The base class of the different vertex classes. More...

#include <OpenMS/VISUAL/TOPPASVertex.h>

Inheritance diagram for TOPPASVertex:

Collaboration diagram for TOPPASVertex:

Classes
class	TOPPASFilenames

struct	VertexRoundPackage
	Info for one edge and round, to be passed to next node. More...

Public Types
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
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	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
	TOPPASVertex ()
	Default Constructor. More...

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

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

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

virtual std::unique_ptr< TOPPASVertex >	clone () const =0
	Make a copy of this vertex on the heap and return a pointer to it (useful for copying nodes) 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...

QRectF	boundingRect () const override=0
	Returns the bounding rectangle of this item. 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	setTopoNr (UInt nr)
	Sets the topological sort number (overridden in tool and output vertices) More...

virtual void	reset (bool reset_all_files=false)

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...

virtual void	run ()

virtual bool	invertRecylingMode ()
	invert status of recycling More...

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

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

virtual String	getName () const =0

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...

Protected Member Functions
reimplemented Qt events
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
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

The base class of the different vertex classes.

This class contains the common functionality (such as event handling for mouse clicks and drags) and holds the common members of all different kinds of vertices (e.g., containers for all in and out edges, the vertex ID, the number of a topological sort of the whole graph, etc.)

Class Documentation

◆ OpenMS::TOPPASVertex::VertexRoundPackage

struct OpenMS::TOPPASVertex::VertexRoundPackage

Info for one edge and round, to be passed to next node.

Collaboration diagram for TOPPASVertex::VertexRoundPackage:

[legend]

Class Members
TOPPASEdge *	edge	edge that connects the upstream node to the current one
TOPPASFilenames	filenames	filenames passed from upstream node in this round

Member Typedef Documentation

◆ ConstEdgeIterator

typedef EdgeContainer::const_iterator ConstEdgeIterator

A const iterator for in/out edges.

◆ EdgeContainer

typedef QList<TOPPASEdge *> EdgeContainer

The container for in/out edges.

◆ EdgeIterator

typedef EdgeContainer::iterator EdgeIterator

A mutable iterator for in/out edges.

◆ RoundPackage

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

all infos to process one round for a vertex (from all incoming vertices) indexing via "parameter_index" of adjacent edge (could later be param_name) -> filenames Index for input and output edges is (-1) implicitly, thus we need signed type warning: the index refers to either input OR output (depending on if this structure is used for input files storage or output files storage)

◆ RoundPackageConstIt

using RoundPackageConstIt = RoundPackage::const_iterator

◆ RoundPackageIt

using RoundPackageIt = RoundPackage::iterator

◆ RoundPackages

using RoundPackages = std::vector<RoundPackage>

all information a node needs to process all rounds

Member Enumeration Documentation

◆ DFS_COLOR

enum DFS_COLOR

The color of a vertex during depth-first search.

Enumerator
DFS_WHITE
DFS_GRAY
DFS_BLACK

◆ SUBSTREESTATUS

enum SUBSTREESTATUS

The color of a vertex during depth-first search.

Enumerator
TV_ALLFINISHED	all downstream nodes are done (including the ones which are feed by a parallel subtree)
TV_UNFINISHED	some direct downstream node is not done
TV_UNFINISHED_INBRANCH	a parallel subtree which merged with some downstream node A was not done (which prevented processing of the node A)

Constructor & Destructor Documentation

◆ TOPPASVertex() [1/2]

TOPPASVertex ( )

Default Constructor.

◆ TOPPASVertex() [2/2]

TOPPASVertex ( const TOPPASVertex & rhs )

Copy constructor.

◆ ~TOPPASVertex()

~TOPPASVertex ( )

overridedefault

Destructor.

Member Function Documentation

◆ addInEdge()

void addInEdge ( TOPPASEdge * edge )

Adds an incoming edge.

◆ addOutEdge()

void addOutEdge ( TOPPASEdge * edge )

Adds an outgoing edge.

◆ allInputsReady()

bool allInputsReady ( ) const

check if all upstream nodes are finished

◆ boundingRect()

QRectF boundingRect ( ) const

overridepure virtual

Returns the bounding rectangle of this item.

Implemented in TOPPASToolVertex, TOPPASSplitterVertex, TOPPASOutputFolderVertex, TOPPASOutputFileListVertex, TOPPASMergerVertex, and TOPPASInputFileListVertex.

◆ buildRoundPackages()

bool buildRoundPackages	(	RoundPackages &	pkg,
		String &	error_msg
	)

get the round package for this node from upstream – indices in 'RoundPackage' mapping are thus referring to incoming edges of this node returns false on failure

◆ clicked

void clicked ( )

signal

Emitted when this item is clicked.

◆ clone()

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

pure virtual

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

Implemented in TOPPASToolVertex, TOPPASSplitterVertex, TOPPASOutputFolderVertex, TOPPASOutputFileListVertex, TOPPASMergerVertex, and TOPPASInputFileListVertex.

◆ contextMenuEvent()

void contextMenuEvent ( QGraphicsSceneContextMenuEvent * event )

overrideprotected

◆ debugOut_()

void debugOut_ ( const String & ) const

inlineprotected

Displays the debug output message, if TOPPAS_DEBUG is defined.

◆ finishHoveringEdge

void finishHoveringEdge ( )

signal

Emitted when the mouse is released after having dragged a new edge somewhere.

◆ get3CharsNumber_()

String get3CharsNumber_ ( UInt number ) const

protected

Returns a three character string (i.e. 001 instead of 1) for the given number.

◆ getDFSColor()

DFS_COLOR getDFSColor ( )

Returns the DFS color of this node.

◆ getFileNames() [1/2]

QStringList getFileNames ( ) const

get all output files for all parameters for all rounds

◆ getFileNames() [2/2]

QStringList getFileNames	(	int	param_index,
		int	round
	)		const

gets filenames for a certain output parameter (from this vertex), for a certain TOPPAS round

◆ getName()

virtual String getName ( ) const

pure virtual

Implemented in TOPPASToolVertex, TOPPASSplitterVertex, TOPPASOutputFolderVertex, TOPPASOutputFileListVertex, TOPPASMergerVertex, and TOPPASInputFileListVertex.

◆ getOutputFiles()

const RoundPackages& getOutputFiles ( ) const

◆ getSubtreeStatus()

TOPPASVertex::SUBSTREESTATUS getSubtreeStatus ( ) const

Checks if all tools in the subtree below this node are finished.

◆ getTopoNr()

UInt getTopoNr ( ) const

Returns the topological sort number.

Referenced by TOPPASBase::toolStarted().

◆ hoveringEdgePosChanged

void hoveringEdgePosChanged ( const QPointF & new_pos )

signal

Emitted when the position of the hovering edge changes.

◆ incomingEdgesCount()

Size incomingEdgesCount ( )

Returns the number of incoming edges.

◆ inEdgeHasChanged

virtual void inEdgeHasChanged ( )

virtualslot

Called by an incoming edge when it has changed.

◆ inEdgesBegin()

ConstEdgeIterator inEdgesBegin ( ) const

Returns begin() iterator of incoming edges.

◆ inEdgesEnd()

ConstEdgeIterator inEdgesEnd ( ) const

Returns end() iterator of incoming edges.

◆ invertRecylingMode()

virtual bool invertRecylingMode ( )

virtual

invert status of recycling

Reimplemented in TOPPASToolVertex.

◆ isFinished()

bool isFinished ( ) const

Returns whether this node has already been processed during the current pipeline execution.

◆ isReachable()

bool isReachable ( ) const

Returns whether this node is reachable.

◆ isRecyclingEnabled()

bool isRecyclingEnabled ( ) const

get status of recycling

◆ isTopoSortMarked()

bool isTopoSortMarked ( ) const

Returns whether the vertex has been marked already (during topological sort)

◆ isUpstreamFinished()

bool isUpstreamFinished ( ) const

check if all upstream nodes are ready to go ( 'finished_' is true)

◆ itemDragged

void itemDragged	(	qreal	dx,
		qreal	dy
	)

signal

Emitted when the item is dragged.

◆ markUnreachable()

virtual void markUnreachable ( )

virtual

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

Reimplemented in TOPPASSplitterVertex, and TOPPASMergerVertex.

◆ mouseDoubleClickEvent()

void mouseDoubleClickEvent ( QGraphicsSceneMouseEvent * e )

overrideprotected

◆ mouseMoveEvent()

void mouseMoveEvent ( QGraphicsSceneMouseEvent * e )

overrideprotected

◆ mousePressEvent()

void mousePressEvent ( QGraphicsSceneMouseEvent * e )

overrideprotected

◆ mouseReleaseEvent()

void mouseReleaseEvent ( QGraphicsSceneMouseEvent * e )

overrideprotected

◆ moveNewEdgeTo_()

virtual void moveNewEdgeTo_ ( const QPointF & pos )

protectedvirtual

Moves the target pos of the edge which is just being created to pos.

◆ newHoveringEdge

void newHoveringEdge ( const QPointF & pos )

signal

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

◆ operator=()

TOPPASVertex& operator= ( const TOPPASVertex & rhs )

Assignment operator.

◆ outEdgeHasChanged

virtual void outEdgeHasChanged ( )

virtualslot

Called by an outgoing edge when it has changed.

◆ outEdgesBegin()

ConstEdgeIterator outEdgesBegin ( ) const

Returns begin() iterator of outgoing edges.

◆ outEdgesEnd()

ConstEdgeIterator outEdgesEnd ( ) const

Returns end() iterator of outgoing edges.

◆ outgoingEdgesCount()

Size outgoingEdgesCount ( )

Returns the number of outgoing edges.

◆ paint()

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

◆ parameterChanged

void parameterChanged ( const bool invalidates_running_pipeline )

signal

Emitted if an INI parameter or recycling mode or whatever was edited by the user - depending on the current state of the tool an action is taken each node type decides itself if this will invalidate the pipeline, depending on its internal status

◆ released

void released ( )

signal

Emitted when this item is released.

◆ removeInEdge()

void removeInEdge ( TOPPASEdge * edge )

Removes an incoming edge.

◆ removeOutEdge()

void removeOutEdge ( TOPPASEdge * edge )

Removes an outgoing edge.

◆ reset()

virtual void reset ( bool reset_all_files = false )

virtual

Resets the status

Parameters

reset_all_files Not used in this implementation, but in derived classes

Reimplemented in TOPPASToolVertex, and TOPPASOutputVertex.

◆ run()

virtual void run ( )

virtual

run the tool (either ToolVertex, Merger, or OutputNode)

Exceptions

NotImplemented

Reimplemented in TOPPASToolVertex, TOPPASSplitterVertex, TOPPASOutputFolderVertex, TOPPASOutputFileListVertex, TOPPASMergerVertex, and TOPPASInputFileListVertex.

◆ setDFSColor()

void setDFSColor ( DFS_COLOR color )

Sets the DFS color of this node.

◆ setRecycling()

void setRecycling ( const bool is_enabled )

set status of recycling

◆ setTopoNr()

virtual void setTopoNr ( UInt nr )

virtual

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

Reimplemented in TOPPASToolVertex, and TOPPASOutputVertex.

◆ setTopoSortMarked()

void setTopoSortMarked ( bool b )

(Un)marks the vertex (during topological sort)

◆ shape()

QPainterPath shape ( ) const

final

Returns a more precise shape.

◆ somethingHasChanged

void somethingHasChanged ( )

signal

Emitted when something has changed.

Member Data Documentation

◆ allow_output_recycling_

bool allow_output_recycling_ {false}

protected

shall subsequent tools be allowed to recycle the output of this node to match the number of rounds imposed by other parent nodes?

◆ brush_color_

QColor brush_color_ { Qt::lightGray}

protected

The color of the brush.

◆ dfs_color_

DFS_COLOR dfs_color_ {DFS_WHITE}

protected

The DFS color of this node.

◆ edge_being_created_

bool edge_being_created_ {false}

protected

Indicates whether a new out edge is currently being created.

◆ finished_

bool finished_ {false}

protected

Stores whether this node has already been processed during the current pipeline execution.

◆ in_edges_

EdgeContainer in_edges_

protected

The list of incoming edges.

◆ out_edges_

EdgeContainer out_edges_

protected

The list of outgoing edges.

◆ output_files_

RoundPackages output_files_

protected

Stores the current output file names for each output parameter.

◆ pen_color_

QColor pen_color_ {Qt::black}

protected

The color of the pen.

◆ reachable_

bool reachable_ {true}

protected

Indicates whether this node is reachable (i.e. there is an input node somewhere further upstream)

◆ round_counter_

int round_counter_ {0}

protected

currently finished number of rounds (TODO: do we need that?)

◆ round_total_

int round_total_ {-1}

protected

number of rounds this node will do ('Merge All' nodes will pass everything, thus do only one round)

◆ topo_nr_

UInt topo_nr_

protected

The number in a topological sort of the entire graph.

◆ topo_sort_marked_

bool topo_sort_marked_ {false}

protected

"marked" flag for topological sort

Classes

Public Types

Public Slots

Signals

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Class Documentation

◆ OpenMS::TOPPASVertex::VertexRoundPackage

Member Typedef Documentation

◆ ConstEdgeIterator

◆ EdgeContainer

◆ EdgeIterator

◆ RoundPackage

◆ RoundPackageConstIt

◆ RoundPackageIt

◆ RoundPackages

Member Enumeration Documentation

◆ DFS_COLOR

◆ SUBSTREESTATUS

Constructor & Destructor Documentation

◆ TOPPASVertex() [1/2]

◆ TOPPASVertex() [2/2]

◆ ~TOPPASVertex()

Member Function Documentation

◆ addInEdge()

◆ addOutEdge()

◆ allInputsReady()

◆ boundingRect()

◆ buildRoundPackages()

◆ clicked

◆ clone()

◆ contextMenuEvent()

◆ debugOut_()

◆ finishHoveringEdge

◆ get3CharsNumber_()

◆ getDFSColor()

◆ getFileNames() [1/2]

◆ getFileNames() [2/2]

◆ getName()

◆ getOutputFiles()

◆ getSubtreeStatus()

◆ getTopoNr()

◆ hoveringEdgePosChanged

◆ incomingEdgesCount()

◆ inEdgeHasChanged

◆ inEdgesBegin()

◆ inEdgesEnd()

◆ invertRecylingMode()

◆ isFinished()

◆ isReachable()

◆ isRecyclingEnabled()

◆ isTopoSortMarked()

◆ isUpstreamFinished()

◆ itemDragged

◆ markUnreachable()

◆ mouseDoubleClickEvent()

◆ mouseMoveEvent()

◆ mousePressEvent()

◆ mouseReleaseEvent()

◆ moveNewEdgeTo_()

◆ newHoveringEdge

◆ operator=()

◆ outEdgeHasChanged

◆ outEdgesBegin()

◆ outEdgesEnd()

◆ outgoingEdgesCount()

◆ paint()

◆ parameterChanged

◆ released

◆ removeInEdge()

◆ removeOutEdge()

◆ reset()

◆ run()

◆ setDFSColor()

◆ setRecycling()

◆ setTopoNr()

◆ setTopoSortMarked()

◆ shape()