A vertex representing a TOPP tool. More...

#include <OpenMS/VISUAL/TOPPASToolVertex.h>

Inheritance diagram for TOPPASToolVertex:

Collaboration diagram for TOPPASToolVertex:

Classes
struct	IOInfo
	Stores the information for input/output files/lists. More...

Public Types
enum	TOOLSTATUS { TOOL_READY , TOOL_SCHEDULED , TOOL_RUNNING , TOOL_SUCCESS , TOOL_CRASH , TOOLSTATUS_SIZE }
	current status of the vertex More...

Public Types inherited from TOPPASVertex
enum	DFS_COLOR { DFS_WHITE , DFS_GRAY , DFS_BLACK }
	The color of a vertex during depth-first search. More...

enum	SUBSTREESTATUS { TV_ALLFINISHED , TV_UNFINISHED , TV_UNFINISHED_INBRANCH }
	The color of a vertex during depth-first search. More...

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

typedef EdgeContainer::iterator	EdgeIterator
	A mutable iterator for in/out edges. More...

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

using	RoundPackage = std::map< Int, VertexRoundPackage >

using	RoundPackageConstIt = RoundPackage::const_iterator

using	RoundPackageIt = RoundPackage::iterator

using	RoundPackages = std::vector< RoundPackage >
	all information a node needs to process all rounds More...

Public Slots
void	executionFinished (int ec, QProcess::ExitStatus es)
	Called when the execution of this tool has finished. More...

void	forwardTOPPOutput ()
	Called when the running TOPP tool produces output. More...

void	toolStartedSlot ()
	Called when the tool is started. More...

void	toolFinishedSlot ()
	Called when the tool has finished. More...

void	toolCrashedSlot ()
	Called when the tool has crashed. More...

void	toolFailedSlot ()
	Called when the tool has failed. More...

virtual void	toolScheduledSlot ()
	Called when the tool was scheduled for running. More...

void	inEdgeHasChanged () override
	Called by an incoming edge when it has changed. More...

void	outEdgeHasChanged () override
	Called by an outgoing edge when it has changed. More...

Public Slots inherited from TOPPASVertex
virtual void	inEdgeHasChanged ()
	Called by an incoming edge when it has changed. More...

virtual void	outEdgeHasChanged ()
	Called by an outgoing edge when it has changed. More...

Signals
void	toolStarted ()
	Emitted when the tool is started. More...

void	toolFinished ()
	Emitted when the tool is finished. More...

void	toolCrashed ()
	Emitted when the tool crashes. More...

void	toolFailed (int return_code=-1, const QString &message="")
	Emitted when the tool execution fails. More...

void	toppOutputReady (const QString &out)
	Emitted from forwardTOPPOutput() to forward the signal outside. More...

Signals inherited from TOPPASVertex
void	clicked ()
	Emitted when this item is clicked. More...

void	released ()
	Emitted when this item is released. More...

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

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

void	finishHoveringEdge ()
	Emitted when the mouse is released after having dragged a new edge somewhere. More...

void	somethingHasChanged ()
	Emitted when something has changed. More...

void	itemDragged (qreal dx, qreal dy)
	Emitted when the item is dragged. More...

void	parameterChanged (const bool invalidates_running_pipeline)

Public Member Functions
	TOPPASToolVertex ()
	Default constructor. More...

	TOPPASToolVertex (const String &name, const String &type="")
	Constructor. More...

	TOPPASToolVertex (const TOPPASToolVertex &rhs)
	Copy constructor. More...

	~TOPPASToolVertex () override=default
	Destructor. More...

TOPPASToolVertex &	operator= (const TOPPASToolVertex &rhs)
	Assignment operator. More...

virtual std::unique_ptr< TOPPASVertex >	clone () const override
	Make a copy of this vertex on the heap and return a pointer to it (useful for copying nodes) More...

String	getName () const override
	returns the name of the TOPP tool More...

const String &	getType () const
	Returns the type of the tool. More...

QVector< IOInfo >	getInputParameters () const
	Returns input file/list parameters together with their valid types. More...

QVector< IOInfo >	getOutputParameters () const
	Returns output file/list/dir parameters together with their valid types. More...

void	paint (QPainter painter, const QStyleOptionGraphicsItem option, QWidget *widget) override

QRectF	boundingRect () const override
	Returns the bounding rectangle of this item. More...

void	setTopoNr (UInt nr) override
	Sets the topological sort number (overridden in tool and output vertices) More...

void	reset (bool reset_all_files=false) override

void	setParam (const Param &param)
	Sets the Param object of this tool. More...

const Param &	getParam ()
	Returns the Param object of this tool. More...

void	run () override
	Checks if all parent nodes have finished the tool execution and, if so, runs the tool. More...

bool	updateCurrentOutputFileNames (const RoundPackages &pkg, String &error_message)

TOOLSTATUS	getStatus () const
	return if tool failed or is ready etc. More...

void	editParam ()
	Lets the user edit the parameters of the tool. More...

int	numIterations ()
	Returns the number of iterations this tool has to perform. More...

String	getFullOutputDirectory () const
	Returns the full directory (including preceding tmp path) More...

String	getOutputDir () const
	Returns the directory where this tool stores its output files. More...

void	createDirs ()
	Creates all necessary directories. More...

void	openContainingFolder () const
	Opens the folder where the file is contained. More...

void	openInTOPPView ()
	Opens the files in TOPPView. More...

bool	refreshParameters ()
	Refreshes the parameters of this tool, returns if their has been a change. More...

bool	isToolReady () const
	underlying TOPP tool found and parameters fetched?! (done in C'Tor) More...

void	toggleBreakpoint ()
	Toggle breakpoint. More...

virtual void	emitToolStarted ()
	Called when the QProcess in the queue is called: emits 'toolStarted()'. More...

bool	invertRecylingMode () override
	invert status of recycling (overriding base class) More...

Public Member Functions inherited from TOPPASVertex
	TOPPASVertex ()
	Default Constructor. More...

	TOPPASVertex (const TOPPASVertex &rhs)
	Copy constructor. More...

	~TOPPASVertex () override=default
	Destructor. More...

TOPPASVertex &	operator= (const TOPPASVertex &rhs)
	Assignment operator. More...

void	paint (QPainter painter, const QStyleOptionGraphicsItem , QWidget *, bool round_shape=true)
	base paint method for all derived classes. should be called first in child-class paint More...

bool	buildRoundPackages (RoundPackages &pkg, String &error_msg)

bool	isUpstreamFinished () const
	check if all upstream nodes are ready to go ( 'finished_' is true) More...

QPainterPath	shape () const final
	Returns a more precise shape. More...

ConstEdgeIterator	outEdgesBegin () const
	Returns begin() iterator of outgoing edges. More...

ConstEdgeIterator	outEdgesEnd () const
	Returns end() iterator of outgoing edges. More...

ConstEdgeIterator	inEdgesBegin () const
	Returns begin() iterator of incoming edges. More...

ConstEdgeIterator	inEdgesEnd () const
	Returns end() iterator of incoming edges. More...

Size	incomingEdgesCount ()
	Returns the number of incoming edges. More...

Size	outgoingEdgesCount ()
	Returns the number of outgoing edges. More...

void	addInEdge (TOPPASEdge *edge)
	Adds an incoming edge. More...

void	addOutEdge (TOPPASEdge *edge)
	Adds an outgoing edge. More...

void	removeInEdge (TOPPASEdge *edge)
	Removes an incoming edge. More...

void	removeOutEdge (TOPPASEdge *edge)
	Removes an outgoing edge. More...

DFS_COLOR	getDFSColor ()
	Returns the DFS color of this node. More...

void	setDFSColor (DFS_COLOR color)
	Sets the DFS color of this node. More...

TOPPASVertex::SUBSTREESTATUS	getSubtreeStatus () const
	Checks if all tools in the subtree below this node are finished. More...

bool	isTopoSortMarked () const
	Returns whether the vertex has been marked already (during topological sort) More...

void	setTopoSortMarked (bool b)
	(Un)marks the vertex (during topological sort) More...

UInt	getTopoNr () const
	Returns the topological sort number. More...

virtual void	markUnreachable ()
	Marks this node (and everything further downstream) as unreachable. Overridden behavior in mergers. More...

bool	isReachable () const
	Returns whether this node is reachable. More...

bool	isFinished () const
	Returns whether this node has already been processed during the current pipeline execution. More...

bool	isRecyclingEnabled () const
	get status of recycling More...

void	setRecycling (const bool is_enabled)
	set status of recycling More...

QStringList	getFileNames (int param_index, int round) const
	gets filenames for a certain output parameter (from this vertex), for a certain TOPPAS round More...

QStringList	getFileNames () const
	get all output files for all parameters for all rounds More...

const RoundPackages &	getOutputFiles () const

bool	allInputsReady () const
	check if all upstream nodes are finished More...

reimplemented Qt events
String	name_
	The name of the tool. More...

String	type_
	The type of the tool, or "" if it does not have a type. More...

String	tmp_path_
	The temporary path. More...

Param	param_
	The parameters of the tool. More...

TOOLSTATUS	status_ {TOOL_READY}
	current status of the tool More...

bool	tool_ready_ {true}
	tool initialization status: if C'tor was successful in finding the TOPP tool, this is set to 'true' More...

bool	breakpoint_set_ {false}
	Breakpoint set? More...

void	mouseDoubleClickEvent (QGraphicsSceneMouseEvent *e) override

TOPPASScene *	getScene_ () const
	get parent Scene More...

bool	doesParamChangeInvalidate_ ()
	determines if according to current status_, a parameter change would invalidate the pipeline status (e.g., because this node was already processed) More...

bool	renameOutput_ ()
	renames SUFFICES of the output files created by the TOPP tool by inspecting file content More...

bool	initParam_ (const QString &old_ini_file="")
	Initializes the parameters with standard values (from -write_ini), uses the parameters from the old_ini_file if given, returns if parameters have changed (if old_ini_file was given) More...

QVector< IOInfo >	getParameters_ (bool input_params) const
	returns input/output file/list parameters. If `input_params` is true, input params are returned, otherwise output params. More...

void	writeParam_ (const Param &param, const QString &ini_file)
	Writes `param` to the `ini_file`. More...

QString	toolnameWithWhitespacesForFancyWordWrapping_ (QPainter *painter, const QString &str)
	Helper method for finding good boundaries for wrapping the tool name. Returns a string with whitespaces at the preferred boundaries. More...

void	smartFileNames_ (std::vector< QStringList > &filenames)

Additional Inherited Members
Protected Member Functions inherited from TOPPASVertex
void	mouseReleaseEvent (QGraphicsSceneMouseEvent *e) override

void	mousePressEvent (QGraphicsSceneMouseEvent *e) override

void	mouseDoubleClickEvent (QGraphicsSceneMouseEvent *e) override

void	mouseMoveEvent (QGraphicsSceneMouseEvent *e) override

void	contextMenuEvent (QGraphicsSceneContextMenuEvent *event) override

virtual void	moveNewEdgeTo_ (const QPointF &pos)
	Moves the target pos of the edge which is just being created to `pos`. More...

String	get3CharsNumber_ (UInt number) const
	Returns a three character string (i.e. 001 instead of 1) for the given `number`. More...

void	debugOut_ (const String &) const
	Displays the debug output `message`, if TOPPAS_DEBUG is defined. More...

Protected Attributes inherited from TOPPASVertex
EdgeContainer	in_edges_
	The list of incoming edges. More...

EdgeContainer	out_edges_
	The list of outgoing edges. More...

bool	edge_being_created_ {false}
	Indicates whether a new out edge is currently being created. More...

QColor	pen_color_ {Qt::black}
	The color of the pen. More...

QColor	brush_color_ { Qt::lightGray}
	The color of the brush. More...

DFS_COLOR	dfs_color_ {DFS_WHITE}
	The DFS color of this node. More...

bool	topo_sort_marked_ {false}
	"marked" flag for topological sort More...

UInt	topo_nr_
	The number in a topological sort of the entire graph. More...

RoundPackages	output_files_
	Stores the current output file names for each output parameter. More...

int	round_total_ {-1}
	number of rounds this node will do ('Merge All' nodes will pass everything, thus do only one round) More...

int	round_counter_ {0}
	currently finished number of rounds (TODO: do we need that?) More...

bool	finished_ {false}
	Stores whether this node has already been processed during the current pipeline execution. More...

bool	reachable_ {true}
	Indicates whether this node is reachable (i.e. there is an input node somewhere further upstream) More...

bool	allow_output_recycling_ {false}
	shall subsequent tools be allowed to recycle the output of this node to match the number of rounds imposed by other parent nodes? More...

Detailed Description

A vertex representing a TOPP tool.

Besides TOPPASScene, this class contains most of the remaining functionality of TOPPAS regarding the execution of pipelines. Once a pipeline run is started from TOPPASScene, the execution is propagated from tool to tool and the TOPP tools are actually called from here.

Member Enumeration Documentation

◆ TOOLSTATUS

enum TOOLSTATUS

current status of the vertex

Enumerator
TOOL_READY
TOOL_SCHEDULED
TOOL_RUNNING
TOOL_SUCCESS
TOOL_CRASH
TOOLSTATUS_SIZE

Constructor & Destructor Documentation

◆ TOPPASToolVertex() [1/3]

TOPPASToolVertex ( )

Default constructor.

◆ TOPPASToolVertex() [2/3]

TOPPASToolVertex	(	const String &	name,
		const String &	type = `""`
	)

Constructor.

◆ TOPPASToolVertex() [3/3]

TOPPASToolVertex ( const TOPPASToolVertex & rhs )

Copy constructor.

◆ ~TOPPASToolVertex()

~TOPPASToolVertex ( )

overridedefault

Destructor.

Member Function Documentation

◆ boundingRect()

QRectF boundingRect ( ) const

overridevirtual

Returns the bounding rectangle of this item.

Implements TOPPASVertex.

◆ clone()

virtual std::unique_ptr<TOPPASVertex> clone ( ) const

overridevirtual

Make a copy of this vertex on the heap and return a pointer to it (useful for copying nodes)

Implements TOPPASVertex.

◆ createDirs()

void createDirs ( )

Creates all necessary directories.

◆ doesParamChangeInvalidate_()

bool doesParamChangeInvalidate_ ( )

protected

determines if according to current status_, a parameter change would invalidate the pipeline status (e.g., because this node was already processed)

◆ editParam()

void editParam ( )

Lets the user edit the parameters of the tool.

◆ emitToolStarted()

virtual void emitToolStarted ( )

virtual

Called when the QProcess in the queue is called: emits 'toolStarted()'.

◆ executionFinished

void executionFinished	(	int	ec,
		QProcess::ExitStatus	es
	)

slot

Called when the execution of this tool has finished.

◆ forwardTOPPOutput

void forwardTOPPOutput ( )

slot

Called when the running TOPP tool produces output.

◆ getFullOutputDirectory()

String getFullOutputDirectory ( ) const

Returns the full directory (including preceding tmp path)

◆ getInputParameters()

QVector<IOInfo> getInputParameters ( ) const

Returns input file/list parameters together with their valid types.

◆ getName()

String getName ( ) const

overridevirtual

returns the name of the TOPP tool

Implements TOPPASVertex.

Referenced by TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), and TOPPASBase::toolStarted().

◆ getOutputDir()

String getOutputDir ( ) const

Returns the directory where this tool stores its output files.

◆ getOutputParameters()

QVector<IOInfo> getOutputParameters ( ) const

Returns output file/list/dir parameters together with their valid types.

◆ getParam()

const Param& getParam ( )

Returns the Param object of this tool.

◆ getParameters_()

QVector<IOInfo> getParameters_ ( bool input_params ) const

protected

returns input/output file/list parameters. If input_params is true, input params are returned, otherwise output params.

◆ getScene_()

TOPPASScene* getScene_ ( ) const

protected

get parent Scene

◆ getStatus()

TOOLSTATUS getStatus ( ) const

return if tool failed or is ready etc.

◆ getType()

const String& getType ( ) const

Returns the type of the tool.

Referenced by TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), and TOPPASBase::toolStarted().

◆ inEdgeHasChanged

void inEdgeHasChanged ( )

overrideslot

Called by an incoming edge when it has changed.

◆ initParam_()

bool initParam_ ( const QString & old_ini_file = "" )

protected

Initializes the parameters with standard values (from -write_ini), uses the parameters from the old_ini_file if given, returns if parameters have changed (if old_ini_file was given)

◆ invertRecylingMode()

bool invertRecylingMode ( )

overridevirtual

invert status of recycling (overriding base class)

Reimplemented from TOPPASVertex.

◆ isToolReady()

bool isToolReady ( ) const

underlying TOPP tool found and parameters fetched?! (done in C'Tor)

Referenced by TOPPASBase::insertNewVertex_().

◆ mouseDoubleClickEvent()

void mouseDoubleClickEvent ( QGraphicsSceneMouseEvent * e )

overrideprotected

◆ numIterations()

int numIterations ( )

Returns the number of iterations this tool has to perform.

◆ openContainingFolder()

void openContainingFolder ( ) const

Opens the folder where the file is contained.

◆ openInTOPPView()

void openInTOPPView ( )

Opens the files in TOPPView.

◆ operator=()

TOPPASToolVertex& operator= ( const TOPPASToolVertex & rhs )

Assignment operator.

◆ outEdgeHasChanged

void outEdgeHasChanged ( )

overrideslot

Called by an outgoing edge when it has changed.

◆ paint()

void paint	(	QPainter *	painter,
		const QStyleOptionGraphicsItem *	option,
		QWidget *	widget
	)

override

◆ refreshParameters()

bool refreshParameters ( )

Refreshes the parameters of this tool, returns if their has been a change.

◆ renameOutput_()

bool renameOutput_ ( )

protected

renames SUFFICES of the output files created by the TOPP tool by inspecting file content

◆ reset()

void reset ( bool reset_all_files = false )

overridevirtual

Resets the status

Parameters

reset_all_files Not used in this implementation, but in derived classes

Reimplemented from TOPPASVertex.

◆ run()

void run ( )

overridevirtual

Checks if all parent nodes have finished the tool execution and, if so, runs the tool.

Reimplemented from TOPPASVertex.

◆ setParam()

void setParam ( const Param & param )

Sets the Param object of this tool.

◆ setTopoNr()

void setTopoNr ( UInt nr )

overridevirtual

Sets the topological sort number (overridden in tool and output vertices)

Reimplemented from TOPPASVertex.

◆ smartFileNames_()

void smartFileNames_ ( std::vector< QStringList > & filenames )

protected

smart naming of round-based filenames when basename is not unique we take the preceding directory name

◆ toggleBreakpoint()

void toggleBreakpoint ( )

Toggle breakpoint.

◆ toolCrashed

void toolCrashed ( )

signal

Emitted when the tool crashes.

◆ toolCrashedSlot

void toolCrashedSlot ( )

slot

Called when the tool has crashed.

◆ toolFailed

void toolFailed	(	int	return_code = `-1`,
		const QString &	message = `""`
	)

signal

Emitted when the tool execution fails.

◆ toolFailedSlot

void toolFailedSlot ( )

slot

Called when the tool has failed.

◆ toolFinished

void toolFinished ( )

signal

Emitted when the tool is finished.

◆ toolFinishedSlot

void toolFinishedSlot ( )

slot

Called when the tool has finished.

◆ toolnameWithWhitespacesForFancyWordWrapping_()

QString toolnameWithWhitespacesForFancyWordWrapping_	(	QPainter *	painter,
		const QString &	str
	)

protected

Helper method for finding good boundaries for wrapping the tool name. Returns a string with whitespaces at the preferred boundaries.

◆ toolScheduledSlot

virtual void toolScheduledSlot ( )

virtualslot

Called when the tool was scheduled for running.

◆ toolStarted

void toolStarted ( )

signal

Emitted when the tool is started.

◆ toolStartedSlot

void toolStartedSlot ( )

slot

Called when the tool is started.

◆ toppOutputReady

void toppOutputReady ( const QString & out )

signal

Emitted from forwardTOPPOutput() to forward the signal outside.

◆ updateCurrentOutputFileNames()

bool updateCurrentOutputFileNames	(	const RoundPackages &	pkg,
		String &	error_message
	)

Updates the vector containing the lists of current output files for all output parameters using the input files as guidance Returns true on success, on failure the error_message is filled

◆ writeParam_()

void writeParam_	(	const Param &	param,
		const QString &	ini_file
	)

protected

Writes param to the ini_file.

Member Data Documentation

◆ breakpoint_set_

bool breakpoint_set_ {false}

protected

Breakpoint set?

◆ name_

String name_

protected

The name of the tool.

◆ param_

Param param_

protected

The parameters of the tool.

◆ status_

TOOLSTATUS status_ {TOOL_READY}

protected

current status of the tool

◆ tmp_path_

String tmp_path_

protected

The temporary path.

◆ tool_ready_

bool tool_ready_ {true}

protected

tool initialization status: if C'tor was successful in finding the TOPP tool, this is set to 'true'

◆ type_

String type_

protected

The type of the tool, or "" if it does not have a type.

Classes

Public Types

Public Slots

Signals

Public Member Functions

reimplemented Qt events

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ TOOLSTATUS

Constructor & Destructor Documentation

◆ TOPPASToolVertex() [1/3]

◆ TOPPASToolVertex() [2/3]

◆ TOPPASToolVertex() [3/3]

◆ ~TOPPASToolVertex()

Member Function Documentation

◆ boundingRect()

◆ clone()

◆ createDirs()

◆ doesParamChangeInvalidate_()

◆ editParam()

◆ emitToolStarted()

◆ executionFinished

◆ forwardTOPPOutput

◆ getFullOutputDirectory()

◆ getInputParameters()

◆ getName()

◆ getOutputDir()

◆ getOutputParameters()

◆ getParam()

◆ getParameters_()

◆ getScene_()

◆ getStatus()

◆ getType()

◆ inEdgeHasChanged

◆ initParam_()

◆ invertRecylingMode()

◆ isToolReady()

◆ mouseDoubleClickEvent()

◆ numIterations()

◆ openContainingFolder()

◆ openInTOPPView()

◆ operator=()

◆ outEdgeHasChanged

◆ paint()

◆ refreshParameters()

◆ renameOutput_()

◆ reset()

◆ run()

◆ setParam()

◆ setTopoNr()

◆ smartFileNames_()

◆ toggleBreakpoint()

◆ toolCrashed

◆ toolCrashedSlot

◆ toolFailed

◆ toolFailedSlot

◆ toolFinished

◆ toolFinishedSlot

◆ toolnameWithWhitespacesForFancyWordWrapping_()

◆ toolScheduledSlot

◆ toolStarted

◆ toolStartedSlot

◆ toppOutputReady

◆ updateCurrentOutputFileNames()

◆ writeParam_()

Member Data Documentation

◆ breakpoint_set_

◆ name_

◆ param_

◆ status_

◆ tmp_path_

◆ tool_ready_

◆ type_