS::StringUtils::toQString(), and TOPPViewBase::updateMenu().

Referenced by TOPPViewBase::runTOPPTool_().

◆ getActive1DWidget()

Plot1DWidget * getActive1DWidget ( ) const

returns a pointer to the active Plot1DWidget (0 the active window is no Plot1DWidget or there is no active window)

References TOPPViewBase::getActivePlotWidget().

Referenced by TOPPViewBase::setDrawMode1D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::toggleInterestingMZs(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateToolBar().

◆ getActive2DWidget()

Plot2DWidget * getActive2DWidget ( ) const

returns a pointer to the active Plot2DWidget (0 the active window is no Plot2DWidget or there is no active window)

References TOPPViewBase::getActivePlotWidget().

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::loadFiles(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::toggleProjections(), and TOPPViewBase::updateToolBar().

◆ getActive3DWidget()

Plot3DWidget * getActive3DWidget ( ) const

returns a pointer to the active Plot3DWidget (0 the active window is no Plot2DWidget or there is no active window)

References TOPPViewBase::getActivePlotWidget().

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

◆ getActiveCanvas()

PlotCanvas * getActiveCanvas ( ) const

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

References PlotWidget::canvas(), and TOPPViewBase::getActivePlotWidget().

Referenced by TOPPViewBase::annotateWithAMS(), TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::getCurrentLayer(), TOPPViewBase::layerFilterVisibilityChange(), 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::TOPPViewBase(), TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), and TOPPViewBase::updateMenu().

◆ getActivePlotWidget()

PlotWidget * getActivePlotWidget ( ) const

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

References TOPPViewBase::tab_bar_, and TOPPViewBase::ws_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::layerStatistics(), TOPPViewBase::loadFiles(), TOPPViewBase::resetZoom(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::setIntensityMode(), TOPPViewBase::showGoToDialog(), TOPPViewBase::toggleAxisLegends(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateToolBar(), and TOPPViewBase::zoomOtherWindows().

◆ getCanvasParameters()

Param getCanvasParameters ( UInt dim ) const

Returns the parameters for a PlotCanvas of dimension dim.

References Param::copy(), Param::getValue(), DefaultParamHandler::param_, Param::setValue(), ParamValue::toString(), and OpenMS::user_section.

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

◆ getCurrentLayer() [1/2]

LayerDataBase * getCurrentLayer ( )

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

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

◆ getCurrentLayer() [2/2]

const LayerDataBase * getCurrentLayer ( ) const

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

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

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::changeLabel(), TOPPViewBase::loadFiles(), TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), and TOPPViewBase::updateMenu().

◆ getWorkspace()

EnhancedWorkspace * getWorkspace ( )

returns a pointer to the EnhancedWorkspace containing PlotWidgets

References TOPPViewBase::ws_.

◆ initializeDefaultParameters_()

void initializeDefaultParameters_ ( )

protected

Initializes the default parameters on TOPPView construction.

References DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), DefaultParamHandler::getDefaults(), File::getUserDirectory(), Param::insert(), Param::setSectionDescription(), Param::setValidStrings(), Param::setValue(), DefaultParamHandler::subsections_, and OpenMS::user_section.

Referenced by TOPPViewBase::TOPPViewBase().

◆ layerActivated

void layerActivated ( )

slot

gets called if a layer got activated

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

Referenced by TOPPViewBase::fileChanged_(), TOPPViewBase::showPlotWidgetInWindow(), and TOPPViewBase::updateBarsAndMenus().

◆ layerDeactivated

void layerDeactivated ( )

slot

gets called if a layer got deactivated

◆ layerFilterVisibilityChange

void layerFilterVisibilityChange ( bool on ) const

slot

Enables/disables the data filters for the current layer.

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

◆ layerStatistics

void layerStatistics ( ) const

slot

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

References TOPPViewBase::getActivePlotWidget(), and PlotWidget::showStatistics().

◆ linkZoom

void linkZoom ( )

slot

link the zoom of individual windows

References TOPPViewBase::zoom_together_.

◆ loadFiles()

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

Opens all the files in the string list.

References TOPPViewBase::addDataFile(), LogWindow::appendNewHeader(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActivePlotWidget(), LayerAnnotatorBase::getAnnotatorWhichSupports(), TOPPViewBase::getCurrentLayer(), PlotCanvas::getCurrentLayer(), OpenMS::Helpers::indexOf(), TOPPViewBase::log_, LayerDataBase::param, PlotCanvas::setCurrentLayerParameters(), Param::setValue(), and OpenMS::StringUtils::toQString().

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::copy(), Param::exists(), File::exists(), TOPPViewBase::FORCE_SCAN, File::getUserDirectory(), Param::getValue(), VersionInfo::getVersion(), Param::hasSection(), Param::insert(), ParamXMLFile::load(), TVToolDiscovery::loadToolParams(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, TOPPViewBase::scan_mode_, RecentFilesMenu::setFromParam(), DefaultParamHandler::setParameters(), TVToolDiscovery::setPluginPath(), Param::setValue(), TOPPViewBase::SKIP_SCAN, TOPPViewBase::tool_scanner_, ParamValue::toString(), and OpenMS::user_section.

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

◆ metadataFileDialog

void metadataFileDialog ( )

slot

dialog for inspecting database meta data

References MetaDataBrowser::add(), TOPPViewBase::chooseFilesDialog_(), FileHandler::getOptions(), and PeakFileOptions::setMetadataOnly().

◆ openFile

void openFile ( const String & filename )

slot

list of the recently opened files called when RecentFileMenu items is clicked

References TOPPViewBase::addDataFile().

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

◆ openFilesByDialog

void openFilesByDialog ( const String & initial_directory = "" )

slot

shows the file dialog for opening files (a starting directory, e.g. for the example files can be provided; otherwise, uses the current_path_)

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

◆ preferencesDialog

void preferencesDialog ( )

slot

shows the preferences dialog

References Param::copy(), TOPPViewPrefDialog::getParam(), Param::insert(), DefaultParamHandler::param_, Param::remove(), TOPPViewBase::savePreferences(), TOPPViewPrefDialog::setParam(), and OpenMS::user_section.

◆ rerunTOPPTool

void rerunTOPPTool ( )

slot

returns the last invoked TOPP tool with the same parameters

References LogWindow::appendNewHeader(), TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), TOPPViewBase::log_, TOPPViewBase::runTOPPTool_(), TOPPViewBase::topp_, and LayerDataBase::visible.

◆ resetZoom

void resetZoom ( ) const

slot

References PlotWidget::canvas(), TOPPViewBase::getActivePlotWidget(), and PlotCanvas::resetZoom().

Referenced by TOPPViewBase::TOPPViewBase().

◆ runTOPPTool_()

void runTOPPTool_ ( )

protected

◆ saveLayerAll

void saveLayerAll ( ) const

slot

Saves the whole current layer data.

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

◆ saveLayerVisible

void saveLayerVisible ( ) const

slot

Saves the visible layer data.

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

◆ savePreferences()

void savePreferences ( )

Stores the preferences (used when this window is closed)

References Param::copy(), RecentFilesMenu::getAsParam(), TVToolDiscovery::getPluginPath(), TVToolDiscovery::getToolParams(), Param::getValue(), VersionInfo::getVersion(), Param::hasSection(), Param::insert(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, Param::removeAll(), TOPPViewBase::scan_mode_, TVToolDiscovery::setPluginPath(), Param::setValue(), TOPPViewBase::SKIP_SCAN, ParamXMLFile::store(), TOPPViewBase::tool_scanner_, ParamValue::toString(), OpenMS::user_section, and TVToolDiscovery::waitForToolParams().

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

◆ setDrawMode1D

void setDrawMode1D ( int index ) const

slot

References Plot1DWidget::canvas(), TOPPViewBase::getActive1DWidget(), and Plot1DCanvas::setDrawMode().

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

◆ setIntensityMode

void setIntensityMode ( int index )

slot

References TOPPViewBase::getActivePlotWidget(), TOPPViewBase::intensity_button_group_, and PlotWidget::setIntensityMode().

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

◆ showCurrentPeaksAs2D

void showCurrentPeaksAs2D ( )

slot

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

References PlotCanvas::addPeakLayer(), Plot2DWidget::canvas(), LayerDataBase::filename, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getCurrentLayer(), LayerDataPeak::getPeakDataMuteable(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ showCurrentPeaksAs3D

void showCurrentPeaksAs3D ( )

slot

◆ showCurrentPeaksAsDIA

void showCurrentPeaksAsDIA	(	const Precursor &	pc,
		const MSExperiment &	exp
	)

slot

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

References PlotCanvas::addPeakLayer(), Plot2DWidget::canvas(), LayerDataBase::filename, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getCurrentLayer(), PlotCanvas::getCurrentLayerIndex(), Precursor::getIsolationWindowLowerOffset(), Precursor::getIsolationWindowUpperOffset(), Peak1D::getMZ(), LayerDataBase::getName(), OpenMS::Constants::k, PlotCanvas::setLayerName(), MSSpectrum::setMSLevel(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ showCurrentPeaksAsIonMobility

void showCurrentPeaksAsIonMobility ( const MSSpectrum & spec )

slot

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

References PlotCanvas::addPeakLayer(), Plot2DWidget::canvas(), LayerDataBase::filename, IMTypes::fromIMUnit(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getCurrentLayer(), OpenMS::MZ, Plot2DWidget::setMapper(), TOPPViewBase::showPlotWidgetInWindow(), IMDataConverter::splitByIonMobility(), TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ showCursorStatus

void showCursorStatus	(	const String &	x,
		const String &	y
	)

slot

shows X/Y axis mouse values in the status bar

References TOPPViewBase::message_label_, String::toQString(), TOPPViewBase::x_label_, and TOPPViewBase::y_label_.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

◆ showGoToDialog

void showGoToDialog ( ) const

slot

shows the DB dialog for opening files

References TOPPViewBase::getActivePlotWidget(), and PlotWidget::showGoToDialog().

◆ showPlotWidgetInWindow()

void showPlotWidgetInWindow ( PlotWidget * sw )

Opens the provided spectrum widget in a new window.

References EnhancedWorkspace::addSubWindow(), EnhancedTabBarWidgetInterface::addToTabBar(), PlotWidget::canvas(), TOPPViewBase::copyLayer(), PlotWidget::dropReceived(), PlotCanvas::getCurrentLayer(), LayerDataBase::getDecoratedName(), Plot2DWidget::getProjectionOntoX(), Plot2DWidget::getProjectionOntoY(), EnhancedTabBarWidgetInterface::getWindowId(), TOPPViewBase::layerActivated(), PlotCanvas::layerActivated(), PlotCanvas::layerModficationChange(), PlotCanvas::layerZoomChanged(), PlotCanvas::preferencesChange(), TOPPViewBase::selection_view_, PlotWidget::sendCursorStatus(), PlotWidget::sendStatusMessage(), TOPPViewBase::showCurrentPeaksAs2D(), Plot1DWidget::showCurrentPeaksAs2D(), Plot3DWidget::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), Plot1DWidget::showCurrentPeaksAs3D(), Plot2DWidget::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), Plot1DWidget::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), Plot1DWidget::showCurrentPeaksAsIonMobility(), Plot2DWidget::showCurrentPeaksAsIonMobility(), TOPPViewBase::showCursorStatus(), DataSelectionTabs::showSpectrumAsNew1D(), Plot2DWidget::showSpectrumAsNew1D(), TOPPViewBase::showStatusMessage(), TOPPViewBase::showWindow(), TOPPViewBase::tab_bar_, TOPPViewBase::updateLayerBar(), TOPPViewBase::ws_, and TOPPViewBase::zoomOtherWindows().

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

◆ showPreferences

void showPreferences ( ) const

slot

Shows current layer preferences.

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

◆ showSpectrumAlignmentDialog

void showSpectrumAlignmentDialog ( )

slot

Shows the spectrum alignment dialog.

References Plot1DWidget::canvas(), SpectrumAlignmentDialog::get1stLayerIndex(), SpectrumAlignmentDialog::get2ndLayerIndex(), TOPPViewBase::getActive1DWidget(), Plot1DCanvas::getAlignmentScore(), Plot1DCanvas::getAlignmentSize(), SpectrumAlignmentDialog::getTolerance(), SpectrumAlignmentDialog::isPPM(), Plot1DCanvas::mirrorModeActive(), Plot1DWidget::performAlignment(), and Param::setValue().

◆ showSpectrumBrowser

void showSpectrumBrowser ( )

protectedslot

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(), Plot1DCanvas::DM_PEAKS, TOPPViewBase::draw_group_1d_, LayerDataDefs::DT_PEAK, TheoreticalSpectrumGenerationDialog::getSequence(), TheoreticalSpectrumGenerationDialog::getSpectrum(), TOPPViewBase::setDrawMode1D(), and TOPPViewBase::spec_gen_dialog_.

◆ showSpectrumMetaData

void showSpectrumMetaData ( int spectrum_index ) const

slot

shows a spectrum's metadata with index spectrum_index from the currently active canvas

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

◆ showStatusMessage

void showStatusMessage	(	const 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::showPlotWidgetInWindow().

◆ showTOPPDialog

void showTOPPDialog ( )

slot

Apply TOPP tool.

References TOPPViewBase::showTOPPDialog_().

◆ 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 LogWindow::appendNewHeader(), TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), ToolsDialog::getInput(), LayerDataBase::getName(), ToolsDialog::getOutput(), File::getTempDirectory(), ToolsDialog::getTool(), TVToolDiscovery::getToolParams(), File::getUniqueName(), Param::hasSection(), Param::insert(), TOPPViewBase::log_, DefaultParamHandler::param_, TOPPViewBase::runTOPPTool_(), TOPPViewBase::tool_scanner_, TOPPViewBase::topp_, LayerDataBase::type, LayerDataBase::visible, TVToolDiscovery::waitForToolParams(), and File::writable().

Referenced by TOPPViewBase::showTOPPDialog().

◆ showWindow

void showWindow ( int id )

protectedslot

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

References EnhancedWorkspace::getWidget(), and TOPPViewBase::ws_.

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

◆ toggleAxisLegends

void toggleAxisLegends ( ) const

slot

Toggles the axis legends.

References TOPPViewBase::getActivePlotWidget(), and PlotWidget::showLegend().

◆ toggleGridLines

void toggleGridLines ( ) const

slot

Toggles the grid lines.

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

◆ toggleInterestingMZs

void toggleInterestingMZs ( ) const

slot

Toggles drawing of interesting MZs.

References TOPPViewBase::getActive1DWidget().

◆ toggleProjections

void toggleProjections ( )

slot

References TOPPViewBase::getActive2DWidget(), Plot2DWidget::projectionsVisible(), and Plot2DWidget::toggleProjections().

Referenced by TOPPViewBase::TOPPViewBase().

◆ updateBarsAndMenus

void updateBarsAndMenus ( )

slot

calls update*Bar and updateMenu_() to make sure the interface matches the current data

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

Referenced by TOPPViewBase::closeByTab(), and 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_, File::path(), ParamValue::toString(), and OpenMS::user_section.

Referenced by TOPPViewBase::layerActivated().

◆ updateFilterBar

void updateFilterBar ( )

slot

adapts the filter bar to the active window

References TOPPViewBase::filter_list_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), PlotCanvas::getLayerCount(), and FilterList::set().

Referenced by TOPPViewBase::layerActivated().

◆ updateLayerBar

void updateLayerBar ( )

slot

adapts the layer bar to the active window

References TOPPViewBase::getActivePlotWidget(), TOPPViewBase::layers_view_, and LayerListView::update().

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

◆ updateMenu

void updateMenu ( )

slot

◆ updateProcessLog

void updateProcessLog ( )

protectedslot

Appends process output to log window.

References LogWindow::appendText(), TOPPViewBase::log_, and TOPPViewBase::topp_.

Referenced by TOPPViewBase::runTOPPTool_().

◆ updateToolBar

void updateToolBar ( )

slot

updates the toolbar

References LogWindow::appendNewHeader(), LayerDataDefs::C_ELEMENTS, PlotWidget::canvas(), Plot1DWidget::canvas(), Plot2DWidget::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_, LayerDataDefs::DT_CONSENSUS, LayerDataDefs::DT_FEATURE, LayerDataDefs::DT_IDENT, LayerDataDefs::DT_PEAK, LayerDataDefs::F_HULL, LayerDataDefs::F_HULLS, LayerDataDefs::F_UNASSIGNED, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActivePlotWidget(), PlotCanvas::getCurrentLayer(), Plot1DCanvas::getDrawMode(), PlotCanvas::getIntensityMode(), PlotCanvas::getLayerCount(), PlotCanvas::getLayerFlag(), LayerDataDefs::I_PEPTIDEMZ, TOPPViewBase::intensity_button_group_, LayerDataDefs::L_NONE, LayerDataBase::label, TOPPViewBase::log_, LayerDataDefs::P_PRECURSORS, 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 LayerDataBase::type.

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

◆ updateViewBar

void updateViewBar ( )

slot

adapts view bar to the active window

References DataSelectionTabs::callUpdateEntries(), and TOPPViewBase::selection_view_.

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

◆ zoomOtherWindows

void zoomOtherWindows ( ) const

slot

gets called when a layer changes in zoom; will apply the same zoom to other windows (if linked)

References PlotWidget::canvas(), LayerDataDefs::DT_CHROMATOGRAM, TOPPViewBase::getActivePlotWidget(), PlotCanvas::getCurrentLayer(), DefaultParamHandler::getName(), PlotCanvas::getVisibleArea(), PlotCanvas::setVisibleArea(), LayerDataBase::type, TOPPViewBase::ws_, and TOPPViewBase::zoom_together_.

Referenced by TOPPViewBase::showPlotWidgetInWindow().

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_

staticprivate

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

◆ 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::annotateWithAMS(), TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::chooseFilesDialog_(), 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().

◆ filter_list_

FilterList* filter_list_

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().

◆ intensity_button_group_

QButtonGroup* intensity_button_group_

protected

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

◆ lastActiveSubwindow_

QMdiSubWindow* lastActiveSubwindow_ = nullptr

protected

LAST active subwindow (~ corresponding to tab) in the MDI container. Since subwindows can lose focus, we want to make sure that things like the ID tables only update when a NEW window is activated. (Actually, we should check for the underlying data but this might be a

Todo:: ).

Referenced by TOPPViewBase::TOPPViewBase().

◆ layer_dock_widget_

QDockWidget* layer_dock_widget_

protected

Referenced by TOPPViewBase::TOPPViewBase().

◆ layers_view_

LayerListView* layers_view_

protected

Layer management widget.

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateLayerBar().

◆ log_

LogWindow* log_

protected

Log output window.

Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::addDataFile(), TOPPViewBase::annotateWithAMS(), TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::loadFiles(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateProcessLog(), and TOPPViewBase::updateToolBar().

◆ menu_

TOPPViewMenu menu_

protected

manages the menu items (active/inactive) and recent files etc

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

◆ message_label_

QLabel* message_label_

protected

Label for messages in the status bar.

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

◆ projections_2d_

QAction* projections_2d_

protected

Referenced by TOPPViewBase::TOPPViewBase().

◆ recent_files_

RecentFilesMenu recent_files_

protected

manages recent list of filenames and the menu that goes with it

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

◆ scan_mode_

TOOL_SCAN scan_mode_

protected

Determines TVToolDiscovery scans for tools and generates new params.

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

◆ selection_view_

DataSelectionTabs* selection_view_

protected

Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateViewBar().

◆ spec_gen_dialog_

TheoreticalSpectrumGenerationDialog spec_gen_dialog_

private

This dialog is a member so that its settings can be perserved upon closing.

Referenced by TOPPViewBase::showSpectrumGenerationDialog().

◆ 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::getActivePlotWidget(), TOPPViewBase::showPlotWidgetInWindow(), and TOPPViewBase::TOPPViewBase().

◆ 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().

◆ tool_scanner_

TVToolDiscovery tool_scanner_

protected

Scans for tools and generates a param for each.

Referenced by TOPPViewBase::loadPreferences(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::savePreferences(), TOPPViewBase::showTOPPDialog_(), and TOPPViewBase::TOPPViewBase().

◆

struct { ... } topp_

Information needed for execution of TOPP tools.

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

◆ verbosity_

VERBOSITY verbosity_

protected

Verbosity of TV.

Referenced by TOPPViewBase::TOPPViewBase().

◆ views_dockwidget_

QDockWidget* views_dockwidget_

protected

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

◆ watcher_

FileWatcher* watcher_ = nullptr

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_ = false

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::closeByTab(), TOPPViewBase::closeEvent(), TOPPViewBase::closeTab(), TOPPViewBase::fileChanged_(), TOPPViewBase::getActivePlotWidget(), TOPPViewBase::getWorkspace(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::showWindow(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::zoomOtherWindows().

◆ x_label_

QLabel* x_label_

protected

x-axis label for messages in the status bar

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

◆ y_label_

QLabel* y_label_

protected

y-axis label for messages in the status bar

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

◆ zoom_together_

bool zoom_together_ = false

protected

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

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

Protected Member Functions

Protected Attributes

Friends

Type definitions

TOPP tool execution

reimplemented Qt events

Toolbar slots

Tabbar slots

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConsensusMapSharedPtrType

◆ ConsensusMapType

◆ ExperimentSharedPtrType

◆ ExperimentType

◆ FeatureMapSharedPtrType

◆ FeatureMapType

◆ ODExperimentSharedPtrType

◆ SpectrumType

Member Enumeration Documentation

◆ LOAD_RESULT

◆ TOOL_SCAN

◆ VERBOSITY

Constructor & Destructor Documentation

◆ TOPPViewBase()

◆ ~TOPPViewBase()

Member Function Documentation

◆ abortTOPPTool

◆ addData()

◆ addDataFile()

◆ addRecentFile_()

◆ annotateWithAMS

◆ annotateWithID

◆ annotateWithOSW

◆ changeLabel

◆ changeLayerFlag

◆ changeUnassigned

◆ checkPreferences_()

◆ chooseFilesDialog_()

◆ closeByTab

◆ closeEvent()

◆ closeTab

◆ copyLayer

◆ editMetadata

◆ fileChanged_

◆ finishTOPPToolExecution

◆ getActive1DWidget()

◆ getActive2DWidget()

◆ getActive3DWidget()

◆ getActiveCanvas()

◆ getActivePlotWidget()

◆ getCanvasParameters()

◆ getCurrentLayer() [1/2]

◆ getCurrentLayer() [2/2]

◆ getWorkspace()

◆ initializeDefaultParameters_()

◆ layerActivated

◆ layerDeactivated

◆ layerFilterVisibilityChange

◆ layerStatistics

◆ linkZoom

◆ loadFiles()

◆ loadPreferences()

◆ metadataFileDialog

◆ openFile

◆ openFilesByDialog

◆ preferencesDialog

◆ rerunTOPPTool

◆ resetZoom

◆ runTOPPTool_()

◆ saveLayerAll

◆ saveLayerVisible

◆ savePreferences()

◆ setDrawMode1D

◆ setIntensityMode

◆ showCurrentPeaksAs2D

◆ showCurrentPeaksAs3D

◆ showCurrentPeaksAsDIA

◆ showCurrentPeaksAsIonMobility

◆ showCursorStatus