Main window of the TOPPAS tool. More...

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

Inheritance diagram for TOPPASBase:

Collaboration diagram for TOPPASBase:

Public Slots
void	addTOPPASFile (const String &file_name, bool in_new_window=true)
	opens the file in a new window More...

void	openFilesByDialog ()
	shows the dialog for opening files More...

void	openExampleDialog ()
	shows the dialog for opening example files More...

void	newPipeline ()
	creates a new tab More...

void	includePipeline ()
	shows the dialog for including another workflow in the currently opened one More...

void	saveCurrentPipelineAs ()
	shows the dialog for saving the current file and updates the current tab caption More...

void	savePipeline ()
	saves the pipeline (determined by Qt's sender mechanism) More...

void	exportAsImage ()
	exports the current pipeline as image More...

void	loadPipelineResourceFile ()
	shows a file dialog for selecting the resource file to load More...

void	savePipelineResourceFile ()
	shows a file dialog for selecting the resource file to write to More...

void	openOnlinePipelineRepository ()
	opens the OpenMS Homepage to download example workflows More...

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

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

void	updateTabBar (QMdiSubWindow *w)
	brings the tab corresponding to the active window in front More...

void	showAboutDialog ()
	Shows the 'About' dialog. More...

void	showURL ()
	shows the URL stored in the data of the sender QAction More...

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

void	showCursorStatus (double x, double y)
	shows x,y coordinates in the status bar More...

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

void	updateToolBar ()
	updates the toolbar More...

void	runPipeline ()
	Runs the pipeline of the current window. More...

void	abortPipeline ()
	Terminates the current pipeline. More...

void	toolStarted ()
	Called when a tool is started. More...

void	toolFinished ()
	Called when a tool is finished. More...

void	toolCrashed ()
	Called when a tool crashes. More...

void	toolFailed ()
	Called when a tool execution fails. More...

void	outputVertexFinished (const String &file)
	Called when a file was successfully written to an output vertex. More...

void	updateTOPPOutputLog (const QString &out)
	Called when a TOPP tool produces (error) output. More...

void	showPipelineFinishedLogMessage ()
	Called by the scene if the pipeline execution finishes successfully. More...

void	saveToClipboard (TOPPASScene *scene)
	Saves `scene` to the clipboard. More...

void	sendClipboardContent ()
	Sends the clipboard content to the sender of the connected signal. More...

void	refreshParameters ()
	Refreshes the parameters of the TOPP tools of the current workflow and stores an updated workflow including the current parameters. More...

void	openFilesInTOPPView (QStringList all_files)
	Open files in a new TOPPView instance. More...

void	openToppasFile (const QString &filename)
	Opens a toppas file. More...

Public Member Functions
	TOPPASBase (QWidget *parent=nullptr)
	Constructor. More...

	~TOPPASBase () override
	Destructor. 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...

void	loadFiles (const std::vector< String > &list, QSplashScreen *splash_screen)
	loads the files and updates the splash screen 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...

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
common functions used in TOPPAS and TOPPView
static TOPPASTreeView *	createTOPPToolsTreeWidget (QWidget *parent_widget=nullptr)
	Creates and fills a tree widget with all available tools. More...

static QString	savePipelineAs (TOPPASWidget *w, const QString &current_path)

static QString	loadPipelineResourceFile (TOPPASWidget *w, const QString &current_path)
	Loads and sets the resources of the TOPPASWidget. More...

static QString	savePipelineResourceFile (TOPPASWidget *w, const QString &current_path)
	Saves the resources of the TOPPASWidget. More...

static QString	refreshPipelineParameters (TOPPASWidget *tw, QString current_path)
	Refreshes the TOPP tools parameters of the pipeline. 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...

Protected Attributes
Toolbar
QToolBar *	tool_bar_

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

EnhancedWorkspace *	ws_
	Main workspace. More...

QWebView *	webview_
	OpenMS homepage workflow browser. More...

QNetworkAccessManager *	network_manager_
	download .toppas files from homepage More...

QNetworkReply *	network_reply_
	the content of the network request More...

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

TOPPASTreeView *	tools_tree_view_
	Tree view of all available TOPP tools. More...

QLineEdit *	tools_filter_
	Filter for the Tree view. More...

QPushButton *	tools_expand_all_
	Expand button for the Tree view. More...

QPushButton *	tools_collapse_all_
	Collapse button for the Tree view. More...

QListWidget *	blocks_list_
	List of ready analysis pipelines. 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...

Tab bar slots
LogWindow *	log_
	Log output window. More...

QTextEdit *	desc_
	Workflow Description window. More...

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

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

void	updateMenu ()
	enable/disable menu entries depending on the current state More...

void	showAsWindow_ (TOPPASWidget *sw, const String &caption)
	Shows the widget as window in the workspace. More...

void	insertNewVertex_ (double x, double y, QTreeWidgetItem *item=nullptr)
	Inserts a new TOPP tool in the current window at (x,y) More...

void	insertNewVertexInCenter_ (QTreeWidgetItem *item)
	Inserts the `item` in the middle of the current window. More...

void	downloadTOPPASfromHomepage_ (const QUrl &url)
	triggered when user clicks a link - if it ends in .TOPPAS we're done More...

void	toppasFileDownloaded_ (QNetworkReply *r)
	triggered when download of .toppas file is finished, so we can store & open it More...

void	TOPPASreadyRead ()
	debug... More...

void	descriptionUpdated_ ()
	user edited the workflow description More...

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

String	current_path_

String	tmp_path_
	The path for temporary files. More...

static int	node_offset_ = 0
	Offset counter for new inserted nodes (to avoid invisible stacking) More...

static qreal	z_value_ = 42.0
	z-value counter for new inserted nodes (new nodes should be on top) More...

TOPPASWidget *	window_ (int id) const
	returns the window with id `id` More...

void	filterToolTree_ ()

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

reimplemented Qt events
TOPPASScene *	clipboard_scene_
	The clipboard. More...

void	closeEvent (QCloseEvent *event) override

void	keyPressEvent (QKeyEvent *e) override

Additional Inherited Members
Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Detailed Description

Main window of the TOPPAS tool.

Constructor & Destructor Documentation

◆ TOPPASBase()

TOPPASBase ( QWidget * parent = nullptr )

Constructor.

References TOPPASBase::abortPipeline(), EnhancedTabBar::addTab(), TOPPASBase::addTOPPASFile(), TOPPASBase::closeByTab(), TOPPASBase::closeFile(), EnhancedTabBar::closeRequested(), TOPPASTreeView::collapseAll(), TOPPASBase::createTOPPToolsTreeWidget(), TOPPASBase::current_path_, EnhancedTabBar::currentIdChanged(), DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), TOPPASBase::desc_, TOPPASBase::descriptionUpdated_(), TOPPASTreeView::expandAll(), TOPPASBase::exportAsImage(), TOPPASBase::filterToolTree_(), TOPPASBase::focusByTab(), RecentFilesMenu::getMenu(), File::getTempDirectory(), File::getUniqueName(), Param::getValue(), TOPPASBase::includePipeline(), TOPPASBase::insertNewVertexInCenter_(), TOPPASBase::loadPipelineResourceFile(), TOPPASBase::loadPreferences(), TOPPASBase::log_, TOPPASBase::message_label_, TOPPASBase::network_manager_, TOPPASBase::newPipeline(), TOPPASBase::openExampleDialog(), TOPPASBase::openFilesByDialog(), DefaultParamHandler::param_, TOPPASBase::recent_files_menu_, RecentFilesMenu::recentFileClicked(), TOPPASBase::refreshParameters(), EnhancedTabBar::removeId(), TOPPASBase::runPipeline(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineResourceFile(), LogWindow::setMaxLength(), Param::setValidStrings(), Param::setValue(), TOPPASBase::showAboutDialog(), TOPPASBase::showURL(), DefaultParamHandler::subsections_, TOPPASBase::tab_bar_, TOPPASBase::tmp_path_, TOPPASBase::tools_collapse_all_, TOPPASBase::tools_expand_all_, TOPPASBase::tools_filter_, TOPPASBase::tools_tree_view_, TOPPASBase::toppasFileDownloaded_(), String::toQString(), OpenMS::StringUtils::toQString(), ParamValue::toString(), TOPPASBase::updateMenu(), TOPPASBase::updateTabBar(), and TOPPASBase::ws_.

◆ ~TOPPASBase()

~TOPPASBase ( )

override

Destructor.

References File::getTempDirectory(), OpenMS::StringUtils::hasPrefix(), File::removeDirRecursively(), TOPPASBase::savePreferences(), OpenMS::StringUtils::substitute(), and TOPPASBase::tmp_path_.

Member Function Documentation

◆ abortPipeline

void abortPipeline ( )

slot

Terminates the current pipeline.

References TOPPASScene::abortPipeline(), TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASBase::updateMenu().

Referenced by TOPPASBase::TOPPASBase().

◆ activeSubWindow_()

TOPPASWidget * activeSubWindow_ ( ) const

protected

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

References TOPPASBase::ws_.

Referenced by TOPPASBase::abortPipeline(), TOPPASBase::addTOPPASFile(), TOPPASBase::descriptionUpdated_(), TOPPASBase::exportAsImage(), TOPPASBase::insertNewVertex_(), TOPPASBase::insertNewVertexInCenter_(), TOPPASBase::keyPressEvent(), TOPPASBase::loadPipelineResourceFile(), TOPPASBase::refreshParameters(), TOPPASBase::runPipeline(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineResourceFile(), and TOPPASBase::updateMenu().

◆ addTOPPASFile

void addTOPPASFile	(	const String &	file_name,
		bool	in_new_window = `true`
	)

slot

opens the file in a new window

References TOPPASBase::activeSubWindow_(), RecentFilesMenu::add(), File::basename(), TOPPASBase::closeByTab(), EnhancedTabBarWidgetInterface::getFirstWindowID(), TOPPASWidget::getScene(), TOPPASScene::include(), TOPPASScene::load(), OPENMS_LOG_ERROR, TOPPASBase::outputVertexFinished(), TOPPASBase::recent_files_menu_, TOPPASBase::showAsWindow_(), TOPPASBase::tmp_path_, TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), TOPPASBase::toolStarted(), String::toQString(), TOPPASBase::updateTOPPOutputLog(), TOPPASScene::verticesBegin(), TOPPASScene::verticesEnd(), TOPPASScene::wasChanged(), TOPPASBase::window_(), and TOPPASBase::ws_.

Referenced by TOPPASBase::includePipeline(), TOPPASBase::loadFiles(), TOPPASBase::openExampleDialog(), TOPPASBase::openFilesByDialog(), TOPPASBase::openToppasFile(), TOPPASBase::showAsWindow_(), and TOPPASBase::TOPPASBase().

◆ closeByTab

void closeByTab ( int id )

protectedslot

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

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

Referenced by TOPPASBase::addTOPPASFile(), and TOPPASBase::TOPPASBase().

◆ closeEvent()

void closeEvent ( QCloseEvent * event )

overrideprotected

References TOPPASWidget::getScene(), TOPPASScene::saveIfChanged(), and TOPPASBase::ws_.

◆ closeFile

void closeFile ( )

slot

closes the active window

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

Referenced by TOPPASBase::TOPPASBase().

◆ createTOPPToolsTreeWidget()

TOPPASTreeView * createTOPPToolsTreeWidget ( QWidget * parent_widget = nullptr )

static

Creates and fills a tree widget with all available tools.

References ToolHandler::getTOPPToolList(), ToolHandler::getTypes(), and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ descriptionUpdated_

void descriptionUpdated_ ( )

protectedslot

user edited the workflow description

References TOPPASBase::activeSubWindow_(), TOPPASBase::desc_, TOPPASWidget::getScene(), TOPPASScene::setChanged(), and TOPPASScene::setDescription().

Referenced by TOPPASBase::TOPPASBase().

◆ downloadTOPPASfromHomepage_

void downloadTOPPASfromHomepage_ ( const QUrl & url )

protectedslot

triggered when user clicks a link - if it ends in .TOPPAS we're done

References LogWindow::appendNewHeader(), TOPPASBase::log_, TOPPASBase::network_manager_, TOPPASBase::network_reply_, and TOPPASBase::TOPPASreadyRead().

◆ exportAsImage

void exportAsImage ( )

slot

exports the current pipeline as image

References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, TOPPASWidget::getScene(), TOPPASScene::setDescription(), and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ filterToolTree_()

void filterToolTree_ ( )

protected

References TOPPASTreeView::filter(), TOPPASBase::tools_filter_, and TOPPASBase::tools_tree_view_.

Referenced by TOPPASBase::TOPPASBase().

◆ focusByTab

void focusByTab ( int id )

protectedslot

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

References TOPPASBase::desc_, TOPPASScene::getDescription(), TOPPASWidget::getScene(), and TOPPASBase::window_().

Referenced by TOPPASBase::TOPPASBase().

◆ includePipeline

void includePipeline ( )

slot

shows the dialog for including another workflow in the currently opened one

References TOPPASBase::addTOPPASFile(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ insertNewVertex_

void insertNewVertex_	(	double	x,
		double	y,
		QTreeWidgetItem *	item = `nullptr`
	)

protectedslot

◆ insertNewVertexInCenter_

void insertNewVertexInCenter_ ( QTreeWidgetItem * item )

protectedslot

Inserts the item in the middle of the current window.

References TOPPASBase::activeSubWindow_(), TOPPASBase::insertNewVertex_(), TOPPASBase::node_offset_, and TOPPASBase::tools_tree_view_.

Referenced by TOPPASBase::TOPPASBase().

◆ keyPressEvent()

void keyPressEvent ( QKeyEvent * e )

overrideprotected

References TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASScene::runPipeline().

◆ loadFiles()

void loadFiles	(	const std::vector< String > &	list,
		QSplashScreen *	splash_screen
	)

loads the files and updates the splash screen

References TOPPASBase::addTOPPASFile(), and OpenMS::StringUtils::toQString().

Referenced by main().

◆ loadPipelineResourceFile [1/2]

void loadPipelineResourceFile ( )

slot

shows a file dialog for selecting the resource file to load

References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ loadPipelineResourceFile() [2/2]

QString loadPipelineResourceFile	(	TOPPASWidget *	w,
		const QString &	current_path
	)

static

Loads and sets the resources of the TOPPASWidget.

References TOPPASWidget::getScene(), TOPPASResources::load(), and TOPPASScene::loadResources().

◆ 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(), Param::getValue(), VersionInfo::getVersion(), ParamXMLFile::load(), DefaultParamHandler::param_, TOPPASBase::recent_files_menu_, RecentFilesMenu::setFromParam(), DefaultParamHandler::setParameters(), Param::setValue(), and ParamValue::toString().

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

◆ newPipeline

void newPipeline ( )

slot

creates a new tab

References TOPPASBase::showAsWindow_(), TOPPASBase::tmp_path_, and TOPPASBase::ws_.

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

◆ openExampleDialog

void openExampleDialog ( )

slot

shows the dialog for opening example files

References TOPPASBase::addTOPPASFile(), File::getOpenMSDataPath(), and OpenMS::StringUtils::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ openFilesByDialog

void openFilesByDialog ( )

slot

shows the dialog for opening files

References TOPPASBase::addTOPPASFile(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ openFilesInTOPPView

void openFilesInTOPPView ( QStringList all_files )

slot

Open files in a new TOPPView instance.

References OpenMS::GUIHelpers::startTOPPView().

Referenced by TOPPASBase::showAsWindow_().

◆ openOnlinePipelineRepository

void openOnlinePipelineRepository ( )

slot

opens the OpenMS Homepage to download example workflows

◆ openToppasFile

void openToppasFile ( const QString & filename )

slot

Opens a toppas file.

References TOPPASBase::addTOPPASFile().

Referenced by main().

◆ outputVertexFinished

void outputVertexFinished ( const String & file )

slot

Called when a file was successfully written to an output vertex.

References LogWindow::appendNewHeader(), and TOPPASBase::log_.

Referenced by TOPPASBase::addTOPPASFile(), and TOPPASBase::insertNewVertex_().

◆ preferencesDialog

void preferencesDialog ( )

slot

shows the preferences dialog

References TOPPASBase::savePreferences().

◆ refreshParameters

void refreshParameters ( )

slot

Refreshes the parameters of the TOPP tools of the current workflow and stores an updated workflow including the current parameters.

References TOPPASBase::activeSubWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::refreshPipelineParameters(), EnhancedTabBar::setTabText(), TOPPASBase::tab_bar_, String::toQString(), and OpenMS::StringUtils::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ refreshPipelineParameters()

QString refreshPipelineParameters	(	TOPPASWidget *	tw,
		QString	current_path
	)

static

Refreshes the TOPP tools parameters of the pipeline.

References TOPPASWidget::getScene(), TOPPASScene::refreshParameters(), TOPPASBase::savePipelineAs(), TOPPASScene::setChanged(), TOPPASScene::ST_REFRESH_CHANGEINVALID, TOPPASScene::ST_REFRESH_NOCHANGE, TOPPASScene::ST_REFRESH_REMAINSINVALID, and TOPPASScene::updateEdgeColors().

Referenced by TOPPASBase::refreshParameters().

◆ runPipeline

void runPipeline ( )

slot

Runs the pipeline of the current window.

References TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASScene::runPipeline().

Referenced by TOPPASBase::TOPPASBase().

◆ saveCurrentPipelineAs

void saveCurrentPipelineAs ( )

slot

shows the dialog for saving the current file and updates the current tab caption

References TOPPASBase::activeSubWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::savePipelineAs(), EnhancedTabBar::setTabText(), TOPPASBase::tab_bar_, String::toQString(), and OpenMS::StringUtils::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ savePipeline

void savePipeline ( )

slot

saves the pipeline (determined by Qt's sender mechanism)

References TOPPASBase::activeSubWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASScene::getSaveFileName(), TOPPASWidget::getScene(), TOPPASBase::savePipelineAs(), EnhancedTabBar::setTabText(), TOPPASScene::store(), TOPPASBase::tab_bar_, String::toQString(), and OpenMS::StringUtils::toQString().

Referenced by TOPPASBase::showAsWindow_(), and TOPPASBase::TOPPASBase().

◆ savePipelineAs()

QString savePipelineAs	(	TOPPASWidget *	w,
		const QString &	current_path
	)

static

Saves the workflow in the provided TOPPASWidget to a user defined location. Returns the full file name or "" if no valid one is selected.

References File::basename(), TOPPASWidget::getScene(), TOPPASScene::store(), and String::toQString().

Referenced by TOPPASBase::refreshPipelineParameters(), TOPPASBase::saveCurrentPipelineAs(), and TOPPASBase::savePipeline().

◆ savePipelineResourceFile [1/2]

void savePipelineResourceFile ( )

slot

shows a file dialog for selecting the resource file to write to

References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

◆ savePipelineResourceFile() [2/2]

QString savePipelineResourceFile	(	TOPPASWidget *	w,
		const QString &	current_path
	)

static

Saves the resources of the TOPPASWidget.

References TOPPASScene::createResources(), TOPPASWidget::getScene(), and TOPPASResources::store().

◆ savePreferences()

void savePreferences ( )

stores the preferences (used when this window is closed)

References Param::copy(), RecentFilesMenu::getAsParam(), Param::getValue(), VersionInfo::getVersion(), Param::insert(), DefaultParamHandler::param_, TOPPASBase::recent_files_menu_, Param::removeAll(), Param::setValue(), and ParamXMLFile::store().

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

◆ saveToClipboard

void saveToClipboard ( TOPPASScene * scene )

slot

Saves scene to the clipboard.

References TOPPASBase::clipboard_scene_.

Referenced by TOPPASBase::showAsWindow_().

◆ sendClipboardContent

void sendClipboardContent ( )

slot

Sends the clipboard content to the sender of the connected signal.

References TOPPASBase::clipboard_scene_, and TOPPASScene::setClipboard().

Referenced by TOPPASBase::showAsWindow_().

◆ showAboutDialog

void showAboutDialog ( )

slot

Shows the 'About' dialog.

References QApplicationTOPP::showAboutDialog().

Referenced by TOPPASBase::TOPPASBase().

◆ showAsWindow_

void showAsWindow_	(	TOPPASWidget *	sw,
		const String &	caption
	)

protectedslot

◆ showCursorStatus

void showCursorStatus	(	double	x,
		double	y
	)

slot

shows x,y coordinates in the status bar

Referenced by TOPPASBase::showAsWindow_().

◆ showPipelineFinishedLogMessage

void showPipelineFinishedLogMessage ( )

slot

Called by the scene if the pipeline execution finishes successfully.

References LogWindow::appendNewHeader(), and TOPPASBase::log_.

Referenced by TOPPASBase::showAsWindow_().

◆ 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 TOPPASBase::message_label_.

Referenced by TOPPASBase::showAsWindow_().

◆ showURL

void showURL ( )

slot

shows the URL stored in the data of the sender QAction

References OpenMS::GUIHelpers::openURL().

Referenced by TOPPASBase::TOPPASBase().

◆ toolCrashed

void toolCrashed ( )

slot

Called when a tool crashes.

References LogWindow::appendNewHeader(), TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::log_, and TOPPASBase::updateMenu().

Referenced by TOPPASBase::addTOPPASFile(), and TOPPASBase::insertNewVertex_().

◆ toolFailed

void toolFailed ( )

slot

Called when a tool execution fails.

References LogWindow::appendNewHeader(), TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::log_, and TOPPASBase::updateMenu().

Referenced by TOPPASBase::addTOPPASFile(), and TOPPASBase::insertNewVertex_().

◆ toolFinished

void toolFinished ( )

slot

Called when a tool is finished.

References LogWindow::appendNewHeader(), TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::log_, and TOPPASBase::updateMenu().

Referenced by TOPPASBase::addTOPPASFile(), and TOPPASBase::insertNewVertex_().

◆ toolStarted

void toolStarted ( )

slot

Called when a tool is started.

References LogWindow::appendNewHeader(), TOPPASToolVertex::getName(), TOPPASVertex::getTopoNr(), TOPPASToolVertex::getType(), TOPPASBase::log_, and TOPPASBase::updateMenu().

Referenced by TOPPASBase::addTOPPASFile(), and TOPPASBase::insertNewVertex_().

◆ toppasFileDownloaded_

void toppasFileDownloaded_ ( QNetworkReply * r )

protectedslot

triggered when download of .toppas file is finished, so we can store & open it

Referenced by TOPPASBase::TOPPASBase().

◆ TOPPASreadyRead

void TOPPASreadyRead ( )

protectedslot

debug...

References TOPPASBase::network_reply_, and OPENMS_LOG_DEBUG.

Referenced by TOPPASBase::downloadTOPPASfromHomepage_().

◆ updateCurrentPath

void updateCurrentPath ( )

slot

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

References TOPPASBase::current_path_, Param::getValue(), DefaultParamHandler::param_, and ParamValue::toString().

◆ updateMenu

void updateMenu ( )

protectedslot

enable/disable menu entries depending on the current state

References TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), TOPPASScene::isPipelineRunning(), EnhancedTabBar::setTabText(), TOPPASBase::tab_bar_, and TOPPASScene::wasChanged().

Referenced by TOPPASBase::abortPipeline(), TOPPASBase::closeByTab(), TOPPASBase::closeFile(), TOPPASBase::showAsWindow_(), TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), TOPPASBase::toolStarted(), and TOPPASBase::TOPPASBase().

◆ updateTabBar

void updateTabBar ( QMdiSubWindow * w )

slot

brings the tab corresponding to the active window in front

References EnhancedTabBarWidgetInterface::getWindowId(), EnhancedTabBar::show(), and TOPPASBase::tab_bar_.

Referenced by TOPPASBase::TOPPASBase().

◆ updateToolBar

void updateToolBar ( )

slot

updates the toolbar

◆ updateTOPPOutputLog

void updateTOPPOutputLog ( const QString & out )

slot

Called when a TOPP tool produces (error) output.

References TOPPASBase::log_.

Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::insertNewVertex_(), and TOPPASBase::showAsWindow_().

◆ window_()

TOPPASWidget * window_ ( int id ) const

protected

returns the window with id id

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

Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::closeByTab(), and TOPPASBase::focusByTab().

Member Data Documentation

◆ blocks_list_

QListWidget* blocks_list_

protected

List of ready analysis pipelines.

◆ clipboard_scene_

TOPPASScene* clipboard_scene_

protected

The clipboard.

Referenced by TOPPASBase::saveToClipboard(), and TOPPASBase::sendClipboardContent().

◆ 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 TOPPASBase::exportAsImage(), TOPPASBase::includePipeline(), TOPPASBase::loadPipelineResourceFile(), TOPPASBase::openFilesByDialog(), TOPPASBase::refreshParameters(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineResourceFile(), TOPPASBase::TOPPASBase(), and TOPPASBase::updateCurrentPath().

◆ desc_

QTextEdit* desc_

protected

Workflow Description window.

Referenced by TOPPASBase::descriptionUpdated_(), TOPPASBase::focusByTab(), TOPPASBase::showAsWindow_(), and TOPPASBase::TOPPASBase().

◆ log_

LogWindow* log_

protected

Log output window.

Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), TOPPASBase::outputVertexFinished(), TOPPASBase::showPipelineFinishedLogMessage(), TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), TOPPASBase::toolStarted(), TOPPASBase::TOPPASBase(), and TOPPASBase::updateTOPPOutputLog().

◆ message_label_

QLabel* message_label_

protected

Label for messages in the status bar.

Referenced by TOPPASBase::showStatusMessage(), and TOPPASBase::TOPPASBase().

◆ network_manager_

QNetworkAccessManager* network_manager_

protected

download .toppas files from homepage

Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), and TOPPASBase::TOPPASBase().

◆ network_reply_

QNetworkReply* network_reply_

protected

the content of the network request

Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), and TOPPASBase::TOPPASreadyRead().

◆ node_offset_

int node_offset_ = 0

staticprotected

Offset counter for new inserted nodes (to avoid invisible stacking)

Referenced by TOPPASBase::insertNewVertexInCenter_().

◆ recent_files_menu_

RecentFilesMenu recent_files_menu_

protected

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

Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::loadPreferences(), TOPPASBase::savePreferences(), and TOPPASBase::TOPPASBase().

◆ 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 TOPPASBase::refreshParameters(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::showAsWindow_(), TOPPASBase::TOPPASBase(), TOPPASBase::updateMenu(), and TOPPASBase::updateTabBar().

◆ tmp_path_

String tmp_path_

protected

The path for temporary files.

Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::newPipeline(), TOPPASBase::TOPPASBase(), and TOPPASBase::~TOPPASBase().

◆ tool_bar_

QToolBar* tool_bar_

protected

◆ tools_collapse_all_

QPushButton* tools_collapse_all_

protected

Collapse button for the Tree view.

Referenced by TOPPASBase::TOPPASBase().

◆ tools_expand_all_

QPushButton* tools_expand_all_

protected

Expand button for the Tree view.

Referenced by TOPPASBase::TOPPASBase().

◆ tools_filter_

QLineEdit* tools_filter_

protected

Filter for the Tree view.

Referenced by TOPPASBase::filterToolTree_(), and TOPPASBase::TOPPASBase().

◆ tools_tree_view_

TOPPASTreeView* tools_tree_view_

protected

Tree view of all available TOPP tools.

Referenced by TOPPASBase::filterToolTree_(), TOPPASBase::insertNewVertex_(), TOPPASBase::insertNewVertexInCenter_(), and TOPPASBase::TOPPASBase().

◆ webview_

QWebView* webview_

protected

OpenMS homepage workflow browser.

◆ ws_

EnhancedWorkspace* ws_

protected

Main workspace.

Referenced by TOPPASBase::activeSubWindow_(), TOPPASBase::addTOPPASFile(), TOPPASBase::closeEvent(), TOPPASBase::closeFile(), TOPPASBase::newPipeline(), TOPPASBase::showAsWindow_(), TOPPASBase::TOPPASBase(), and TOPPASBase::window_().

◆ z_value_

qreal z_value_ = 42.0

staticprotected

z-value counter for new inserted nodes (new nodes should be on top)

Referenced by TOPPASBase::insertNewVertex_().

Public Slots

Public Member Functions

Static Public Member Functions

Protected Attributes

Tab bar slots

Status bar

reimplemented Qt events

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TOPPASBase()

◆ ~TOPPASBase()

Member Function Documentation

◆ abortPipeline

◆ activeSubWindow_()

◆ addTOPPASFile

◆ closeByTab

◆ closeEvent()

◆ closeFile

◆ createTOPPToolsTreeWidget()

◆ descriptionUpdated_

◆ downloadTOPPASfromHomepage_

◆ exportAsImage

◆ filterToolTree_()

◆ focusByTab

◆ includePipeline

◆ insertNewVertex_

◆ insertNewVertexInCenter_

◆ keyPressEvent()

◆ loadFiles()

◆ loadPipelineResourceFile [1/2]

◆ loadPipelineResourceFile() [2/2]

◆ loadPreferences()

◆ newPipeline

◆ openExampleDialog

◆ openFilesByDialog

◆ openFilesInTOPPView

◆ openOnlinePipelineRepository

◆ openToppasFile

◆ outputVertexFinished

◆ preferencesDialog

◆ refreshParameters

◆ refreshPipelineParameters()

◆ runPipeline

◆ saveCurrentPipelineAs

◆ savePipeline

◆ savePipelineAs()

◆ savePipelineResourceFile [1/2]

◆ savePipelineResourceFile() [2/2]

◆ savePreferences()

◆ saveToClipboard

◆ sendClipboardContent

◆ showAboutDialog

◆ showAsWindow_

◆ showCursorStatus

◆ showPipelineFinishedLogMessage

◆ showStatusMessage

◆ showURL

◆ toolCrashed

◆ toolFailed

◆ toolFinished

◆ toolStarted

◆ toppasFileDownloaded_

◆ TOPPASreadyRead

◆ updateCurrentPath

◆ updateMenu

◆ updateTabBar

◆ updateToolBar

◆ updateTOPPOutputLog

◆ window_()

Member Data Documentation

◆ blocks_list_

◆ clipboard_scene_

◆ current_path_

◆ desc_

◆ log_

◆ message_label_

◆ network_manager_

◆ network_reply_

◆ node_offset_