OpenMS
TOPPASToolVertex Class Reference

A vertex representing a TOPP tool. More...

#include <OpenMS/VISUAL/TOPPASToolVertex.h>

Inheritance diagram for TOPPASToolVertex:
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Collaboration diagram for TOPPASToolVertex:
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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...
 
typedef std::map< Int, VertexRoundPackageRoundPackage
 
typedef RoundPackage::const_iterator RoundPackageConstIt
 
typedef RoundPackage::iterator RoundPackageIt
 
typedef std::vector< RoundPackageRoundPackages
 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 (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...
 
TOPPASToolVertexoperator= (const TOPPASToolVertex &rhs)
 Assignment operator. More...
 
String getName () const override
 returns the name of the TOPP tool More...
 
const StringgetType () const
 Returns the type of the tool. More...
 
void getInputParameters (QVector< IOInfo > &input_infos) const
 Fills input_infos with the required input file/list parameters together with their valid types. More...
 
void getOutputParameters (QVector< IOInfo > &output_infos) const
 Fills output_infos with the required output file/list 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 ParamgetParam ()
 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...
 
TOPPASVertexoperator= (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 RoundPackagesgetOutputFiles () 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
 
TOPPASScenegetScene_ () 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...
 
void getParameters_ (QVector< IOInfo > &io_infos, bool input_params) const
 Fills io_infos with the required 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]

Default constructor.

◆ TOPPASToolVertex() [2/3]

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

Constructor.

◆ TOPPASToolVertex() [3/3]

Copy constructor.

◆ ~TOPPASToolVertex()

~TOPPASToolVertex ( )
overridedefault

Destructor.

Member Function Documentation

◆ boundingRect()

QRectF boundingRect ( ) const
overridevirtual

Returns the bounding rectangle of this item.

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()

void getInputParameters ( QVector< IOInfo > &  input_infos) const

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

◆ getName()

String getName ( ) const
overridevirtual

◆ getOutputDir()

String getOutputDir ( ) const

Returns the directory where this tool stores its output files.

◆ getOutputParameters()

void getOutputParameters ( QVector< IOInfo > &  output_infos) const

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

◆ getParam()

const Param& getParam ( )

Returns the Param object of this tool.

◆ getParameters_()

void getParameters_ ( QVector< IOInfo > &  io_infos,
bool  input_params 
) const
protected

Fills io_infos with the required 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

◆ 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_filesNot 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 ( 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.