A vertex representing a TOPP tool. More...

#include <OpenMS/VISUAL/TOPPASToolVertex.h>

Inheritance 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 Slots
void	executionFinished (int ec, QProcess::ExitStatus es)
	Called when the execution of this tool has finished.
void	forwardTOPPOutput ()
	Called when the running TOPP tool produces output.
void	toolStartedSlot ()
	Called when the tool is started.
void	toolFinishedSlot ()
	Called when the tool has finished.
void	toolCrashedSlot ()
	Called when the tool has crashed.
void	toolFailedSlot ()
	Called when the tool has failed.
virtual void	toolScheduledSlot ()
	Called when the tool was scheduled for running.
virtual void	inEdgeHasChanged ()
	Called by an incoming edge when it has changed.
virtual void	outEdgeHasChanged ()
	Called by an outgoing edge when it has changed.
Signals
void	toolStarted ()
	Emitted when the tool is started.
void	toolFinished ()
	Emitted when the tool is finished.
void	toolCrashed ()
	Emitted when the tool crashes.
void	toolFailed (const QString &message="")
	Emitted when the tool execution fails.
void	toppOutputReady (const QString &out)
	Emitted from forwardTOPPOutput() to forward the signal outside.
Public Member Functions
	TOPPASToolVertex ()
	Default constructor.
	TOPPASToolVertex (const String &name, const String &type="")
	Constructor.
	TOPPASToolVertex (const TOPPASToolVertex &rhs)
	Copy constructor.
virtual	~TOPPASToolVertex ()
	Destructor.
TOPPASToolVertex &	operator= (const TOPPASToolVertex &rhs)
	Assignment operator.
virtual String	getName () const
	returns the name of the TOPP tool
const String &	getType () const
	Returns the type of the tool.
void	getInputParameters (QVector< IOInfo > &input_infos)
	Fills `input_infos` with the required input file/list parameters together with their valid types.
void	getOutputParameters (QVector< IOInfo > &output_infos)
	Fills `output_infos` with the required output file/list parameters together with their valid types.
virtual void	paint (QPainter painter, const QStyleOptionGraphicsItem option, QWidget *widget)
	Paints the item.
virtual QRectF	boundingRect () const
	Returns the bounding rectangle of this item.
virtual QPainterPath	shape () const
	Returns a more precise shape.
virtual void	setTopoNr (UInt nr)
	Sets the topological sort number (overridden in tool and output vertices).
virtual void	reset (bool reset_all_files=false)
	Resets the status.
void	setParam (const Param &param)
	Sets the Param object of this tool.
const Param &	getParam ()
	Returns the Param object of this tool.
void	run ()
	Checks if all parent nodes have finished the tool execution and, if so, runs the tool.
bool	updateCurrentOutputFileNames (const RoundPackages &pkg, String &error_message)
TOOLSTATUS	getStatus () const
	return if tool failed or is ready etc.
void	editParam ()
	Lets the user edit the parameters of the tool.
int	numIterations ()
	Returns the number of iterations this tool has to perform.
String	getFullOutputDirectory () const
	Returns the full directory (including preceding tmp path).
String	getOutputDir () const
	Returns the directory where this tool stores its output files.
void	createDirs ()
	Creates all necessary directories.
void	openContainingFolder ()
	Opens the folder where the file is contained.
void	openInTOPPView ()
	Opens the files in TOPPView.
bool	refreshParameters ()
	Refreshes the parameters of this tool, returns if their has been a change.
bool	isToolReady () const
	underlying TOPP tool found and parameters fetched?! (done in C'Tor)
void	toggleBreakpoint ()
	Toggle breakpoint.
virtual void	emitToolStarted ()
	Called when the QProcess in the queue is called: emits 'toolStarted()'.
virtual bool	invertRecylingMode ()
	invert status of recycling (overriding base class)
Protected Member Functions
bool	doesParamChangeInvalidate_ ()
	determines if according to current status_, a parameter change would invalidate the pipeline status (e.g., because this node was already processed)
bool	renameOutput_ ()
	renames SUFFICES of the output files created by the TOPP tool by inspecting file content
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).
void	getParameters_ (QVector< IOInfo > &io_infos, bool input_params)
	Fills `io_infos` with the required input/output file/list parameters. If `input_params` is true, input params are returned, otherwise output params.
void	writeParam_ (const Param &param, const QString &ini_file)
	Writes `param` to the `ini_file`.
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.
void	smartFileNames_ (std::vector< QStringList > &filenames)
reimplemented Qt events

void	mouseDoubleClickEvent (QGraphicsSceneMouseEvent *e)
Protected Attributes
String	name_
	The name of the tool.
String	type_
	The type of the tool, or "" if it does not have a type.
String	tmp_path_
	The temporary path.
Param	param_
	The parameters of the tool.
TOOLSTATUS	status_
	current status of the tool
bool	tool_ready_
	tool initialization status: if C'tor was successful in finding the TOPP tool, this is set to 'true'
bool	breakpoint_set_
	Breakpoint set?
Static Protected Attributes
static UInt	uid_
	UID for output files.

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

enum TOOLSTATUS

current status of the vertex

Enumerator:

TOOL_READY
TOOL_SCHEDULED
TOOL_RUNNING
TOOL_SUCCESS
TOOL_CRASH
TOOLSTATUS_SIZE

Constructor & Destructor Documentation

TOPPASToolVertex ( )

Default constructor.

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

Constructor.

TOPPASToolVertex ( const TOPPASToolVertex & rhs )

Copy constructor.

virtual ~TOPPASToolVertex ( ) [virtual]

Destructor.

Member Function Documentation

virtual QRectF boundingRect ( ) const [virtual]

Returns the bounding rectangle of this item.

Implements TOPPASVertex.

void createDirs ( )

Creates all necessary directories.

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)

void editParam ( )

Lets the user edit the parameters of the tool.

virtual void emitToolStarted ( ) [virtual]

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

void executionFinished	(	int	ec,
		QProcess::ExitStatus	es
	)			`[slot]`

Called when the execution of this tool has finished.

void forwardTOPPOutput ( ) [slot]

Called when the running TOPP tool produces output.

String getFullOutputDirectory ( ) const

Returns the full directory (including preceding tmp path).

void getInputParameters ( QVector< IOInfo > & input_infos )

Fills input_infos with the required input file/list parameters together with their valid types.

virtual String getName ( ) const [virtual]

returns the name of the TOPP tool

Implements TOPPASVertex.

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

String getOutputDir ( ) const

Returns the directory where this tool stores its output files.

void getOutputParameters ( QVector< IOInfo > & output_infos )

Fills output_infos with the required output file/list parameters together with their valid types.

const Param& getParam ( )

Returns the Param object of this tool.

void getParameters_	(	QVector< IOInfo > &	io_infos,
		bool	input_params
	)			`[protected]`

Fills io_infos with the required input/output file/list parameters. If input_params is true, input params are returned, otherwise output params.

TOOLSTATUS getStatus ( ) const

return if tool failed or is ready etc.

const String& getType ( ) const

Returns the type of the tool.

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

virtual void inEdgeHasChanged ( ) [virtual, slot]

Called by an incoming edge when it has changed.

Reimplemented from TOPPASVertex.

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).

virtual bool invertRecylingMode ( ) [virtual]

invert status of recycling (overriding base class)

Reimplemented from TOPPASVertex.

bool isToolReady ( ) const

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

Referenced by TOPPASBase::insertNewVertex_().

void mouseDoubleClickEvent ( QGraphicsSceneMouseEvent * e ) [protected]

Reimplemented from TOPPASVertex.

int numIterations ( )

Returns the number of iterations this tool has to perform.

void openContainingFolder ( )

Opens the folder where the file is contained.

void openInTOPPView ( )

Opens the files in TOPPView.

TOPPASToolVertex& operator= ( const TOPPASToolVertex & rhs )

Assignment operator.

virtual void outEdgeHasChanged ( ) [virtual, slot]

Called by an outgoing edge when it has changed.

Reimplemented from TOPPASVertex.

virtual void paint	(	QPainter *	painter,
		const QStyleOptionGraphicsItem *	option,
		QWidget *	widget
	)			`[virtual]`

Paints the item.

Implements TOPPASVertex.

bool refreshParameters ( )

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

bool renameOutput_ ( ) [protected]

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

virtual void reset ( bool reset_all_files = false ) [virtual]

Resets the status.

Reimplemented from TOPPASVertex.

void run ( ) [virtual]

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

Reimplemented from TOPPASVertex.

void setParam ( const Param & param )

Sets the Param object of this tool.

virtual void setTopoNr ( UInt nr ) [virtual]

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

Reimplemented from TOPPASVertex.

virtual QPainterPath shape ( ) const [virtual]

Returns a more precise shape.

Implements TOPPASVertex.

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

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

void toggleBreakpoint ( )

Toggle breakpoint.

void toolCrashed ( ) [signal]

Emitted when the tool crashes.

void toolCrashedSlot ( ) [slot]

Called when the tool has crashed.

void toolFailed ( const QString & message = "" ) [signal]

Emitted when the tool execution fails.

void toolFailedSlot ( ) [slot]

Called when the tool has failed.

void toolFinished ( ) [signal]

Emitted when the tool is finished.

void toolFinishedSlot ( ) [slot]

Called when the tool has finished.

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.

virtual void toolScheduledSlot ( ) [virtual, slot]

Called when the tool was scheduled for running.

void toolStarted ( ) [signal]

Emitted when the tool is started.

void toolStartedSlot ( ) [slot]

Called when the tool is started.

void toppOutputReady ( const QString & out ) [signal]

Emitted from forwardTOPPOutput() to forward the signal outside.

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

void writeParam_	(	const Param &	param,
		const QString &	ini_file
	)			`[protected]`

Writes param to the ini_file.

Member Data Documentation

bool breakpoint_set_ [protected]

Breakpoint set?

String name_ [protected]

The name of the tool.

Param param_ [protected]

The parameters of the tool.

TOOLSTATUS status_ [protected]

current status of the tool

String tmp_path_ [protected]

The temporary path.

bool tool_ready_ [protected]

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

String type_ [protected]

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

UInt uid_ [static, protected]

UID for output files.

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:58 using doxygen 1.7.1

TOPPASToolVertex Class Reference [TOPPAS]

Classes

Public Types

Public Slots

Signals

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

TOPPASToolVertex Class Reference
[TOPPAS]