Main window of the TOPPAS tool. More...

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

Inheritance diagram for TOPPASBase:

Public Slots
void	addTOPPASFile (const String &file_name, bool in_new_window=true)
	opens the file in a new window
void	openFileDialog ()
	shows the dialog for opening files
void	openExampleDialog ()
	shows the dialog for opening example files
void	newPipeline (const int id=-1)
	shows the dialog for creating a new file (pass IDINITIALUNTITLED as `id` if its the first call)
void	includePipeline ()
	shows the dialog for including another workflow in the currently opened one
void	saveCurrentPipelineAs ()
	shows the dialog for saving the current file and updates the current tab caption
void	savePipeline ()
	saves the pipeline (determined by Qt's sender mechanism)
void	exportAsImage ()
	exports the current pipeline as image
void	loadPipelineResourceFile ()
	shows a file dialog for selecting the resource file to load
void	savePipelineResourceFile ()
	shows a file dialog for selecting the resource file to write to
void	openOnlinePipelineRepository ()
	opens the OpenMS Homepage to download example workflows
void	preferencesDialog ()
	shows the preferences dialog
void	updateCurrentPath ()
	changes the current path according to the currently active window/layer
void	updateTabBar (QWidget *w)
	brings the tab corresponding to the active window in front
void	showAboutDialog ()
	Shows the 'About' dialog.
void	showURL ()
	shows the URL stored in the data of the sender QAction
void	showStatusMessage (std::string msg, OpenMS::UInt time)
	Shows a status message in the status bar.
void	showCursorStatus (double x, double y)
	shows x,y coordinates in the status bar
void	closeFile ()
	closes the active window
void	updateToolBar ()
	updates the toolbar
void	runPipeline ()
	Runs the pipeline of the current window.
void	abortPipeline ()
	Terminates the current pipeline.
void	toolStarted ()
	Called when a tool is started.
void	toolFinished ()
	Called when a tool is finished.
void	toolCrashed ()
	Called when a tool crashes.
void	toolFailed ()
	Called when a tool execution fails.
void	outputVertexFinished (const String &file)
	Called when a file was successfully written to an output vertex.
void	updateTOPPOutputLog (const QString &out)
	Called when a TOPP tool produces (error) output.
void	showPipelineFinishedLogMessage ()
	Called by the scene if the pipeline execution finishes successfully.
void	saveToClipboard (TOPPASScene *scene)
	Saves `scene` to the clipboard.
void	sendClipboardContent ()
	Sends the clipboard content to the sender of the connected signal.
void	refreshParameters ()
	Refreshes the parameters of the TOPP tools of the current workflow and stores an updated workflow including the current parameters.
void	openFilesInTOPPView (QStringList all_files)
	Open files in a new TOPPView instance.
void	openToppasFile (QString filename)
	Opens a toppas file.
Public Member Functions
	TOPPASBase (QWidget *parent=0)
	Constructor.
virtual	~TOPPASBase ()
	Destructor.
void	loadPreferences (String filename="")
	Loads the preferences from the filename given.
void	savePreferences ()
	stores the preferences (used when this window is closed)
void	loadFiles (const StringList &list, QSplashScreen *splash_screen)
	loads the files and updates the splash screen
Static Public Member Functions
common functions used in TOPPAS and TOPPView

static TOPPASTreeView *	createTOPPToolsTreeWidget (QWidget *parent_widget=0)
	Creates and fills a tree widget with all available tools.
static QString	savePipelineAs (TOPPASWidget *w, QString current_path)
static QString	loadPipelineResourceFile (TOPPASWidget *w, QString current_path)
	Loads and sets the resources of the TOPPASWidget.
static QString	savePipelineResourceFile (TOPPASWidget *w, QString current_path)
	Saves the resources of the TOPPASWidget.
static QString	refreshPipelineParameters (TOPPASWidget *tw, QString current_path)
	Refreshes the TOPP tools parameters of the pipeline.
Static Public Attributes
static int const	IDINITIALUNTITLED = 1000
	use this for the first call to newPipeline(), to ensure that the first empty (and unmodified) workspace is closed iff existing workflows are loaded
Protected Types
enum	LogState { LS_NOTICE, LS_WARNING, LS_ERROR }
	Log message states. More...
Protected Slots
void	updateMenu ()
	enable/disable menu entries depending on the current state
void	showAsWindow_ (TOPPASWidget *sw, const String &caption, const int special_id=-1)
	Shows the widget as window in the workspace (the special_id is only used for the first untitled widget (to be able to auto-close it later).
void	insertNewVertex_ (double x, double y, QTreeWidgetItem *item=0)
	Inserts a new TOPP tool in the current window at (x,y).
void	insertNewVertexInCenter_ (QTreeWidgetItem *item)
	Inserts the `item` in the middle of the current window.
void	downloadTOPPASfromHomepage_ (const QUrl &url)
	triggered when user clicks a link - if it ends in .TOPPAS we're done
void	toppasFileDownloaded_ (QNetworkReply *r)
	triggered when download of .toppas file is finished, so we can store & open it
void	descriptionUpdated_ ()
	user edited the workflow description
Tab bar slots

void	closeByTab (int id)
	Closes the window corresponding to the data of the tab with identifier `id`.
void	focusByTab (int id)
	Raises the window corresponding to the data of the tab with identifier `id`.
Protected Member Functions
TOPPASWidget *	window_ (int id) const
	returns the window with id `id`
TOPPASWidget *	activeWindow_ () const
	returns a pointer to the active TOPPASWidget (0 if none is active)
void	showLogMessage_ (LogState state, const String &heading, const String &body)
	Shows a log message in the log_ window.
reimplemented Qt events

void	closeEvent (QCloseEvent *event)
void	keyPressEvent (QKeyEvent *e)
Protected Attributes
TOPPASLogWindow *	log_
	Log output window.
QTextEdit *	desc_
	Workflow Description window.
QWorkspace *	ws_
	Main workspace.
QWebView *	webview_
	OpenMS homepage workflow browser.
QNetworkAccessManager *	network_manager_
	download .toppas files from homepage
TOPPASTabBar *	tab_bar_
	Tab bar. The address of the corresponding window to a tab is stored as an int in tabData().
QTreeWidget *	tools_tree_view_
	Tree view of all available TOPP tools.
QListWidget *	blocks_list_
	List of ready analysis pipelines.
String	current_path_
String	tmp_path_
	The path for temporary files.
TOPPASScene *	clipboard_scene_
	The clipboard.
Toolbar

QToolBar *	tool_bar_
Status bar

QLabel *	message_label_
	Label for messages in the status bar.
Static Protected Attributes
static int	node_offset_ = 0
	Offset counter for new inserted nodes (to avoid invisible stacking).
static qreal	z_value_ = 42.0
	z-value counter for new inserted nodes (new nodes should be on top)

Detailed Description

Main window of the TOPPAS tool.

Member Enumeration Documentation

enum LogState [protected]

Log message states.

Enumerator:

LS_NOTICE	Notice.
LS_WARNING	Warning.
LS_ERROR	Fatal error.

Constructor & Destructor Documentation

TOPPASBase ( QWidget * parent = 0 )

Constructor.

References TOPPASBase::abortPipeline(), TOPPASTabBar::addTab(), TOPPASBase::closeByTab(), TOPPASBase::closeFile(), StringList::create(), TOPPASBase::createTOPPToolsTreeWidget(), TOPPASBase::current_path_, DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), TOPPASBase::desc_, TOPPASBase::descriptionUpdated_(), TOPPASBase::downloadTOPPASfromHomepage_(), File::exists(), TOPPASBase::exportAsImage(), TOPPASBase::focusByTab(), File::getOpenMSDataPath(), 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::openFileDialog(), TOPPASBase::openOnlinePipelineRepository(), DefaultParamHandler::param_, TOPPASBase::refreshParameters(), TOPPASTabBar::removeId(), TOPPASBase::runPipeline(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineResourceFile(), Param::setValidStrings(), Param::setValue(), TOPPASBase::showAboutDialog(), TOPPASBase::showURL(), TOPPASBase::tab_bar_, TOPPASBase::tmp_path_, TOPPASBase::tools_tree_view_, TOPPASBase::toppasFileDownloaded_(), String::toQString(), TOPPASBase::updateMenu(), TOPPASBase::updateTabBar(), TOPPASBase::webview_, and TOPPASBase::ws_.

~TOPPASBase ( ) [virtual]

Destructor.

References File::getTempDirectory(), File::removeDirRecursively(), TOPPASBase::savePreferences(), and TOPPASBase::tmp_path_.

Member Function Documentation

void abortPipeline ( ) [slot]

Terminates the current pipeline.

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

Referenced by TOPPASBase::TOPPASBase().

TOPPASWidget * activeWindow_ ( ) 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().

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

opens the file in a new window

References TOPPASBase::activeWindow_(), File::basename(), TOPPASBase::closeByTab(), TOPPASWidget::getScene(), TOPPASBase::IDINITIALUNTITLED, TOPPASScene::include(), TOPPASScene::load(), LOG_ERROR, TOPPASBase::outputVertexFinished(), 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::openFileDialog(), TOPPASBase::openToppasFile(), TOPPASBase::showAsWindow_(), and TOPPASBase::toppasFileDownloaded_().

void closeByTab ( int id ) [protected, slot]

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

References TOPPASTabBar::removeId(), TOPPASBase::tab_bar_, TOPPASBase::updateMenu(), and TOPPASBase::window_().

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

void closeEvent ( QCloseEvent * event ) [protected]

References TOPPASBase::ws_.

void closeFile ( ) [slot]

closes the active window

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

Referenced by TOPPASBase::TOPPASBase().

TOPPASTreeView * createTOPPToolsTreeWidget ( QWidget * parent_widget = 0 ) [static]

Creates and fills a tree widget with all available tools.

References ToolHandler::getTOPPToolList(), ToolHandler::getTypes(), and ToolHandler::getUtilList().

Referenced by TOPPASBase::TOPPASBase().

void descriptionUpdated_ ( ) [protected, slot]

user edited the workflow description

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

Referenced by TOPPASBase::TOPPASBase().

void downloadTOPPASfromHomepage_ ( const QUrl & url ) [protected, slot]

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

References TOPPASBase::LS_NOTICE, TOPPASBase::network_manager_, TOPPASBase::showLogMessage_(), and TOPPASBase::webview_.

Referenced by TOPPASBase::TOPPASBase().

void exportAsImage ( ) [slot]

exports the current pipeline as image

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

Referenced by TOPPASBase::TOPPASBase().

void focusByTab ( int id ) [protected, slot]

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().

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().

void insertNewVertex_	(	double	x,
		double	y,
		QTreeWidgetItem *	item = `0`
	)			`[protected, slot]`

void insertNewVertexInCenter_ ( QTreeWidgetItem * item ) [protected, slot]

Inserts the item in the middle of the current window.

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

Referenced by TOPPASBase::TOPPASBase().

void keyPressEvent ( QKeyEvent * e ) [protected]

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

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

loads the files and updates the splash screen

References TOPPASBase::addTOPPASFile().

Referenced by main().

void loadPipelineResourceFile ( ) [slot]

shows a file dialog for selecting the resource file to load

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

Referenced by TOPPASBase::TOPPASBase().

QString loadPipelineResourceFile	(	TOPPASWidget *	w,
		QString	current_path
	)			`[static]`

Loads and sets the resources of the TOPPASWidget.

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

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::exists(), File::exists(), Param::getValue(), VersionInfo::getVersion(), ParamXMLFile::load(), DefaultParamHandler::param_, DefaultParamHandler::setParameters(), Param::setValue(), and DataValue::toString().

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

void newPipeline ( const int id = -1 ) [slot]

shows the dialog for creating a new file (pass IDINITIALUNTITLED as id if its the first call)

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

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

void openExampleDialog ( ) [slot]

shows the dialog for opening example files

References TOPPASBase::addTOPPASFile(), and File::getOpenMSDataPath().

Referenced by TOPPASBase::TOPPASBase().

void openFileDialog ( ) [slot]

shows the dialog for opening files

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

Referenced by TOPPASBase::TOPPASBase().

void openFilesInTOPPView ( QStringList all_files ) [slot]

Open files in a new TOPPView instance.

References File::exists(), File::findExecutable(), and File::getExecutablePath().

Referenced by TOPPASBase::showAsWindow_().

void openOnlinePipelineRepository ( ) [slot]

opens the OpenMS Homepage to download example workflows

References TOPPASBase::webview_.

Referenced by TOPPASBase::TOPPASBase().

void openToppasFile ( QString filename ) [slot]

Opens a toppas file.

References TOPPASBase::addTOPPASFile().

void outputVertexFinished ( const String & file ) [slot]

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

References TOPPASBase::LS_NOTICE, and TOPPASBase::showLogMessage_().

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

void preferencesDialog ( ) [slot]

shows the preferences dialog

References TOPPASBase::savePreferences().

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::activeWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::refreshPipelineParameters(), TOPPASBase::tab_bar_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

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, and TOPPASScene::updateEdgeColors().

Referenced by TOPPASBase::refreshParameters().

void runPipeline ( ) [slot]

Runs the pipeline of the current window.

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

Referenced by TOPPASBase::TOPPASBase().

void saveCurrentPipelineAs ( ) [slot]

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

References TOPPASBase::activeWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::savePipelineAs(), TOPPASBase::tab_bar_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

void savePipeline ( ) [slot]

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

References TOPPASBase::activeWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASScene::getSaveFileName(), TOPPASWidget::getScene(), TOPPASBase::savePipelineAs(), TOPPASScene::store(), TOPPASBase::tab_bar_, and String::toQString().

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

QString savePipelineAs	(	TOPPASWidget *	w,
		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(), NULL, TOPPASScene::store(), and String::toQString().

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

void savePipelineResourceFile ( ) [slot]

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

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

Referenced by TOPPASBase::TOPPASBase().

QString savePipelineResourceFile	(	TOPPASWidget *	w,
		QString	current_path
	)			`[static]`

Saves the resources of the TOPPASWidget.

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

void savePreferences ( )

stores the preferences (used when this window is closed)

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

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

void saveToClipboard ( TOPPASScene * scene ) [slot]

Saves scene to the clipboard.

References TOPPASBase::clipboard_scene_.

Referenced by TOPPASBase::showAsWindow_().

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_().

void showAboutDialog ( ) [slot]

Shows the 'About' dialog.

References VersionInfo::getVersion().

Referenced by TOPPASBase::TOPPASBase().

void showAsWindow_	(	TOPPASWidget *	sw,
		const String &	caption,
		const int	special_id = `-1`
	)			`[protected, slot]`

Shows the widget as window in the workspace (the special_id is only used for the first untitled widget (to be able to auto-close it later).

References TOPPASTabBar::addTab(), TOPPASBase::addTOPPASFile(), TOPPASBase::desc_, TOPPASScene::getDescription(), TOPPASWidget::getScene(), TOPPASWidget::getWindowId(), TOPPASBase::insertNewVertex_(), TOPPASBase::openFilesInTOPPView(), TOPPASBase::savePipeline(), TOPPASBase::saveToClipboard(), TOPPASBase::sendClipboardContent(), TOPPASTabBar::setCurrentId(), TOPPASWidget::setWindowId(), TOPPASBase::showCursorStatus(), TOPPASBase::showPipelineFinishedLogMessage(), TOPPASBase::showStatusMessage(), TOPPASBase::tab_bar_, String::toQString(), TOPPASBase::updateMenu(), TOPPASBase::updateTOPPOutputLog(), and TOPPASBase::ws_.

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

void showCursorStatus	(	double	x,
		double	y
	)			`[slot]`

shows x,y coordinates in the status bar

Referenced by TOPPASBase::showAsWindow_().

void showLogMessage_	(	TOPPASBase::LogState	state,
		const String &	heading,
		const String &	body
	)			`[protected]`

Shows a log message in the log_ window.

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

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

void showPipelineFinishedLogMessage ( ) [slot]

Called by the scene if the pipeline execution finishes successfully.

References TOPPASBase::LS_NOTICE, and TOPPASBase::showLogMessage_().

Referenced by TOPPASBase::showAsWindow_().

void showStatusMessage	(	std::string	msg,
		OpenMS::UInt	time
	)			`[slot]`

Shows a status message in the status bar.

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

References TOPPASBase::message_label_.

Referenced by TOPPASBase::showAsWindow_().

void showURL ( ) [slot]

shows the URL stored in the data of the sender QAction

Referenced by TOPPASBase::TOPPASBase().

void toolCrashed ( ) [slot]

Called when a tool crashes.

References TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::LS_ERROR, TOPPASBase::showLogMessage_(), and TOPPASBase::updateMenu().

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

void toolFailed ( ) [slot]

Called when a tool execution fails.

References TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::LS_ERROR, TOPPASBase::showLogMessage_(), and TOPPASBase::updateMenu().