A container for all visual items of a TOPPAS workflow. More...

#include <OpenMS/VISUAL/TOPPASScene.h>

Inheritance diagram for TOPPASScene:

Collaboration diagram for TOPPASScene:

Classes
struct	TOPPProcess
	Stores the information for a TOPP process. More...

Public Types
enum	ActionMode { AM_NEW_EDGE , AM_MOVE }
	The current action mode (creation of a new edge, or panning of the widget) More...

enum	RefreshStatus { ST_REFRESH_NOCHANGE , ST_REFRESH_CHANGED , ST_REFRESH_CHANGEINVALID , ST_REFRESH_REMAINSINVALID }
	Pipeline status after refreshParameters() was called. More...

typedef QList< TOPPASEdge * >	EdgeContainer
	The container for edges. More...

typedef EdgeContainer::iterator	EdgeIterator
	A mutable iterator for edges. More...

typedef EdgeContainer::const_iterator	ConstEdgeIterator
	A const iterator for edges. More...

typedef QList< TOPPASVertex * >	VertexContainer
	The container for vertices. More...

typedef VertexContainer::iterator	VertexIterator
	A mutable iterator for vertices. More...

typedef VertexContainer::const_iterator	ConstVertexIterator
	A const iterator for vertices. More...

Public Slots
void	abortPipeline ()
	Terminates the currently running pipeline. More...

void	itemClicked ()
	Called when an item is clicked. More...

void	itemReleased ()
	Called when an item is released. More...

void	updateHoveringEdgePos (const QPointF &new_pos)
	Called when the position of the hovering edge changes. More...

void	addHoveringEdge (const QPointF &pos)
	Called when a new out edge is supposed to be created. More...

void	finishHoveringEdge ()
	Called when the new edge is being "released". More...

void	pipelineErrorSlot (const QString msg="")
	Called by vertices at which an error occurred during pipeline execution. More...

void	moveSelectedItems (qreal dx, qreal dy)
	Moves all selected items by dx, dy. More...

void	snapToGrid ()
	Makes all vertices snap to the grid. More...

void	setPipelineRunning (bool b=true)

void	changedParameter (const bool invalidates_running_pipeline)
	Invoked by TTV or other vertices if a parameter was edited. More...

void	changedOutputFolder ()
	Invoked by OutfilelistVertex of user changed the folder name. More...

void	processFinished ()
	Called by a finished QProcess to indicate that we are free to start a new one. More...

void	quitWithError ()
	dirty solution: when using ExecutePipeline this slot is called when the pipeline crashes. This will quit the app More...

Public Member Functions
	TOPPASScene (QObject *parent, const QString &tmp_path, bool gui=true)
	Constructor. More...

	~TOPPASScene () override
	Destructor. More...

void	addVertex (TOPPASVertex *tv)
	Adds a vertex. More...

void	addEdge (TOPPASEdge *te)
	Adds an edge. More...

void	setActionMode (ActionMode mode)
	Sets the action mode. More...

ActionMode	getActionMode ()
	Returns the action mode. More...

VertexIterator	verticesBegin ()
	Returns begin() iterator of all vertices. More...

VertexIterator	verticesEnd ()
	Returns end() iterator of all vertices. More...

EdgeIterator	edgesBegin ()
	Returns begin() iterator of all edges. More...

EdgeIterator	edgesEnd ()
	Returns end() iterator of all edges. More...

void	copySelected ()
	Copies all currently selected edges and vertices. More...

void	paste (QPointF pos=QPointF())
	Pastes the copied items. More...

void	removeSelected ()
	Removes all currently selected edges and vertices. More...

void	unselectAll ()
	Unselects all items. More...

void	updateEdgeColors ()
	Updates all edge colors (color of green and yellow edges can change when edges are added/removed) More...

void	resetDownstream (TOPPASVertex *vertex)
	Called when user fires "Resume" action, to clear downstream nodes from previous results. More...

void	runPipeline ()
	Runs the pipeline. More...

bool	store (const String &file)
	Stores the pipeline to `file`, returns true on success. More...

void	load (const String &file)
	Loads the pipeline from `file`. More...

void	include (TOPPASScene *new_scene, QPointF pos=QPointF())
	Includes the pipeline `scene`. More...

const String &	getSaveFileName ()
	Returns the file name. More...

void	setSaveFileName (const String &name)
	Sets the file name. More...

void	topoSort (bool resort_all=true)
	Performs a topological sort of all vertices. More...

const QString &	getOutDir () const
	Returns the name of the directory for output files. More...

const QString &	getTempDir () const
	Returns the name of the directory for temporary files. More...

void	setOutDir (const QString &dir)
	Sets the name of the directory for output files. More...

bool	saveIfChanged ()
	Saves the pipeline if it has been changed since the last save. More...

void	setChanged (bool b)
	Sets the changed flag. More...

bool	isPipelineRunning () const
	Returns if a pipeline is currently running. More...

bool	askForOutputDir (bool always_ask=true)
	Shows a dialog that allows to specify the output directory. If `always_ask` == false, the dialog won't be shown if a directory has been set, already. More...

void	enqueueProcess (const TOPPProcess &process)
	Enqueues the process, it will be run when the currently pending processes have finished. More...

void	runNextProcess ()
	Runs the next process in the queue, if any. More...

void	resetProcessesQueue ()
	Resets the processes queue. More...

void	setClipboard (TOPPASScene *clipboard)
	Sets the clipboard content. More...

void	connectVertexSignals (TOPPASVertex *tv)
	Connects the signals to slots. More...

void	connectToolVertexSignals (TOPPASToolVertex *ttv)
	Connects the signals to slots. More...

void	connectOutputVertexSignals (TOPPASOutputFileListVertex *oflv)
	Connects the signals to slots. More...

void	connectMergerVertexSignals (TOPPASMergerVertex *tmv)
	Connects the signals to slots. More...

void	connectEdgeSignals (TOPPASEdge *e)
	Connects the signals to slots. More...

void	loadResources (const TOPPASResources &resources)
	Loads the `resources` into the input nodes of this workflow. More...

void	createResources (TOPPASResources &resources)
	Create `resources` from the current workflow. More...

bool	wasChanged () const
	Returns whether the workflow has been changed since the latest "save". More...

RefreshStatus	refreshParameters ()
	Refreshes the parameters of the TOPP tools in this workflow. More...

bool	isGUIMode () const
	is TOPPASScene run in GUI or non-GUI (ExecutePipeline) mode, i.e. are MessageBoxes allowed? More...

bool	isDryRun () const
	determine dry run status (are tools actually called?) More...

QString	getDescription () const
	workflow description (to be displayed in TOPPAS window) More...

void	setDescription (const QString &desc)
	when description is updated by user, use this to update the description for later storage in file More...

void	setAllowedThreads (int num_threads)
	sets the maximum number of jobs More...

TOPPASEdge *	getHoveringEdge ()
	returns the hovering edge More...

void	checkIfWeAreDone ()
	Checks whether all output vertices are finished, and if yes, emits entirePipelineFinished() (called by finished output vertices) More...

Protected Member Functions
reimplemented Qt events
void	contextMenuEvent (QGraphicsSceneContextMenuEvent *event) override

void	writeToLogFile_ (const QString &text)
	Writes the `text` to the logfile. More...

Slots for printing log/error output when no GUI is available
ActionMode	action_mode_
	The current action mode. More...

VertexContainer	vertices_
	The list of all vertices. More...

EdgeContainer	edges_
	The list of all edges. More...

TOPPASEdge *	hover_edge_
	The hovering edge which is currently being created. More...

TOPPASVertex *	potential_target_
	The current potential target vertex of the hovering edge. More...

String	file_name_
	The file name of this pipeline. More...

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

bool	gui_
	Are we in a GUI or is the scene used by ExecutePipeline (at the command line)? More...

QString	out_dir_
	The directory where the output files will be written. More...

bool	changed_
	Flag that indicates if the pipeline has been changed since the last save. More...

bool	running_
	Indicates if a pipeline is currently running. More...

bool	error_occured_
	true if an error occurred during pipeline execution More...

bool	user_specified_out_dir_
	Indicates if the output directory has been specified by the user already. More...

QList< TOPPProcess >	topp_processes_queue_
	The queue of pending TOPP processes. More...

TOPPASScene *	clipboard_
	Stores the clipboard content when requested from TOPPASBase. More...

bool	dry_run_
	dry run mode (no tools are actually called) More...

int	threads_active_
	currently running processes... More...

QString	description_text_
	description text More...

int	allowed_threads_
	maximum number of allowed threads More...

TOPPASToolVertex *	resume_source_
	last node where 'resume' was started More...

void	logTOPPOutput (const QString &out)
	Writes the TOPP tool output to the logfile (and to stdout if no gui available) More...

void	logToolStarted ()
	Writes the "tool started" message to the logfile (and to stdout if no gui available) More...

void	logToolFinished ()
	Writes the "tool finished" message to the logfile (and to stdout if no gui available) More...

void	logToolFailed ()
	Writes the "tool failed" message to the logfile (and to stdout if no gui available) More...

void	logToolCrashed ()
	Writes the "tool crashed" message to the logfile (and to stdout if no gui available) More...

void	logOutputFileWritten (const String &file)
	Writes the "output file written" message to the logfile (and to stdout if no gui available) More...

void	entirePipelineFinished ()
	Emitted when the entire pipeline execution is finished. More...

void	pipelineExecutionFailed ()
	Emitted when the pipeline execution has failed. More...

void	saveMe ()
	Emitted when the pipeline should be saved (showing a save as file dialog and so on) More...

void	terminateCurrentPipeline ()
	Kills all connected TOPP processes. More...

void	selectionCopied (TOPPASScene *ts)
	Emitted when a selection is copied to the clipboard. More...

void	requestClipboardContent ()
	Requests the clipboard content from TOPPASBase, will be stored in clipboard_. More...

void	mainWindowNeedsUpdate ()
	Emitted when the main window needs to be updated. More...

void	openInTOPPView (QStringList all_files)
	Emitted when files are triggered for opening in TOPPView. More...

void	dryRunFinished (int, QProcess::ExitStatus)
	Emitted when in dry run mode and asked to run a TOPP tool (to fake success) More...

void	messageReady (const QString &msg)
	Emitted when there is an important message that needs to be printed in TOPPAS. More...

TOPPASVertex *	getVertexAt_ (const QPointF &pos)
	Returns the vertex in the foreground at position `pos` , if existent, otherwise 0. More...

bool	isEdgeAllowed_ (TOPPASVertex u, TOPPASVertex v)
	Returns whether an edge between node u and v would be allowed. More...

bool	dfsVisit_ (TOPPASVertex *vertex)
	DFS helper method. Returns true, if a back edge has been discovered. More...

bool	sanityCheck_ (bool allowUserOverride)

Detailed Description

A container for all visual items of a TOPPAS workflow.

TOPPASScene is a subclass of QGraphicsScene and acts as a container for all visual items (i.e. all vertices and edges). It is visualized by a TOPPASWidget (a subclass of QGraphicsView). This class also provides large parts of the functionality of TOPPAS, e.g., the methods for loading, saving, running, and aborting pipelines are located here.

TOPPASScene can also be used without a visualizing TOPPASWidget (i.e., without a gui) which can be indicated via the constructor. In this case, the signals for log message output are connected to standard out. This is utilized for the ExecutePipeline tool.

Temporary files of the pipeline are stored in the member tmp_path_. Update it when loading a pipeline which has tmp data from an old run. TOPPASToolVertex will ask its parent scene() whenever it wants to know the tmp directory.

Member Typedef Documentation

◆ ConstEdgeIterator

typedef EdgeContainer::const_iterator ConstEdgeIterator

A const iterator for edges.

◆ ConstVertexIterator

typedef VertexContainer::const_iterator ConstVertexIterator

A const iterator for vertices.

◆ EdgeContainer

typedef QList<TOPPASEdge *> EdgeContainer

The container for edges.

◆ EdgeIterator

typedef EdgeContainer::iterator EdgeIterator

A mutable iterator for edges.

◆ VertexContainer

typedef QList<TOPPASVertex *> VertexContainer

The container for vertices.

◆ VertexIterator

typedef VertexContainer::iterator VertexIterator

A mutable iterator for vertices.

Member Enumeration Documentation

◆ ActionMode

enum ActionMode

The current action mode (creation of a new edge, or panning of the widget)

Enumerator
AM_NEW_EDGE
AM_MOVE

◆ RefreshStatus

enum RefreshStatus

Pipeline status after refreshParameters() was called.

Enumerator
ST_REFRESH_NOCHANGE	no updates required
ST_REFRESH_CHANGED	some parameters were updated, but pipeline is ok
ST_REFRESH_CHANGEINVALID	updating made pipeline invalid
ST_REFRESH_REMAINSINVALID	pipeline was not valid before and is invalid afterwards

Constructor & Destructor Documentation

◆ TOPPASScene()

TOPPASScene	(	QObject *	parent,
		const QString &	tmp_path,
		bool	gui = `true`
	)

Constructor.

◆ ~TOPPASScene()

~TOPPASScene ( )

override

Destructor.

Member Function Documentation

◆ abortPipeline

void abortPipeline ( )

slot

Terminates the currently running pipeline.

Referenced by TOPPASBase::abortPipeline().

◆ addEdge()

void addEdge ( TOPPASEdge * te )

Adds an edge.

◆ addHoveringEdge

void addHoveringEdge ( const QPointF & pos )

slot

Called when a new out edge is supposed to be created.

◆ addVertex()

void addVertex ( TOPPASVertex * tv )

Adds a vertex.

Referenced by TOPPASBase::insertNewVertex_().

◆ askForOutputDir()

bool askForOutputDir ( bool always_ask = true )

Shows a dialog that allows to specify the output directory. If always_ask == false, the dialog won't be shown if a directory has been set, already.

◆ changedOutputFolder

void changedOutputFolder ( )

slot

Invoked by OutfilelistVertex of user changed the folder name.

◆ changedParameter

void changedParameter ( const bool invalidates_running_pipeline )

slot

Invoked by TTV or other vertices if a parameter was edited.

◆ checkIfWeAreDone()

void checkIfWeAreDone ( )

Checks whether all output vertices are finished, and if yes, emits entirePipelineFinished() (called by finished output vertices)