OpenMS
2.4.0
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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 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 ¶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=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... | |
Main window of the TOPPAS tool.
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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_.
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override |
Destructor.
References File::getTempDirectory(), File::removeDirRecursively(), TOPPASBase::savePreferences(), and TOPPASBase::tmp_path_.
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Terminates the current pipeline.
References TOPPASScene::abortPipeline(), TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASBase::updateMenu().
Referenced by TOPPASBase::TOPPASBase().
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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().
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opens the file in a new window
References TOPPASBase::activeSubWindow_(), 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(), and TOPPASBase::showAsWindow_().
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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().
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overrideprotected |
References TOPPASWidget::getScene(), TOPPASScene::saveIfChanged(), and TOPPASBase::ws_.
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closes the active window
References TOPPASBase::updateMenu(), and TOPPASBase::ws_.
Referenced by TOPPASBase::TOPPASBase().
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Creates and fills a tree widget with all available tools.
References ToolHandler::getTOPPToolList(), ToolHandler::getTypes(), ToolHandler::getUtilList(), and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
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protectedslot |
user edited the workflow description
References TOPPASBase::activeSubWindow_(), TOPPASBase::desc_, TOPPASWidget::getScene(), TOPPASScene::setChanged(), and TOPPASScene::setDescription().
Referenced by TOPPASBase::TOPPASBase().
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protectedslot |
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().
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exports the current pipeline as image
References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, TOPPASWidget::getScene(), TOPPASScene::setDescription(), and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
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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().
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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::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_().
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protectedslot |
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().
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overrideprotected |
References TOPPASBase::activeSubWindow_(), 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().
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shows a file dialog for selecting the resource file to load
References TOPPASBase::activeSubWindow_(), TOPPASBase::current_path_, and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
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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().
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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().
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shows the dialog for opening example files
References TOPPASBase::addTOPPASFile(), and File::getOpenMSDataPath().
Referenced by TOPPASBase::TOPPASBase().
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shows the dialog for opening files
References TOPPASBase::addTOPPASFile(), TOPPASBase::current_path_, and String::toQString().
Referenced by TOPPASBase::TOPPASBase().
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Open files in a new TOPPView instance.
References GUIHelpers::startTOPPView().
Referenced by TOPPASBase::showAsWindow_().
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opens the OpenMS Homepage to download example workflows
Referenced by TOPPASBase::TOPPASBase().
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Opens a toppas file.
References TOPPASBase::addTOPPASFile().
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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_().
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shows the preferences dialog
References TOPPASBase::savePreferences().
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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().
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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().
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Runs the pipeline of the current window.
References TOPPASBase::activeSubWindow_(), TOPPASWidget::getScene(), and TOPPASScene::runPipeline().
Referenced by TOPPASBase::TOPPASBase().
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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().
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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().
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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().
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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().
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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().
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Saves scene
to the clipboard.
References TOPPASBase::clipboard_scene_.
Referenced by TOPPASBase::showAsWindow_().
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Sends the clipboard content to the sender of the connected signal.
References TOPPASBase::clipboard_scene_, and TOPPASScene::setClipboard().
Referenced by TOPPASBase::showAsWindow_().
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Shows the 'About' dialog.
References QApplicationTOPP::showAboutDialog().
Referenced by TOPPASBase::TOPPASBase().
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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_().
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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().
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Called by the scene if the pipeline execution finishes successfully.
References TOPPASBase::LS_NOTICE, and TOPPASBase::showLogMessage_().
Referenced by TOPPASBase::showAsWindow_().
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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_().
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shows the URL stored in the data of the sender QAction
References GUIHelpers::openURL().
Referenced by TOPPASBase::TOPPASBase().
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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_().
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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_().
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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_().
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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_().
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protectedslot |
triggered when download of .toppas file is finished, so we can store & open it
Referenced by TOPPASBase::TOPPASBase().
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protectedslot |
debug...
References LOG_DEBUG, and TOPPASBase::network_reply_.
Referenced by TOPPASBase::downloadTOPPASfromHomepage_().
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changes the current path according to the currently active window/layer
References TOPPASBase::current_path_, Param::getValue(), and DefaultParamHandler::param_.
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protectedslot |
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().
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brings the tab corresponding to the active window in front
References TOPPASWidget::getWindowId(), TOPPASTabBar::setCurrentId(), and TOPPASBase::tab_bar_.
Referenced by TOPPASBase::TOPPASBase().
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updates the toolbar
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Called when a TOPP tool produces (error) output.
References TOPPASBase::log_.
Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::insertNewVertex_(), and TOPPASBase::showAsWindow_().
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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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List of ready analysis pipelines.
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The clipboard.
Referenced by TOPPASBase::saveToClipboard(), and TOPPASBase::sendClipboardContent().
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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().
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Workflow Description window.
Referenced by TOPPASBase::descriptionUpdated_(), TOPPASBase::focusByTab(), TOPPASBase::showAsWindow_(), and TOPPASBase::TOPPASBase().
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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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Log output window.
Referenced by TOPPASBase::showLogMessage_(), TOPPASBase::TOPPASBase(), and TOPPASBase::updateTOPPOutputLog().
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Label for messages in the status bar.
Referenced by TOPPASBase::showStatusMessage(), and TOPPASBase::TOPPASBase().
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download .toppas files from homepage
Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), and TOPPASBase::TOPPASBase().
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the content of the network request
Referenced by TOPPASBase::downloadTOPPASfromHomepage_(), and TOPPASBase::TOPPASreadyRead().
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Offset counter for new inserted nodes (to avoid invisible stacking)
Referenced by TOPPASBase::insertNewVertexInCenter_().
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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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The path for temporary files.
Referenced by TOPPASBase::addTOPPASFile(), TOPPASBase::newPipeline(), TOPPASBase::TOPPASBase(), and TOPPASBase::~TOPPASBase().
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Tree view of all available TOPP tools.
Referenced by TOPPASBase::insertNewVertex_(), TOPPASBase::insertNewVertexInCenter_(), and TOPPASBase::TOPPASBase().
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OpenMS homepage workflow browser.
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z-value counter for new inserted nodes (new nodes should be on top)
Referenced by TOPPASBase::insertNewVertex_().