OpenMS
TOPPASScene Class Reference

#include <OpenMS/VISUAL/TOPPASScene.h>

Inheritance diagram for TOPPASScene:
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Collaboration diagram for TOPPASScene:
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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 StringgetSaveFileName ()
 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...
 
TOPPASEdgegetHoveringEdge ()
 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...
 
TOPPASEdgehover_edge_
 The hovering edge which is currently being created. More...
 
TOPPASVertexpotential_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< TOPPProcesstopp_processes_queue_
 The queue of pending TOPP processes. More...
 
TOPPASSceneclipboard_
 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...
 
TOPPASToolVertexresume_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...
 
TOPPASVertexgetVertexAt_ (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

@brief 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.

@ingroup TOPPAS_elements

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

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)

◆ connectEdgeSignals()

void connectEdgeSignals ( TOPPASEdge e)

Connects the signals to slots.

◆ connectMergerVertexSignals()

void connectMergerVertexSignals ( TOPPASMergerVertex tmv)

Connects the signals to slots.

◆ connectOutputVertexSignals()

void connectOutputVertexSignals ( TOPPASOutputFileListVertex oflv)

Connects the signals to slots.

Referenced by TOPPASBase::insertNewVertex_().

◆ connectToolVertexSignals()

void connectToolVertexSignals ( TOPPASToolVertex ttv)

Connects the signals to slots.

Referenced by TOPPASBase::insertNewVertex_().

◆ connectVertexSignals()

void connectVertexSignals ( TOPPASVertex tv)

Connects the signals to slots.

Referenced by TOPPASBase::insertNewVertex_().

◆ contextMenuEvent()

void contextMenuEvent ( QGraphicsSceneContextMenuEvent *  event)
overrideprotected

◆ copySelected()

void copySelected ( )

Copies all currently selected edges and vertices.

◆ createResources()

void createResources ( TOPPASResources resources)

Create resources from the current workflow.

Referenced by TOPPASBase::savePipelineResourceFile().

◆ dfsVisit_()

bool dfsVisit_ ( TOPPASVertex vertex)
protected

DFS helper method. Returns true, if a back edge has been discovered.

◆ dryRunFinished

void dryRunFinished ( int  ,
QProcess::ExitStatus   
)
signal

Emitted when in dry run mode and asked to run a TOPP tool (to fake success)

◆ edgesBegin()

EdgeIterator edgesBegin ( )

Returns begin() iterator of all edges.

◆ edgesEnd()

EdgeIterator edgesEnd ( )

Returns end() iterator of all edges.

◆ enqueueProcess()

void enqueueProcess ( const TOPPProcess process)

Enqueues the process, it will be run when the currently pending processes have finished.

◆ entirePipelineFinished

void entirePipelineFinished ( )
signal

Emitted when the entire pipeline execution is finished.

◆ finishHoveringEdge

void finishHoveringEdge ( )
slot

Called when the new edge is being "released".

◆ getActionMode()

ActionMode getActionMode ( )

Returns the action mode.

◆ getDescription()

QString getDescription ( ) const

workflow description (to be displayed in TOPPAS window)

Referenced by TOPPASBase::focusByTab(), and TOPPASBase::showAsWindow_().

◆ getHoveringEdge()

TOPPASEdge* getHoveringEdge ( )

returns the hovering edge

◆ getOutDir()

const QString& getOutDir ( ) const

Returns the name of the directory for output files.

◆ getSaveFileName()

const String& getSaveFileName ( )

Returns the file name.

Referenced by TOPPASBase::savePipeline().

◆ getTempDir()

const QString& getTempDir ( ) const

Returns the name of the directory for temporary files.

◆ getVertexAt_()

TOPPASVertex* getVertexAt_ ( const QPointF &  pos)
protected

Returns the vertex in the foreground at position pos , if existent, otherwise 0.

◆ include()

void include ( TOPPASScene new_scene,
QPointF  pos = QPointF() 
)

Includes the pipeline scene.

Referenced by TOPPASBase::addTOPPASFile().

◆ isDryRun()

bool isDryRun ( ) const

determine dry run status (are tools actually called?)

◆ isEdgeAllowed_()

bool isEdgeAllowed_ ( TOPPASVertex u,
TOPPASVertex v 
)
protected

Returns whether an edge between node u and v would be allowed.

◆ isGUIMode()

bool isGUIMode ( ) const

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

◆ isPipelineRunning()

bool isPipelineRunning ( ) const

Returns if a pipeline is currently running.

Referenced by TOPPASBase::updateMenu().

◆ itemClicked

void itemClicked ( )
slot

Called when an item is clicked.

◆ itemReleased

void itemReleased ( )
slot

Called when an item is released.

◆ load()

void load ( const String file)

Loads the pipeline from file.

Referenced by TOPPASBase::addTOPPASFile().

◆ loadResources()

void loadResources ( const TOPPASResources resources)

Loads the resources into the input nodes of this workflow.

Referenced by TOPPASBase::loadPipelineResourceFile().

◆ logOutputFileWritten

void logOutputFileWritten ( const String file)
slot

Writes the "output file written" message to the logfile (and to stdout if no gui available)

◆ logToolCrashed

void logToolCrashed ( )
slot

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

◆ logToolFailed

void logToolFailed ( )
slot

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

◆ logToolFinished

void logToolFinished ( )
slot

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

◆ logToolStarted

void logToolStarted ( )
slot

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

◆ logTOPPOutput

void logTOPPOutput ( const QString &  out)
slot

Writes the TOPP tool output to the logfile (and to stdout if no gui available)

◆ mainWindowNeedsUpdate

void mainWindowNeedsUpdate ( )
signal

Emitted when the main window needs to be updated.

◆ messageReady

void messageReady ( const QString &  msg)
signal

Emitted when there is an important message that needs to be printed in TOPPAS.

◆ moveSelectedItems

void moveSelectedItems ( qreal  dx,
qreal  dy 
)
slot

Moves all selected items by dx, dy.

◆ openInTOPPView

void openInTOPPView ( QStringList  all_files)
signal

Emitted when files are triggered for opening in TOPPView.

◆ paste()

void paste ( QPointF  pos = QPointF())

Pastes the copied items.

◆ pipelineErrorSlot

void pipelineErrorSlot ( const QString &  msg = "")
slot

Called by vertices at which an error occurred during pipeline execution.

◆ pipelineExecutionFailed

void pipelineExecutionFailed ( )
signal

Emitted when the pipeline execution has failed.

◆ processFinished

void processFinished ( )
slot

Called by a finished QProcess to indicate that we are free to start a new one.

◆ quitWithError

void quitWithError ( )
slot

dirty solution: when using ExecutePipeline this slot is called when the pipeline crashes. This will quit the app

◆ refreshParameters()

RefreshStatus refreshParameters ( )

Refreshes the parameters of the TOPP tools in this workflow.

Referenced by TOPPASBase::refreshPipelineParameters().

◆ removeSelected()

void removeSelected ( )

Removes all currently selected edges and vertices.

◆ requestClipboardContent

void requestClipboardContent ( )
signal

Requests the clipboard content from TOPPASBase, will be stored in clipboard_.

◆ resetDownstream()

void resetDownstream ( TOPPASVertex vertex)

Called when user fires "Resume" action, to clear downstream nodes from previous results.

◆ resetProcessesQueue()

void resetProcessesQueue ( )

Resets the processes queue.

◆ runNextProcess()

void runNextProcess ( )

Runs the next process in the queue, if any.

◆ runPipeline()

void runPipeline ( )

Runs the pipeline.

Referenced by TOPPASBase::keyPressEvent(), and TOPPASBase::runPipeline().

◆ sanityCheck_()

bool sanityCheck_ ( bool  allowUserOverride)
protected

Performs a sanity check of the pipeline and notifies user when it finds something strange. Returns if pipeline OK. if 'allowUserOverride' is true, some dialogs are shown which allow the user to ignore some warnings (e.g. disconnected nodes)

◆ saveIfChanged()

bool saveIfChanged ( )

Saves the pipeline if it has been changed since the last save.

Referenced by TOPPASBase::closeEvent().

◆ saveMe

void saveMe ( )
signal

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

◆ selectionCopied

void selectionCopied ( TOPPASScene ts)
signal

Emitted when a selection is copied to the clipboard.

◆ setActionMode()

void setActionMode ( ActionMode  mode)

Sets the action mode.

◆ setAllowedThreads()

void setAllowedThreads ( int  num_threads)

sets the maximum number of jobs

◆ setChanged()

void setChanged ( bool  b)

◆ setClipboard()

void setClipboard ( TOPPASScene clipboard)

Sets the clipboard content.

Referenced by TOPPASBase::sendClipboardContent().

◆ setDescription()

void setDescription ( const QString &  desc)

when description is updated by user, use this to update the description for later storage in file

Referenced by TOPPASBase::descriptionUpdated_(), and TOPPASBase::exportAsImage().

◆ setOutDir()

void setOutDir ( const QString &  dir)

Sets the name of the directory for output files.

◆ setPipelineRunning

void setPipelineRunning ( bool  b = true)
slot

Sets if the running_ flag to true, or false If set to false, the application emits an 'alert' sign, demanding user attention (to let him know it finished)

◆ setSaveFileName()

void setSaveFileName ( const String name)

Sets the file name.

◆ snapToGrid

void snapToGrid ( )
slot

Makes all vertices snap to the grid.

◆ store()

bool store ( const String file)

Stores the pipeline to file, returns true on success.

Referenced by TOPPASBase::savePipeline(), and TOPPASBase::savePipelineAs().

◆ terminateCurrentPipeline

void terminateCurrentPipeline ( )
signal

Kills all connected TOPP processes.

◆ topoSort()

void topoSort ( bool  resort_all = true)

Performs a topological sort of all vertices.

Referenced by TOPPASBase::insertNewVertex_().

◆ unselectAll()

void unselectAll ( )

Unselects all items.

◆ updateEdgeColors()

void updateEdgeColors ( )

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

Referenced by TOPPASBase::refreshPipelineParameters().

◆ updateHoveringEdgePos

void updateHoveringEdgePos ( const QPointF &  new_pos)
slot

Called when the position of the hovering edge changes.

◆ verticesBegin()

VertexIterator verticesBegin ( )

Returns begin() iterator of all vertices.

Referenced by TOPPASBase::addTOPPASFile().

◆ verticesEnd()

VertexIterator verticesEnd ( )

Returns end() iterator of all vertices.

Referenced by TOPPASBase::addTOPPASFile().

◆ wasChanged()

bool wasChanged ( ) const

Returns whether the workflow has been changed since the latest "save".

Referenced by TOPPASBase::addTOPPASFile(), and TOPPASBase::updateMenu().

◆ writeToLogFile_()

void writeToLogFile_ ( const QString &  text)
protected

Writes the text to the logfile.

Member Data Documentation

◆ action_mode_

ActionMode action_mode_
protected

The current action mode.

◆ allowed_threads_

int allowed_threads_
protected

maximum number of allowed threads

◆ changed_

bool changed_
protected

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

◆ clipboard_

TOPPASScene* clipboard_
protected

Stores the clipboard content when requested from TOPPASBase.

◆ description_text_

QString description_text_
protected

description text

◆ dry_run_

bool dry_run_
protected

dry run mode (no tools are actually called)

◆ edges_

EdgeContainer edges_
protected

The list of all edges.

◆ error_occured_

bool error_occured_
protected

true if an error occurred during pipeline execution

◆ file_name_

String file_name_
protected

The file name of this pipeline.

◆ gui_

bool gui_
protected

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

◆ hover_edge_

TOPPASEdge* hover_edge_
protected

The hovering edge which is currently being created.

◆ out_dir_

QString out_dir_
protected

The directory where the output files will be written.

◆ potential_target_

TOPPASVertex* potential_target_
protected

The current potential target vertex of the hovering edge.

◆ resume_source_

TOPPASToolVertex* resume_source_
protected

last node where 'resume' was started

◆ running_

bool running_
protected

Indicates if a pipeline is currently running.

◆ threads_active_

int threads_active_
protected

currently running processes...

◆ tmp_path_

QString tmp_path_
protected

The path for temporary files.

◆ topp_processes_queue_

QList<TOPPProcess> topp_processes_queue_
protected

The queue of pending TOPP processes.

◆ user_specified_out_dir_

bool user_specified_out_dir_
protected

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

◆ vertices_

VertexContainer vertices_
protected

The list of all vertices.