Main window of the TOPPAS tool. More...
#include <OpenMS/VISUAL/APPLICATIONS/TOPPASBase.h>
 
  
 | 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 idif 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 (QWidget *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 sceneto 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=0) | |
| Constructor.  More... | |
| virtual | ~TOPPASBase () | 
| 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 ¶m) | 
| 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=0) | 
| 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=0) | 
| Inserts a new TOPP tool in the current window at (x,y)  More... | |
| void | insertNewVertexInCenter_ (QTreeWidgetItem *item) | 
| Inserts the itemin 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 | 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 idMore... | |
| TOPPASWidget * | activeWindow_ () 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) | 
| void | keyPressEvent (QKeyEvent *e) | 
|  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... | |
| QWorkspace * | ws_ | 
| Main workspace.  More... | |
| QWebView * | webview_ | 
| OpenMS homepage workflow browser.  More... | |
| QNetworkAccessManager * | network_manager_ | 
| download .toppas files from homepage  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... | |
Main window of the TOPPAS tool.
| 
 | protected | 
| TOPPASBase | ( | QWidget * | parent = 0 | ) | 
Constructor.
References TOPPASBase::abortPipeline(), TOPPASTabBar::addTab(), TOPPASBase::closeByTab(), TOPPASBase::closeFile(), StringList::create(), TOPPASBase::createTOPPToolsTreeWidget(), TOPPASBase::current_path_, DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), TOPPASBase::desc_, TOPPASBase::descriptionUpdated_(), TOPPASBase::downloadTOPPASfromHomepage_(), 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(), 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(), TOPPASBase::webview_, and TOPPASBase::ws_.
| 
 | virtual | 
Destructor.
References File::getTempDirectory(), File::removeDirRecursively(), TOPPASBase::savePreferences(), and TOPPASBase::tmp_path_.
| 
 | slot | 
Terminates the current pipeline.
References TOPPASScene::abortPipeline(), TOPPASBase::activeWindow_(), TOPPASWidget::getScene(), and TOPPASBase::updateMenu().
Referenced by TOPPASBase::TOPPASBase().
| 
 | 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().
| 
 | slot | 
opens the file in a new window
References TOPPASBase::activeWindow_(), File::basename(), TOPPASBase::closeByTab(), TOPPASWidget::getScene(), TOPPASBase::IDINITIALUNTITLED, TOPPASScene::include(), TOPPASScene::load(), 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(), TOPPASBase::showAsWindow_(), and TOPPASBase::toppasFileDownloaded_().
| 
 | protectedslot | 
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().
| 
 | protected | 
References TOPPASBase::ws_.
| 
 | slot | 
closes the active window
References TOPPASBase::updateMenu(), and TOPPASBase::ws_.
Referenced by TOPPASBase::TOPPASBase().
| 
 | 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().
| 
 | protectedslot | 
user edited the workflow description
References TOPPASBase::activeWindow_(), TOPPASBase::desc_, TOPPASWidget::getScene(), TOPPASScene::setChanged(), and TOPPASScene::setDescription().
Referenced by TOPPASBase::TOPPASBase().
| 
 | protectedslot | 
triggered when user clicks a link - if it ends in .TOPPAS we're done
References TOPPASBase::LS_NOTICE, TOPPASBase::network_manager_, TOPPASBase::showLogMessage_(), and TOPPASBase::webview_.
Referenced by TOPPASBase::TOPPASBase().
| 
 | slot | 
exports the current pipeline as image
References TOPPASBase::activeWindow_(), TOPPASBase::current_path_, TOPPASWidget::getScene(), TOPPASScene::setDescription(), and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
| 
 | protectedslot | 
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().
| 
 | 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().
Inserts a new TOPP tool in the current window at (x,y)
References TOPPASBase::activeWindow_(), 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_().
| 
 | protectedslot | 
Inserts the item in the middle of the current window. 
References TOPPASBase::activeWindow_(), TOPPASBase::insertNewVertex_(), TOPPASBase::node_offset_, and TOPPASBase::tools_tree_view_.
Referenced by TOPPASBase::TOPPASBase().
| 
 | protected | 
References TOPPASBase::activeWindow_(), TOPPASWidget::getScene(), and TOPPASScene::runPipeline().
| void loadFiles | ( | const StringList & | list, | 
| QSplashScreen * | splash_screen | ||
| ) | 
loads the files and updates the splash screen
References TOPPASBase::addTOPPASFile().
Referenced by main().
| 
 | slot | 
shows a file dialog for selecting the resource file to load
References TOPPASBase::activeWindow_(), TOPPASBase::current_path_, and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
| 
 | static | 
Loads and sets the resources of the TOPPASWidget.
References TOPPASWidget::getScene(), TOPPASResources::load(), and TOPPASScene::loadResources().
| 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().
| 
 | 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().
| 
 | slot | 
shows the dialog for opening example files
References TOPPASBase::addTOPPASFile(), and File::getOpenMSDataPath().
Referenced by TOPPASBase::TOPPASBase().
| 
 | slot | 
shows the dialog for opening files
References TOPPASBase::addTOPPASFile(), TOPPASBase::current_path_, and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
| 
 | slot | 
Open files in a new TOPPView instance.
References File::exists(), File::findExecutable(), and File::getExecutablePath().
Referenced by TOPPASBase::showAsWindow_().
| 
 | slot | 
opens the OpenMS Homepage to download example workflows
References TOPPASBase::webview_.
Referenced by TOPPASBase::TOPPASBase().
| 
 | slot | 
Opens a toppas file.
References TOPPASBase::addTOPPASFile().
| 
 | 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_().
| 
 | slot | 
shows the preferences dialog
References TOPPASBase::savePreferences().
| 
 | slot | 
Refreshes the parameters of the TOPP tools of the current workflow and stores an updated workflow including the current parameters.
References TOPPASBase::activeWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::refreshPipelineParameters(), TOPPASBase::tab_bar_, and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
| 
 | 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().
| 
 | slot | 
Runs the pipeline of the current window.
References TOPPASBase::activeWindow_(), TOPPASWidget::getScene(), and TOPPASScene::runPipeline().
Referenced by TOPPASBase::TOPPASBase().
| 
 | slot | 
shows the dialog for saving the current file and updates the current tab caption
References TOPPASBase::activeWindow_(), File::basename(), TOPPASBase::current_path_, TOPPASBase::savePipelineAs(), TOPPASBase::tab_bar_, and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
| 
 | slot | 
saves the pipeline (determined by Qt's sender mechanism)
References TOPPASBase::activeWindow_(), 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().
| 
 | 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(), NULL, TOPPASScene::store(), and String::toQString().
Referenced by TOPPASBase::refreshPipelineParameters(), TOPPASBase::saveCurrentPipelineAs(), and TOPPASBase::savePipeline().
| 
 | slot | 
shows a file dialog for selecting the resource file to write to
References TOPPASBase::activeWindow_(), TOPPASBase::current_path_, and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
| 
 | static | 
Saves the resources of the TOPPASWidget.
References TOPPASScene::createResources(), TOPPASWidget::getScene(), and TOPPASResources::store().
| 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().
| 
 | slot | 
Saves scene to the clipboard. 
References TOPPASBase::clipboard_scene_.
Referenced by TOPPASBase::showAsWindow_().
| 
 | slot | 
Sends the clipboard content to the sender of the connected signal.
References TOPPASBase::clipboard_scene_, and TOPPASScene::setClipboard().
Referenced by TOPPASBase::showAsWindow_().
| 
 | slot | 
Shows the 'About' dialog.
References VersionInfo::getVersion().
Referenced by TOPPASBase::TOPPASBase().
| 
 | protectedslot | 
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().
shows x,y coordinates in the status bar
Referenced by TOPPASBase::showAsWindow_().
| 
 | 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(), TOPPASBase::toolStarted(), and TOPPASBase::toppasFileDownloaded_().
| 
 | slot | 
Called by the scene if the pipeline execution finishes successfully.
References TOPPASBase::LS_NOTICE, and TOPPASBase::showLogMessage_().
Referenced by TOPPASBase::showAsWindow_().
| 
 | 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_().
| 
 | slot | 
shows the URL stored in the data of the sender QAction
References File::findDoc(), and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
| 
 | 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_().
| 
 | 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_().
| 
 | 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_().
| 
 | 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_().
| 
 | protectedslot | 
triggered when download of .toppas file is finished, so we can store & open it
References TOPPASBase::addTOPPASFile(), TOPPASBase::current_path_, LOG_WARN, TOPPASBase::LS_NOTICE, TOPPASBase::showLogMessage_(), String::toQString(), and String::trim().
Referenced by TOPPASBase::TOPPASBase().
| 
 | slot | 
changes the current path according to the currently active window/layer
References TOPPASBase::current_path_, Param::getValue(), and DefaultParamHandler::param_.
| 
 | protectedslot | 
enable/disable menu entries depending on the current state
References TOPPASBase::activeWindow_(), 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().
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 | slot | 
brings the tab corresponding to the active window in front
References TOPPASTabBar::setCurrentId(), and TOPPASBase::tab_bar_.
Referenced by TOPPASBase::TOPPASBase().
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 | slot | 
updates the toolbar
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 | slot | 
Called when a TOPP tool produces (error) output.
References TOPPASBase::log_.
Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::insertNewVertex_(), and TOPPASBase::showAsWindow_().
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 | protected | 
returns the window with id id 
References TOPPASWidget::getWindowId(), and TOPPASBase::ws_.
Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::closeByTab(), and TOPPASBase::focusByTab().
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 | protected | 
List of ready analysis pipelines.
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 | protected | 
The clipboard.
Referenced by TOPPASBase::saveToClipboard(), and TOPPASBase::sendClipboardContent().
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 | 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(), TOPPASBase::toppasFileDownloaded_(), and TOPPASBase::updateCurrentPath().
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 | protected | 
Workflow Description window.
Referenced by TOPPASBase::descriptionUpdated_(), TOPPASBase::focusByTab(), TOPPASBase::showAsWindow_(), and TOPPASBase::TOPPASBase().
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 | 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().
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 | protected | 
Log output window.
Referenced by TOPPASBase::showLogMessage_(), TOPPASBase::TOPPASBase(), and TOPPASBase::updateTOPPOutputLog().
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 | protected | 
Label for messages in the status bar.
Referenced by TOPPASBase::showStatusMessage(), and TOPPASBase::TOPPASBase().
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 | protected | 
download .toppas files from homepage
Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), and TOPPASBase::TOPPASBase().
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 | staticprotected | 
Offset counter for new inserted nodes (to avoid invisible stacking)
Referenced by TOPPASBase::insertNewVertexInCenter_().
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 | 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().
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 | protected | 
The path for temporary files.
Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::newPipeline(), TOPPASBase::TOPPASBase(), and TOPPASBase::~TOPPASBase().
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 | protected | 
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 | protected | 
Tree view of all available TOPP tools.
Referenced by TOPPASBase::insertNewVertex_(), TOPPASBase::insertNewVertexInCenter_(), and TOPPASBase::TOPPASBase().
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 | protected | 
OpenMS homepage workflow browser.
Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), TOPPASBase::openOnlinePipelineRepository(), and TOPPASBase::TOPPASBase().
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 | protected | 
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 | staticprotected | 
z-value counter for new inserted nodes (new nodes should be on top)
Referenced by TOPPASBase::insertNewVertex_().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5 |