| OpenMS 2.5.0

Public Slots | Public Member Functions | Static Public Attributes | Protected Types | Protected Slots | Protected Member Functions | Protected Attributes | Static Protected Attributes | List of all members
TOPPASBase Class Reference
Visual » TOPPAS

Main window of the TOPPAS tool. More...

`#include <OpenMS/VISUAL/APPLICATIONS/TOPPASBase.h>`

Inheritance diagram for TOPPASBase:

## Public Slots

void | addTOPPASFile (const String &file_name, bool in_new_window=true)
| opens the file in a new window More...
void | openFileDialog ()
| shows the dialog for opening files More...
void | openExampleDialog ()
| shows the dialog for opening example files More...
void | newPipeline (const int id=-1)
| shows the dialog for creating a new file (pass IDINITIALUNTITLED as `id` if its the first call) More...
void | includePipeline ()
| shows the dialog for including another workflow in the currently opened one More...
void | saveCurrentPipelineAs ()
| shows the dialog for saving the current file and updates the current tab caption More...
void | savePipeline ()
| saves the pipeline (determined by Qt's sender mechanism) More...
void | exportAsImage ()
| exports the current pipeline as image More...
void | loadPipelineResourceFile ()
| shows a file dialog for selecting the resource file to load More...
void | savePipelineResourceFile ()
| shows a file dialog for selecting the resource file to write to More...
void | openOnlinePipelineRepository ()
| opens the OpenMS Homepage to download example workflows More...
void | preferencesDialog ()
| shows the preferences dialog More...
void | updateCurrentPath ()
| changes the current path according to the currently active window/layer More...
void | updateTabBar (QMdiSubWindow *w)
| brings the tab corresponding to the active window in front More...
void | showAboutDialog ()
| Shows the 'About' dialog. More...
void | showURL ()
| shows the URL stored in the data of the sender QAction More...
void | showStatusMessage (std::string msg, OpenMS::UInt time)
| Shows a status message in the status bar. More...
void | showCursorStatus (double x, double y)
| shows x,y coordinates in the status bar More...
void | closeFile ()
| closes the active window More...
void | updateToolBar ()
| updates the toolbar More...
void | runPipeline ()
| Runs the pipeline of the current window. More...
void | abortPipeline ()
| Terminates the current pipeline. More...
void | toolStarted ()
| Called when a tool is started. More...
void | toolFinished ()
| Called when a tool is finished. More...
void | toolCrashed ()
| Called when a tool crashes. More...
void | toolFailed ()
| Called when a tool execution fails. More...
void | outputVertexFinished (const String &file)
| Called when a file was successfully written to an output vertex. More...
void | updateTOPPOutputLog (const QString &out)
| Called when a TOPP tool produces (error) output. More...
void | showPipelineFinishedLogMessage ()
| Called by the scene if the pipeline execution finishes successfully. More...
void | saveToClipboard (TOPPASScene *scene)
| Saves `scene` to the clipboard. More...
void | sendClipboardContent ()
| Sends the clipboard content to the sender of the connected signal. More...
void | refreshParameters ()
| Refreshes the parameters of the TOPP tools of the current workflow and stores an updated workflow including the current parameters. More...
void | openFilesInTOPPView (QStringList all_files)
| Open files in a new TOPPView instance. More...
void | openToppasFile (QString filename)
| Opens a toppas file. More...

## Public Member Functions

| TOPPASBase (QWidget *parent=nullptr)
| Constructor. More...
| ~TOPPASBase () override
| Destructor. More...
void | loadPreferences (String filename="")
| Loads the preferences from the filename given. More...
void | savePreferences ()
| stores the preferences (used when this window is closed) More...
void | loadFiles (const StringList &list, QSplashScreen *splash_screen)
| loads the files and updates the splash screen More...
Public Member Functions inherited from DefaultParamHandler
| DefaultParamHandler (const String &name)
| Constructor with name that is displayed in error messages. More...
| DefaultParamHandler (const DefaultParamHandler &rhs)
| Copy constructor. More...
virtual | ~DefaultParamHandler ()
| Destructor. More...
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs)
| Assignment operator. More...
virtual bool | operator== (const DefaultParamHandler &rhs) const
| Equality operator. More...
void | setParameters (const Param &param)
| Sets the parameters. More...
const Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () const
| Non-mutable access to the name. More...
void | setName (const String &name)
| Mutable access to the name. More...
const std::vector< String > & | getSubsections () const
| Non-mutable access to the registered subsections. More...

## Static Public Member Functions

common functions used in TOPPAS and TOPPView
static TOPPASTreeView * | createTOPPToolsTreeWidget (QWidget *parent_widget=nullptr)
| Creates and fills a tree widget with all available tools. More...
static QString | savePipelineAs (TOPPASWidget *w, QString current_path)
static QString | loadPipelineResourceFile (TOPPASWidget *w, QString current_path)
| Loads and sets the resources of the TOPPASWidget. More...
static QString | savePipelineResourceFile (TOPPASWidget *w, QString current_path)
| Saves the resources of the TOPPASWidget. More...
static QString | refreshPipelineParameters (TOPPASWidget *tw, QString current_path)
| Refreshes the TOPP tools parameters of the pipeline. More...

## Static Public Attributes

static int const | IDINITIALUNTITLED = 1000
| use this for the first call to newPipeline(), to ensure that the first empty (and unmodified) workspace is closed iff existing workflows are loaded More...

## Protected Types

enum | LogState { LS_NOTICE, LS_WARNING, LS_ERROR }
| Log message states. More...

## Protected Slots

void | updateMenu ()
| enable/disable menu entries depending on the current state More...
void | showAsWindow_ (TOPPASWidget *sw, const String &caption, const int special_id=-1)
| Shows the widget as window in the workspace (the special_id is only used for the first untitled widget (to be able to auto-close it later) More...
void | insertNewVertex_ (double x, double y, QTreeWidgetItem *item=nullptr)
| Inserts a new TOPP tool in the current window at (x,y) More...
void | insertNewVertexInCenter_ (QTreeWidgetItem *item)
| Inserts the `item` in the middle of the current window. More...
void | downloadTOPPASfromHomepage_ (const QUrl &url)
| triggered when user clicks a link - if it ends in .TOPPAS we're done More...
void | toppasFileDownloaded_ (QNetworkReply *r)
| triggered when download of .toppas file is finished, so we can store & open it More...
void | TOPPASreadyRead ()
| debug... More...
void | descriptionUpdated_ ()
| user edited the workflow description More...
Tab bar slots
void | closeByTab (int id)
| Closes the window corresponding to the data of the tab with identifier `id`. More...
void | focusByTab (int id)
| Raises the window corresponding to the data of the tab with identifier `id`. More...

## Protected Member Functions

TOPPASWidget * | window_ (int id) const
| returns the window with id `id` More...
TOPPASWidget * | activeSubWindow_ () const
| returns a pointer to the active TOPPASWidget (0 if none is active) More...
void | showLogMessage_ (LogState state, const String &heading, const String &body)
| Shows a log message in the log_ window. More...
reimplemented Qt events
void | closeEvent (QCloseEvent *event) override
void | keyPressEvent (QKeyEvent *e) override
Protected Member Functions inherited from DefaultParamHandler
virtual void | updateMembers_ ()
| This method is used to update extra member variables at the end of the setParameters() method. More...
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

TOPPASLogWindow * | log_
| Log output window. More...
QTextEdit * | desc_
| Workflow Description window. More...
QMdiArea * | ws_
| Main workspace. More...
QWebView * | webview_
| OpenMS homepage workflow browser. More...
QNetworkAccessManager * | network_manager_
| download .toppas files from homepage More...
QNetworkReply * | network_reply_
| the content of the network request More...
TOPPASTabBar * | tab_bar_
| Tab bar. The address of the corresponding window to a tab is stored as an int in tabData() More...
QTreeWidget * | tools_tree_view_
| Tree view of all available TOPP tools. More...
QListWidget * | blocks_list_
| List of ready analysis pipelines. More...
String | current_path_
String | tmp_path_
| The path for temporary files. More...
TOPPASScene * | clipboard_scene_
| The clipboard. More...
Toolbar
QToolBar * | tool_bar_
Status bar
QLabel * | message_label_
| Label for messages in the status bar. More...
Protected Attributes inherited from DefaultParamHandler
Param | param_
| Container for current parameters. More...
Param | defaults_
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
std::vector< String > | subsections_
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
String | error_name_
| Name that is displayed in error messages during the parameter checking. More...
bool | check_defaults_
| If this member is set to false no checking if parameters in done;. More...
bool | warn_empty_defaults_
| If this member is set to false no warning is emitted when defaults are empty;. More...

## Static Protected Attributes

static int | node_offset_ = 0
| Offset counter for new inserted nodes (to avoid invisible stacking) More...
static qreal | z_value_ = 42.0
| z-value counter for new inserted nodes (new nodes should be on top) More...

## Detailed Description

Main window of the TOPPAS tool.

## Member Enumeration Documentation

## ◆ LogState

enum LogState

protected

Log message states.

Enumerator
LS_NOTICE | Notice.
LS_WARNING | Warning.
LS_ERROR | Fatal error.

## Constructor & Destructor Documentation

## ◆ TOPPASBase()

TOPPASBase | ( | QWidget * | parent = `nullptr` | ) |

Constructor.

References TOPPASBase::abortPipeline(), TOPPASTabBar::addTab(), TOPPASBase::closeByTab(), TOPPASBase::closeFile(), TOPPASBase::createTOPPToolsTreeWidget(), TOPPASBase::current_path_, DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), TOPPASBase::desc_, TOPPASBase::descriptionUpdated_(), TOPPASBase::exportAsImage(), TOPPASBase::focusByTab(), File::getTempDirectory(), File::getUniqueName(), Param::getValue(), TOPPASBase::includePipeline(), TOPPASBase::insertNewVertexInCenter_(), TOPPASBase::loadPipelineResourceFile(), TOPPASBase::loadPreferences(), TOPPASBase::log_, TOPPASBase::message_label_, TOPPASBase::network_manager_, TOPPASBase::newPipeline(), TOPPASBase::openExampleDialog(), TOPPASBase::openFileDialog(), TOPPASBase::openOnlinePipelineRepository(), DefaultParamHandler::param_, TOPPASBase::refreshParameters(), TOPPASTabBar::removeId(), TOPPASBase::runPipeline(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineResourceFile(), TOPPASLogWindow::setMaxLength(), Param::setValidStrings(), Param::setValue(), TOPPASBase::showAboutDialog(), TOPPASBase::showURL(), TOPPASBase::tab_bar_, TOPPASBase::tmp_path_, TOPPASBase::tools_tree_view_, TOPPASBase::toppasFileDownloaded_(), String::toQString(), TOPPASBase::updateMenu(), TOPPASBase::updateTabBar(), and TOPPASBase::ws_.

## ◆ ~TOPPASBase()

~TOPPASBase | ( |  | ) |

override

Destructor.

References File::getTempDirectory(), File::removeDirRecursively(), TOPPASBase::savePreferences(), and TOPPASBase::tmp_path_.

## Member Function Documentation

## ◆ abortPipeline

void abortPipeline | ( |  | ) |

slot

Terminates the current pipeline.

References TOPPASScene::abortPipeline(), TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASBase::updateMenu().

Referenced by TOPPASBase::TOPPASBase().

## ◆ activeSubWindow_()

TOPPASWidget * activeSubWindow_ | ( |  | ) | const

protected

returns a pointer to the active TOPPASWidget (0 if none is active)

References TOPPASBase::ws_.

Referenced by TOPPASBase::abortPipeline(), TOPPASBase::addTOPPASFile(), TOPPASBase::descriptionUpdated_(), TOPPASBase::exportAsImage(), TOPPASBase::insertNewVertex_(), TOPPASBase::insertNewVertexInCenter_(), TOPPASBase::keyPressEvent(), TOPPASBase::loadPipelineResourceFile(), TOPPASBase::refreshParameters(), TOPPASBase::runPipeline(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineResourceFile(), and TOPPASBase::updateMenu().

## ◆ addTOPPASFile

void addTOPPASFile | ( | const String & | file_name,
|  | bool | in_new_window = `true`
| ) |  |

slot

opens the file in a new window

References TOPPASBase::activeSubWindow_(), File::basename(), TOPPASBase::closeByTab(), TOPPASWidget::getScene(), TOPPASBase::IDINITIALUNTITLED, TOPPASScene::include(), TOPPASScene::load(), OPENMS_LOG_ERROR, TOPPASBase::outputVertexFinished(), TOPPASBase::showAsWindow_(), TOPPASBase::tmp_path_, TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), TOPPASBase::toolStarted(), String::toQString(), TOPPASBase::updateTOPPOutputLog(), TOPPASScene::verticesBegin(), TOPPASScene::verticesEnd(), TOPPASScene::wasChanged(), TOPPASBase::window_(), and TOPPASBase::ws_.

Referenced by TOPPASBase::includePipeline(), TOPPASBase::loadFiles(), TOPPASBase::openExampleDialog(), TOPPASBase::openFileDialog(), TOPPASBase::openToppasFile(), and TOPPASBase::showAsWindow_().

## ◆ closeByTab

void closeByTab | ( | int | id | ) |

protected slot

Closes the window corresponding to the data of the tab with identifier `id`.

References TOPPASTabBar::removeId(), TOPPASBase::tab_bar_, TOPPASBase::updateMenu(), and TOPPASBase::window_().

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

## ◆ closeEvent()

void closeEvent | ( | QCloseEvent * | event | ) |

override protected

References TOPPASWidget::getScene(), TOPPASScene::saveIfChanged(), and TOPPASBase::ws_.

## ◆ closeFile

void closeFile | ( |  | ) |

slot

closes the active window

References TOPPASBase::updateMenu(), and TOPPASBase::ws_.

Referenced by TOPPASBase::TOPPASBase().

## ◆ createTOPPToolsTreeWidget()

TOPPASTreeView * createTOPPToolsTreeWidget | ( | QWidget * | parent_widget = `nullptr` | ) |

static

Creates and fills a tree widget with all available tools.

References ToolHandler::getTOPPToolList(), ToolHandler::getTypes(), ToolHandler::getUtilList(), and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ descriptionUpdated_

void descriptionUpdated_ | ( |  | ) |

protected slot

user edited the workflow description

References TOPPASBase::activeSubWindow_(), TOPPASBase::desc_, TOPPASWidget::getScene(), TOPPASScene::setChanged(), and TOPPASScene::setDescription().

Referenced by TOPPASBase::TOPPASBase().

## ◆ downloadTOPPASfromHomepage_

void downloadTOPPASfromHomepage_ | ( | const QUrl & | url | ) |

protected slot

triggered when user clicks a link - if it ends in .TOPPAS we're done

References TOPPASBase::LS_NOTICE, TOPPASBase::network_manager_, TOPPASBase::network_reply_, TOPPASBase::showLogMessage_(), and TOPPASBase::TOPPASreadyRead().

## ◆ exportAsImage

void exportAsImage | ( |  | ) |

slot

exports the current pipeline as image

References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, TOPPASWidget::getScene(), TOPPASScene::setDescription(), and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ focusByTab

void focusByTab | ( | int | id | ) |

protected slot

Raises the window corresponding to the data of the tab with identifier `id`.

References TOPPASBase::desc_, TOPPASScene::getDescription(), TOPPASWidget::getScene(), and TOPPASBase::window_().

Referenced by TOPPASBase::TOPPASBase().

## ◆ includePipeline

void includePipeline | ( |  | ) |

slot

shows the dialog for including another workflow in the currently opened one

References TOPPASBase::addTOPPASFile(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ insertNewVertex_

void insertNewVertex_ | ( | double | x,
|  | double | y,
|  | QTreeWidgetItem * | item = `nullptr`
| ) |  |

protected slot

Inserts a new TOPP tool in the current window at (x,y)

References TOPPASBase::activeSubWindow_(), TOPPASScene::addVertex(), TOPPASScene::connectOutputVertexSignals(), TOPPASScene::connectToolVertexSignals(), TOPPASScene::connectVertexSignals(), TOPPASWidget::getScene(), TOPPASToolVertex::isToolReady(), TOPPASBase::outputVertexFinished(), TOPPASScene::setChanged(), tool_name, TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), TOPPASBase::tools_tree_view_, TOPPASBase::toolStarted(), TOPPASScene::topoSort(), TOPPASBase::updateTOPPOutputLog(), and TOPPASBase::z_value_.

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

## ◆ insertNewVertexInCenter_

void insertNewVertexInCenter_ | ( | QTreeWidgetItem * | item | ) |

protected slot

Inserts the `item` in the middle of the current window.

References TOPPASBase::activeSubWindow_(), TOPPASBase::insertNewVertex_(), TOPPASBase::node_offset_, and TOPPASBase::tools_tree_view_.

Referenced by TOPPASBase::TOPPASBase().

## ◆ keyPressEvent()

void keyPressEvent | ( | QKeyEvent * | e | ) |

override protected

References TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASScene::runPipeline().

## ◆ loadFiles()

void loadFiles | ( | const StringList & | list,
|  | QSplashScreen * | splash_screen
| ) |  |

loads the files and updates the splash screen

References TOPPASBase::addTOPPASFile().

Referenced by main().

## ◆ loadPipelineResourceFile [1/2]

void loadPipelineResourceFile | ( |  | ) |

slot

shows a file dialog for selecting the resource file to load

References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ loadPipelineResourceFile() [2/2]

QString loadPipelineResourceFile | ( | TOPPASWidget * | w,
|  | QString | current_path
| ) |  |

static

Loads and sets the resources of the TOPPASWidget.

References TOPPASWidget::getScene(), TOPPASResources::load(), and TOPPASScene::loadResources().

## ◆ loadPreferences()

void loadPreferences | ( | String | filename = `""` | ) |

Loads the preferences from the filename given.

If the filename is empty, the application name + ".ini" is used as filename

References File::exists(), Param::exists(), Param::getValue(), VersionInfo::getVersion(), ParamXMLFile::load(), DefaultParamHandler::param_, DefaultParamHandler::setParameters(), Param::setValue(), and DataValue::toString().

Referenced by main(), and TOPPASBase::TOPPASBase().

## ◆ newPipeline

void newPipeline | ( | const int | id = `-1` | ) |

slot

shows the dialog for creating a new file (pass IDINITIALUNTITLED as `id` if its the first call)

References TOPPASBase::showAsWindow_(), TOPPASBase::tmp_path_, and TOPPASBase::ws_.

Referenced by main(), and TOPPASBase::TOPPASBase().

## ◆ openExampleDialog

void openExampleDialog | ( |  | ) |

slot

shows the dialog for opening example files

References TOPPASBase::addTOPPASFile(), and File::getOpenMSDataPath().

Referenced by TOPPASBase::TOPPASBase().

## ◆ openFileDialog

void openFileDialog | ( |  | ) |

slot

shows the dialog for opening files

References TOPPASBase::addTOPPASFile(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ openFilesInTOPPView

void openFilesInTOPPView | ( | QStringList | all_files | ) |

slot

Open files in a new TOPPView instance.

References GUIHelpers::startTOPPView().

Referenced by TOPPASBase::showAsWindow_().

## ◆ openOnlinePipelineRepository

void openOnlinePipelineRepository | ( |  | ) |

slot

opens the OpenMS Homepage to download example workflows

Referenced by TOPPASBase::TOPPASBase().

## ◆ openToppasFile

void openToppasFile | ( | QString | filename | ) |

slot

Opens a toppas file.

References TOPPASBase::addTOPPASFile().

## ◆ outputVertexFinished

void outputVertexFinished | ( | const String & | file | ) |

slot

Called when a file was successfully written to an output vertex.

References TOPPASBase::LS_NOTICE, and TOPPASBase::showLogMessage_().

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

## ◆ preferencesDialog

void preferencesDialog | ( |  | ) |

slot

shows the preferences dialog

References TOPPASBase::savePreferences().

## ◆ refreshParameters

void refreshParameters | ( |  | ) |

slot

Refreshes the parameters of the TOPP tools of the current workflow and stores an updated workflow including the current parameters.

References TOPPASBase::activeSubWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::refreshPipelineParameters(), TOPPASBase::tab_bar_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ refreshPipelineParameters()

QString refreshPipelineParameters | ( | TOPPASWidget * | tw,
|  | QString | current_path
| ) |  |

static

Refreshes the TOPP tools parameters of the pipeline.

References TOPPASWidget::getScene(), TOPPASScene::refreshParameters(), TOPPASBase::savePipelineAs(), TOPPASScene::setChanged(), TOPPASScene::ST_REFRESH_CHANGEINVALID, TOPPASScene::ST_REFRESH_NOCHANGE, TOPPASScene::ST_REFRESH_REMAINSINVALID, and TOPPASScene::updateEdgeColors().

Referenced by TOPPASBase::refreshParameters().

## ◆ runPipeline

void runPipeline | ( |  | ) |

slot

Runs the pipeline of the current window.

References TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASScene::runPipeline().

Referenced by TOPPASBase::TOPPASBase().

## ◆ saveCurrentPipelineAs

void saveCurrentPipelineAs | ( |  | ) |

slot

shows the dialog for saving the current file and updates the current tab caption

References TOPPASBase::activeSubWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::savePipelineAs(), TOPPASBase::tab_bar_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ savePipeline

void savePipeline | ( |  | ) |

slot

saves the pipeline (determined by Qt's sender mechanism)

References TOPPASBase::activeSubWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASScene::getSaveFileName(), TOPPASWidget::getScene(), TOPPASBase::savePipelineAs(), TOPPASScene::store(), TOPPASBase::tab_bar_, and String::toQString().

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

## ◆ savePipelineAs()

QString savePipelineAs | ( | TOPPASWidget * | w,
|  | QString | current_path
| ) |  |

static

Saves the workflow in the provided TOPPASWidget to a user defined location. Returns the full file name or "" if no valid one is selected.

References File::basename(), TOPPASWidget::getScene(), TOPPASScene::store(), and String::toQString().

Referenced by TOPPASBase::refreshPipelineParameters(), TOPPASBase::saveCurrentPipelineAs(), and TOPPASBase::savePipeline().

## ◆ savePipelineResourceFile [1/2]

void savePipelineResourceFile | ( |  | ) |

slot

shows a file dialog for selecting the resource file to write to

References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, and String::toQString().

Referenced by TOPPASBase::TOPPASBase().

## ◆ savePipelineResourceFile() [2/2]

QString savePipelineResourceFile | ( | TOPPASWidget * | w,
|  | QString | current_path
| ) |  |

static

Saves the resources of the TOPPASWidget.

References TOPPASScene::createResources(), TOPPASWidget::getScene(), and TOPPASResources::store().

## ◆ savePreferences()

void savePreferences | ( |  | ) |

stores the preferences (used when this window is closed)

References Param::copy(), Param::getValue(), VersionInfo::getVersion(), DefaultParamHandler::param_, Param::setValue(), and ParamXMLFile::store().

Referenced by TOPPASBase::preferencesDialog(), and TOPPASBase::~TOPPASBase().

## ◆ saveToClipboard

void saveToClipboard | ( | TOPPASScene * | scene | ) |

slot

Saves `scene` to the clipboard.

References TOPPASBase::clipboard_scene_.

Referenced by TOPPASBase::showAsWindow_().

## ◆ sendClipboardContent

void sendClipboardContent | ( |  | ) |

slot

Sends the clipboard content to the sender of the connected signal.

References TOPPASBase::clipboard_scene_, and TOPPASScene::setClipboard().

Referenced by TOPPASBase::showAsWindow_().

## ◆ showAboutDialog

void showAboutDialog | ( |  | ) |

slot

Shows the 'About' dialog.

References QApplicationTOPP::showAboutDialog().

Referenced by TOPPASBase::TOPPASBase().

## ◆ showAsWindow_

void showAsWindow_ | ( | TOPPASWidget * | sw,
|  | const String & | caption,
|  | const int | special_id = `-1`
| ) |  |

protected slot

Shows the widget as window in the workspace (the special_id is only used for the first untitled widget (to be able to auto-close it later)

References TOPPASTabBar::addTab(), TOPPASBase::addTOPPASFile(), TOPPASBase::desc_, TOPPASScene::getDescription(), TOPPASWidget::getScene(), TOPPASWidget::getWindowId(), TOPPASBase::insertNewVertex_(), TOPPASBase::openFilesInTOPPView(), TOPPASBase::savePipeline(), TOPPASBase::saveToClipboard(), TOPPASBase::sendClipboardContent(), TOPPASTabBar::setCurrentId(), TOPPASWidget::setWindowId(), TOPPASBase::showCursorStatus(), TOPPASBase::showPipelineFinishedLogMessage(), TOPPASBase::showStatusMessage(), TOPPASBase::tab_bar_, String::toQString(), TOPPASBase::updateMenu(), TOPPASBase::updateTOPPOutputLog(), and TOPPASBase::ws_.

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

## ◆ showCursorStatus

void showCursorStatus | ( | double | x,
|  | double | y
| ) |  |

slot

shows x,y coordinates in the status bar

Referenced by TOPPASBase::showAsWindow_().

## ◆ showLogMessage_()

void showLogMessage_ | ( | TOPPASBase::LogState | state,
|  | const String & | heading,
|  | const String & | body
| ) |  |

protected

Shows a log message in the log_ window.

References DateTime::getTime(), TOPPASBase::log_, TOPPASBase::LS_ERROR, TOPPASBase::LS_NOTICE, TOPPASBase::LS_WARNING, DateTime::now(), and String::toQString().

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

## ◆ showPipelineFinishedLogMessage

void showPipelineFinishedLogMessage | ( |  | ) |

slot

Called by the scene if the pipeline execution finishes successfully.

References TOPPASBase::LS_NOTICE, and TOPPASBase::showLogMessage_().

Referenced by TOPPASBase::showAsWindow_().

## ◆ showStatusMessage

void showStatusMessage | ( | std::string | msg,
|  | OpenMS::UInt | time
| ) |  |

slot

Shows a status message in the status bar.

If `time` is 0 the status message is displayed until showStatusMessage is called with an empty message or a new message. Otherwise the message is displayed for `time` ms.

References TOPPASBase::message_label_.

Referenced by TOPPASBase::showAsWindow_().

## ◆ showURL

void showURL | ( |  | ) |

slot

shows the URL stored in the data of the sender QAction

References GUIHelpers::openURL().

Referenced by TOPPASBase::TOPPASBase().

## ◆ toolCrashed

void toolCrashed | ( |  | ) |

slot

Called when a tool crashes.

References TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::LS_ERROR, TOPPASBase::showLogMessage_(), and TOPPASBase::updateMenu().

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

## ◆ toolFailed

void toolFailed | ( |  | ) |

slot

Called when a tool execution fails.

References TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::LS_ERROR, TOPPASBase::showLogMessage_(), and TOPPASBase::updateMenu().

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

## ◆ toolFinished

void toolFinished | ( |  | ) |

slot

Called when a tool is finished.

References TOPPASToolVertex::getName(), TOPPASToolVertex::getType(), TOPPASBase::LS_NOTICE, TOPPASBase::showLogMessage_(), and TOPPASBase::updateMenu().

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

## ◆ toolStarted

void toolStarted | ( |  | ) |

slot

Called when a tool is started.

References TOPPASToolVertex::getName(), TOPPASVertex::getTopoNr(), TOPPASToolVertex::getType(), TOPPASBase::LS_NOTICE, TOPPASBase::showLogMessage_(), and TOPPASBase::updateMenu().

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

## ◆ toppasFileDownloaded_

void toppasFileDownloaded_ | ( | QNetworkReply * | r | ) |

protected slot

triggered when download of .toppas file is finished, so we can store & open it

Referenced by TOPPASBase::TOPPASBase().

## ◆ TOPPASreadyRead

void TOPPASreadyRead | ( |  | ) |

protected slot

debug...

References TOPPASBase::network_reply_, and OPENMS_LOG_DEBUG.

Referenced by TOPPASBase::downloadTOPPASfromHomepage_().

## ◆ updateCurrentPath

void updateCurrentPath | ( |  | ) |

slot

changes the current path according to the currently active window/layer

References TOPPASBase::current_path_, Param::getValue(), and DefaultParamHandler::param_.

## ◆ updateMenu

void updateMenu | ( |  | ) |

protected slot

enable/disable menu entries depending on the current state

References TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), TOPPASScene::isPipelineRunning(), TOPPASBase::tab_bar_, and TOPPASScene::wasChanged().

Referenced by TOPPASBase::abortPipeline(), TOPPASBase::closeByTab(), TOPPASBase::closeFile(), TOPPASBase::showAsWindow_(), TOPPASBase::toolCrashed(), TOPPASBase::toolFailed(), TOPPASBase::toolFinished(), TOPPASBase::toolStarted(), and TOPPASBase::TOPPASBase().

## ◆ updateTabBar

void updateTabBar | ( | QMdiSubWindow * | w | ) |

slot

brings the tab corresponding to the active window in front

References TOPPASWidget::getWindowId(), TOPPASTabBar::setCurrentId(), and TOPPASBase::tab_bar_.

Referenced by TOPPASBase::TOPPASBase().

## ◆ updateToolBar

void updateToolBar | ( |  | ) |

slot

updates the toolbar

## ◆ updateTOPPOutputLog

void updateTOPPOutputLog | ( | const QString & | out | ) |

slot

Called when a TOPP tool produces (error) output.

References TOPPASBase::log_.

Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::insertNewVertex_(), and TOPPASBase::showAsWindow_().

## ◆ window_()

TOPPASWidget * window_ | ( | int | id | ) | const

protected

returns the window with id `id`

References TOPPASWidget::getWindowId(), and TOPPASBase::ws_.

Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::closeByTab(), and TOPPASBase::focusByTab().

## Member Data Documentation

## ◆ blocks_list_

QListWidget* blocks_list_

protected

List of ready analysis pipelines.

## ◆ clipboard_scene_

TOPPASScene* clipboard_scene_

protected

The clipboard.

Referenced by TOPPASBase::saveToClipboard(), and TOPPASBase::sendClipboardContent().

## ◆ current_path_

String current_path_

protected

The current path (used for loading and storing). Depending on the preferences this is static or changes with the current window/layer.

Referenced by TOPPASBase::exportAsImage(), TOPPASBase::includePipeline(), TOPPASBase::loadPipelineResourceFile(), TOPPASBase::openFileDialog(), TOPPASBase::refreshParameters(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::savePipelineResourceFile(), TOPPASBase::TOPPASBase(), and TOPPASBase::updateCurrentPath().

## ◆ desc_

QTextEdit* desc_

protected

Workflow Description window.

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

## ◆ IDINITIALUNTITLED

int const IDINITIALUNTITLED = 1000

static

use this for the first call to newPipeline(), to ensure that the first empty (and unmodified) workspace is closed iff existing workflows are loaded

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

## ◆ log_

TOPPASLogWindow* log_

protected

Log output window.

Referenced by TOPPASBase::showLogMessage_(), TOPPASBase::TOPPASBase(), and TOPPASBase::updateTOPPOutputLog().

## ◆ message_label_

QLabel* message_label_

protected

Label for messages in the status bar.

Referenced by TOPPASBase::showStatusMessage(), and TOPPASBase::TOPPASBase().

## ◆ network_manager_

QNetworkAccessManager* network_manager_

protected

download .toppas files from homepage

Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), and TOPPASBase::TOPPASBase().

## ◆ network_reply_

QNetworkReply* network_reply_

protected

the content of the network request

Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), and TOPPASBase::TOPPASreadyRead().

## ◆ node_offset_

int node_offset_ = 0

static protected

Offset counter for new inserted nodes (to avoid invisible stacking)

Referenced by TOPPASBase::insertNewVertexInCenter_().

## ◆ tab_bar_

TOPPASTabBar* tab_bar_

protected

Tab bar. The address of the corresponding window to a tab is stored as an int in tabData()

Referenced by TOPPASBase::closeByTab(), TOPPASBase::refreshParameters(), TOPPASBase::saveCurrentPipelineAs(), TOPPASBase::savePipeline(), TOPPASBase::showAsWindow_(), TOPPASBase::TOPPASBase(), TOPPASBase::updateMenu(), and TOPPASBase::updateTabBar().

## ◆ tmp_path_

String tmp_path_

protected

The path for temporary files.

Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::newPipeline(), TOPPASBase::TOPPASBase(), and TOPPASBase::~TOPPASBase().

## ◆ tool_bar_

QToolBar* tool_bar_

protected

## ◆ tools_tree_view_

QTreeWidget* tools_tree_view_

protected

Tree view of all available TOPP tools.

Referenced by TOPPASBase::insertNewVertex_(), TOPPASBase::insertNewVertexInCenter_(), and TOPPASBase::TOPPASBase().

## ◆ webview_

QWebView* webview_

protected

OpenMS homepage workflow browser.

## ◆ ws_

QMdiArea* ws_

protected

Main workspace.

Referenced by TOPPASBase::activeSubWindow_(), TOPPASBase::addTOPPASFile(), TOPPASBase::closeEvent(), TOPPASBase::closeFile(), TOPPASBase::newPipeline(), TOPPASBase::showAsWindow_(), TOPPASBase::TOPPASBase(), and TOPPASBase::window_().

## ◆ z_value_

qreal z_value_ = 42.0

static protected

z-value counter for new inserted nodes (new nodes should be on top)

Referenced by TOPPASBase::insertNewVertex_().