OpenMS  3.0.0
TOPPASBase.h
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31 // $Maintainer: Johannes Veit $
32 // $Authors: Johannes Junker, Chris Bielow $
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34 
35 #pragma once
36 
37 // OpenMS_GUI config
38 #include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
39 
40 //OpenMS
45 
46 //QT
47 #include <QtWidgets/QButtonGroup>
48 #include <QtWidgets/QMainWindow>
49 #include <QtWidgets/QMdiArea>
50 #include <QtNetwork/QNetworkReply>
51 #include <QtWidgets/QSplashScreen>
52 
53 class QToolBar;
54 class QListWidget;
55 class QTextEdit;
56 class QMdiArea;
57 class QLabel;
58 class QWidget;
59 class QTreeWidget;
60 class QTreeWidgetItem;
61 class QWebView;
62 class QNetworkAccessManager;
63 
64 
65 namespace OpenMS
66 {
67  class EnhancedWorkSpace;
68  class EnhancedTabBar;
69  class TOPPASWidget;
70  class TOPPASScene;
71  class LogWindow;
72  class TOPPASResources;
73 
79  class OPENMS_GUI_DLLAPI TOPPASBase :
80  public QMainWindow,
81  public DefaultParamHandler
82  {
83  Q_OBJECT
84 
85 public:
86 
88  TOPPASBase(QWidget* parent = nullptr);
90  ~TOPPASBase() override;
91 
97  void loadPreferences(String filename = "");
99  void savePreferences();
101  void loadFiles(const std::vector<String>& list, QSplashScreen* splash_screen);
102 
103 public slots:
105  void addTOPPASFile(const String& file_name, bool in_new_window = true);
107  void openFilesByDialog();
109  void openExampleDialog();
111  void newPipeline();
113  void includePipeline();
115  void saveCurrentPipelineAs();
117  void savePipeline();
119  void exportAsImage();
121  void loadPipelineResourceFile();
123  void savePipelineResourceFile();
125  void openOnlinePipelineRepository();
127  void preferencesDialog();
129  void updateCurrentPath();
131  void updateTabBar(QMdiSubWindow* w);
133  void showAboutDialog();
135  void showURL();
142  void showStatusMessage(std::string msg, OpenMS::UInt time);
144  void showCursorStatus(double x, double y);
146  void closeFile();
148  void updateToolBar();
150  void runPipeline();
152  void abortPipeline();
154  void toolStarted();
156  void toolFinished();
158  void toolCrashed();
160  void toolFailed();
162  void outputVertexFinished(const String& file);
164  void updateTOPPOutputLog(const QString& out);
166  void showPipelineFinishedLogMessage();
168  void saveToClipboard(TOPPASScene* scene);
170  void sendClipboardContent();
172  void refreshParameters();
174  void openFilesInTOPPView(QStringList all_files);
176  void openToppasFile(QString filename);
177 protected slots:
178 
182  void closeByTab(int id);
185  void focusByTab(int id);
187 
189  void updateMenu();
191  void showAsWindow_(TOPPASWidget* sw, const String& caption);
193  void insertNewVertex_(double x, double y, QTreeWidgetItem* item = nullptr);
195  void insertNewVertexInCenter_(QTreeWidgetItem* item);
196 
198  void downloadTOPPASfromHomepage_(const QUrl& url);
200  void toppasFileDownloaded_(QNetworkReply* r);
202  void TOPPASreadyRead();
203 
205  void descriptionUpdated_();
206 
207 protected:
208 
213 
217  QToolBar* tool_bar_;
219 
221  RecentFilesMenu recent_files_menu_; // needs to be declared before 'menu_', because its needed there
222 
225 
227  QWebView* webview_;
229  QNetworkAccessManager* network_manager_;
231  QNetworkReply* network_reply_;
232 
235 
240 
244  QLabel* message_label_;
247 
249  TOPPASWidget* window_(int id) const;
250 
251 
255 
258 
260  static int node_offset_;
261 
263  static qreal z_value_;
264 
266  TOPPASWidget* activeSubWindow_() const;
267 
269 
270  void closeEvent(QCloseEvent* event) override;
271  void keyPressEvent(QKeyEvent* e) override;
273 
276 
277 
278 public:
280 
281  static TOPPASTreeView* createTOPPToolsTreeWidget(QWidget* parent_widget = nullptr);
283 
286  static QString savePipelineAs(TOPPASWidget* w, QString current_path);
287 
289  static QString loadPipelineResourceFile(TOPPASWidget* w, QString current_path);
290 
292  static QString savePipelineResourceFile(TOPPASWidget* w, QString current_path);
293 
295  static QString refreshPipelineParameters(TOPPASWidget* tw, QString current_path);
297  }; //class
298 
299 } //namespace
300 
LogStream.h
DefaultParamHandler.h
OpenMS::TOPPASScene::getSaveFileName
const String & getSaveFileName()
Returns the file name.
OpenMS::TOPPASScene::VertexIterator
VertexContainer::iterator VertexIterator
A mutable iterator for vertices.
Definition: TOPPASScene.h:141
QObject
OpenMS::EnhancedWorkspace
Definition: EnhancedWorkspace.h:51
OpenMS::StringUtils::hasSubstring
static bool hasSubstring(const String &this_s, const String &string)
Definition: StringUtilsSimple.h:137
OpenMS::TOPPASScene::runPipeline
void runPipeline()
Runs the pipeline.
OpenMS::TOPPASBase::recent_files_menu_
RecentFilesMenu recent_files_menu_
manages recent list of filenames and the menu that goes with it
Definition: TOPPASBase.h:221
OpenMS::TOPPASToolVertex::getType
const String & getType() const
Returns the type of the tool.
OpenMS::TOPPASScene::RefreshStatus
RefreshStatus
Pipeline status after refreshParameters() was called.
Definition: TOPPASScene.h:123
OpenMS::TOPPASBase::savePipelineAs
static QString savePipelineAs(TOPPASWidget *w, QString current_path)
Definition: TOPPASBase.cpp:691
OpenMS::TOPPASBase::current_path_
String current_path_
Definition: TOPPASBase.h:254
OpenMS::TOPPASBase::updateCurrentPath
void updateCurrentPath()
changes the current path according to the currently active window/layer
Definition: TOPPASBase.cpp:1189
VersionInfo.h
OpenMS::LogWindow
A log window (QTextEdit) with convenience functions.
Definition: LogWindow.h:53
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
QListWidget
OpenMS::TOPPASToolVertex::getName
String getName() const override
returns the name of the TOPP tool
OpenMS::TOPPASBase::saveCurrentPipelineAs
void saveCurrentPipelineAs()
shows the dialog for saving the current file and updates the current tab caption
Definition: TOPPASBase.cpp:680
OpenMS::TOPPASBase::exportAsImage
void exportAsImage()
exports the current pipeline as image
Definition: TOPPASBase.cpp:716
OpenMS::Param::insert
void insert(const std::string &prefix, const Param &param)
OpenMS::TOPPASBase
Main window of the TOPPAS tool.
Definition: TOPPASBase.h:79
QTextEdit
OpenMS::TOPPASBase::openFilesInTOPPView
void openFilesInTOPPView(QStringList all_files)
Open files in a new TOPPView instance.
Definition: TOPPASBase.cpp:1499
StopWatch.h
OpenMS::LogWindow::appendNewHeader
void appendNewHeader(const LogState state, const String &heading, const String &body)
appends a new block with heading and a body
OpenMS::TOPPASBase::insertNewVertexInCenter_
void insertNewVertexInCenter_(QTreeWidgetItem *item)
Inserts the item in the middle of the current window.
Definition: TOPPASBase.cpp:1408
OpenMS::TOPPASBase::outputVertexFinished
void outputVertexFinished(const String &file)
Called when a file was successfully written to an output vertex.
Definition: TOPPASBase.cpp:1383
OpenMS::TOPPASBase::includePipeline
void includePipeline()
shows the dialog for including another workflow in the currently opened one
Definition: TOPPASBase.cpp:546
OpenMS::File::basename
static String basename(const String &file)
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::StringUtils::toQString
static QString toQString(const String &this_s)
Definition: StringUtils.h:201
TOPPASScene.h
OpenMS::EnhancedTabBar::addTab
int addTab(const String &text, int id)
Adds a new tab with the name text and the identifier id.
OpenMS::TOPPASScene
A container for all visual items of a TOPPAS workflow.
Definition: TOPPASScene.h:85
OpenMS::TOPPASBase::updateTOPPOutputLog
void updateTOPPOutputLog(const QString &out)
Called when a TOPP tool produces (error) output.
Definition: TOPPASBase.cpp:1389
DateTime.h
OpenMS::TOPPASBase::closeEvent
void closeEvent(QCloseEvent *event) override
Definition: TOPPASBase.cpp:892
OpenMS::TOPPASBase::node_offset_
static int node_offset_
Offset counter for new inserted nodes (to avoid invisible stacking)
Definition: TOPPASBase.h:260
OpenMS::TOPPASScene::createResources
void createResources(TOPPASResources &resources)
Create resources from the current workflow.
OpenMS::TOPPASScene::connectOutputVertexSignals
void connectOutputVertexSignals(TOPPASOutputFileListVertex *oflv)
Connects the signals to slots.
OpenMS::TOPPASScene::verticesEnd
VertexIterator verticesEnd()
Returns end() iterator of all vertices.
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TOPPASBase::ws_
EnhancedWorkspace * ws_
Main workspace.
Definition: TOPPASBase.h:224
ParamXMLFile.h
OpenMS::Exception::FileNotFound
File not found exception.
Definition: Exception.h:509
OpenMS::TOPPASBase::showAboutDialog
void showAboutDialog()
Shows the 'About' dialog.
Definition: TOPPASBase.cpp:1095
LogWindow.h
OpenMS::QApplicationTOPP
Extension to the QApplication for running TOPPs GUI tools.
Definition: QApplicationTOPP.h:50
OpenMS::TOPPASScene::wasChanged
bool wasChanged() const
Returns whether the workflow has been changed since the latest "save".
OpenMS::GUIHelpers::startTOPPView
void startTOPPView(const QStringList &args)
Open TOPPView (e.g. from within TOPPAS)
OpenMS::TOPPASScene::include
void include(TOPPASScene *new_scene, QPointF pos=QPointF())
Includes the pipeline scene.
OpenMS::TOPPASScene::store
bool store(const String &file)
Stores the pipeline to file, returns true on success.
OpenMS::TOPPASBase::addTOPPASFile
void addTOPPASFile(const String &file_name, bool in_new_window=true)
opens the file in a new window
Definition: TOPPASBase.cpp:552
OpenMS::TOPPASToolVertex
A vertex representing a TOPP tool.
Definition: TOPPASToolVertex.h:60
OpenMS::GUIHelpers::openURL
void openURL(const QString &target)
OpenMS::ParamXMLFile
The file pendant of the Param class used to load and store the param datastructure as paramXML.
Definition: ParamXMLFile.h:49
OpenMS::TOPPASBase::savePreferences
void savePreferences()
stores the preferences (used when this window is closed)
Definition: TOPPASBase.cpp:1069
OpenMS::EnhancedTabBar::closeRequested
void closeRequested(int id)
Signal that indicates that the tab with identifier id is requested to be removed (double click or con...
OpenMS::TOPPASBase::showURL
void showURL()
shows the URL stored in the data of the sender QAction
Definition: TOPPASBase.cpp:912
OpenMS::EnhancedTabBar::currentIdChanged
void currentIdChanged(int id)
Signal that indicates that the current tab changed, giving the id of the Tab.
OpenMS::TOPPASBase::message_label_
QLabel * message_label_
Label for messages in the status bar.
Definition: TOPPASBase.h:245
RecentFilesMenu.h
OpenMS::TOPPASBase::updateMenu
void updateMenu()
enable/disable menu entries depending on the current state
Definition: TOPPASBase.cpp:1100
OpenMS::File::getUniqueName
static String getUniqueName(bool include_hostname=true)
Returns a string, consisting of date, time, hostname, process id, and a incrementing number....
QWidget
OpenMS::TOPPASBase::descriptionUpdated_
void descriptionUpdated_()
user edited the workflow description
Definition: TOPPASBase.cpp:299
OpenMS::TOPPASBase::loadPipelineResourceFile
void loadPipelineResourceFile()
shows a file dialog for selecting the resource file to load
Definition: TOPPASBase.cpp:778
ListUtils.h
OpenMS::TOPPASScene::refreshParameters
RefreshStatus refreshParameters()
Refreshes the parameters of the TOPP tools in this workflow.
OpenMS::TOPPASScene::loadResources
void loadResources(const TOPPASResources &resources)
Loads the resources into the input nodes of this workflow.
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::Exception::InvalidParameter
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:339
OpenMS::TOPPASBase::openFilesByDialog
void openFilesByDialog()
shows the dialog for opening files
Definition: TOPPASBase.cpp:539
OpenMS::StringUtils::hasPrefix
static bool hasPrefix(const String &this_s, const String &string)
Definition: StringUtilsSimple.h:111
OpenMS::TOPPASBase::showAsWindow_
void showAsWindow_(TOPPASWidget *sw, const String &caption)
Shows the widget as window in the workspace.
Definition: TOPPASBase.cpp:838
OpenMS::TOPPASBase::window_
TOPPASWidget * window_(int id) const
returns the window with id id
Definition: TOPPASBase.cpp:918
OpenMS::RecentFilesMenu::setFromParam
unsigned setFromParam(const Param &filenames)
Extracts all values from all elements in the param object and tries to interpret them as filenames If...
OpenMS::TOPPASBase::blocks_list_
QListWidget * blocks_list_
List of ready analysis pipelines.
Definition: TOPPASBase.h:239
OpenMS::TOPPASScene::abortPipeline
void abortPipeline()
Terminates the currently running pipeline.
OpenMS::RecentFilesMenu::add
void add(const String &filename)
put a new recent file at the top (removing any duplicates in other positions); will update the QMenu
OpenMS::TOPPASBase::openExampleDialog
void openExampleDialog()
shows the dialog for opening example files
Definition: TOPPASBase.cpp:528
TOPPASOutputFileListVertex.h
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::TOPPASBase::closeByTab
void closeByTab(int id)
Closes the window corresponding to the data of the tab with identifier id.
Definition: TOPPASBase.cpp:933
OpenMS::TOPPASBase::saveToClipboard
void saveToClipboard(TOPPASScene *scene)
Saves scene to the clipboard.
Definition: TOPPASBase.cpp:1420
OpenMS::File::exists
static bool exists(const String &file)
Method used to test if a file exists.
OpenMS::ToolHandler::getUtilList
static ToolListType getUtilList()
Returns the list of official UTIL tools contained in the OpenMS/TOPP release.
OpenMS::TOPPASBase::createTOPPToolsTreeWidget
static TOPPASTreeView * createTOPPToolsTreeWidget(QWidget *parent_widget=nullptr)
Creates and fills a tree widget with all available tools.
Definition: TOPPASBase.cpp:439
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::TOPPASBase::updateToolBar
void updateToolBar()
updates the toolbar
Definition: TOPPASBase.cpp:991
QMdiArea
OpenMS::ToolHandler::getTOPPToolList
static ToolListType getTOPPToolList(const bool includeGenericWrapper=false)
Returns the list of official TOPP tools contained in the OpenMS/TOPP release.
OpenMS::TOPPASBase::toolFailed
void toolFailed()
Called when a tool execution fails.
Definition: TOPPASBase.cpp:1365
OpenMS::TOPPASBase::showCursorStatus
void showCursorStatus(double x, double y)
shows x,y coordinates in the status bar
Definition: TOPPASBase.cpp:986
OpenMS::TOPPASBase::tmp_path_
String tmp_path_
The path for temporary files.
Definition: TOPPASBase.h:257
OpenMS::TOPPASScene::verticesBegin
VertexIterator verticesBegin()
Returns begin() iterator of all vertices.
OpenMS::TOPPASInputFileListVertex
A vertex representing an input file list.
Definition: TOPPASInputFileListVertex.h:49
OpenMS::TOPPASScene::isPipelineRunning
bool isPipelineRunning() const
Returns if a pipeline is currently running.
OpenMS::TOPPASTreeView
Tree view implementation for the list of TOPP tools.
Definition: TOPPASTreeView.h:54
OpenMS::TOPPASVertex::getTopoNr
UInt getTopoNr() const
Returns the topological sort number.
TOPPASToolVertex.h
OpenMS::TOPPASScene::saveIfChanged
bool saveIfChanged()
Saves the pipeline if it has been changed since the last save.
OpenMS::TOPPASBase::webview_
QWebView * webview_
OpenMS homepage workflow browser.
Definition: TOPPASBase.h:227
OpenMS::EnhancedWorkspace::getWidget
EnhancedTabBarWidgetInterface * getWidget(int id) const
OpenMS::RecentFilesMenu
Manages recent files opened by the user and provides a QMenu to go with it.
Definition: RecentFilesMenu.h:59
OpenMS::RecentFilesMenu::recentFileClicked
void recentFileClicked(const String &filename)
when a recent file action item from the getMenu() was clicked
OpenMS::StopWatch::getClockTime
double getClockTime() const
OpenMS::TOPPASBase::log_
LogWindow * log_
Log output window.
Definition: TOPPASBase.h:210
OpenMS::TOPPASScene::ST_REFRESH_NOCHANGE
no updates required
Definition: TOPPASScene.h:125
OpenMS::QApplicationTOPP::showAboutDialog
static void showAboutDialog(QWidget *parent, const QString &toolname)
Show the About-Dialog with License and Citation for all GUI tools.
Definition: QApplicationTOPP.cpp:131
OpenMS::TOPPASBase::toppasFileDownloaded_
void toppasFileDownloaded_(QNetworkReply *r)
triggered when download of .toppas file is finished, so we can store & open it
Definition: TOPPASBase.cpp:310
TOPPASResources.h
OpenMS::TOPPASBase::~TOPPASBase
~TOPPASBase() override
Destructor.
Definition: TOPPASBase.cpp:288
OpenMS::Logger::LogStream::insert
void insert(std::ostream &s)
OpenMS::TOPPASBase::sendClipboardContent
void sendClipboardContent()
Sends the clipboard content to the sender of the connected signal.
Definition: TOPPASBase.cpp:1430
OpenMS::TOPPASSplitterVertex
A special vertex that allows to split a list of inputs.
Definition: TOPPASSplitterVertex.h:53
TOPPASTreeView.h
OpenMS::Exception::UnableToCreateFile
Unable to create file exception.
Definition: Exception.h:636
OpenMS::Param::parseCommandLine
void parseCommandLine(const int argc, const char **argv, const std::string &prefix="")
Parses command line arguments.
OpenMS::TOPPASBase::loadPreferences
void loadPreferences(String filename="")
Loads the preferences from the filename given.
Definition: TOPPASBase.cpp:1009
OpenMS::TOPPASScene::setClipboard
void setClipboard(TOPPASScene *clipboard)
Sets the clipboard content.
OpenMS::TOPPASScene::topoSort
void topoSort(bool resort_all=true)
Performs a topological sort of all vertices.
OpenMS::StopWatch::start
void start()
Start the stop watch.
OPENMS_LOG_DEBUG
#define OPENMS_LOG_DEBUG
Macro for general debugging information.
Definition: LogStream.h:470
GUIHelpers.h
tool_name
const char * tool_name
Definition: TOPPAS.cpp:95
OpenMS::TOPPASToolVertex::isToolReady
bool isToolReady() const
underlying TOPP tool found and parameters fetched?! (done in C'Tor)
OpenMS::TOPPASWidget
Widget visualizing and allowing to edit TOPP pipelines.
Definition: TOPPASWidget.h:60
OpenMS::TOPPASResources
A dictionary mapping string keys to lists of TOPPASResource objects.
Definition: TOPPASResources.h:56
OpenMS::TOPPASBase::newPipeline
void newPipeline()
creates a new tab
Definition: TOPPASBase.cpp:622
OpenMS::Exception::BaseException
Exception base class.
Definition: Exception.h:89
OpenMS::TOPPASBase::network_manager_
QNetworkAccessManager * network_manager_
download .toppas files from homepage
Definition: TOPPASBase.h:229
OpenMS::Param::exists
bool exists(const std::string &key) const
Tests if a parameter is set (expecting its fully qualified name, e.g., TextExporter:1:proteins_only)
OpenMS::TOPPASResources::load
void load(const QString &file_name)
Loads the dictionary from file file_name.
OpenMS::StopWatch::stop
void stop()
Stop the stop watch (can be resumed later). If the stop watch was not running an exception is thrown.
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::TOPPASBase::runPipeline
void runPipeline()
Runs the pipeline of the current window.
Definition: TOPPASBase.cpp:1292
OpenMS::String::toQString
QString toQString() const
Conversion to Qt QString.
OpenMS::TOPPASBase::z_value_
static qreal z_value_
z-value counter for new inserted nodes (new nodes should be on top)
Definition: TOPPASBase.h:263
OpenMS::EnhancedTabBar::show
void show(int id)
Selects the tab with identifier id.
OpenMS::EnhancedTabBar
Convenience tab bar implementation.
Definition: EnhancedTabBar.h:60
OpenMS::VersionInfo::getVersion
static String getVersion()
Return the version number of OpenMS.
OpenMS::EnhancedTabBarWidgetInterface::getWindowId
Int getWindowId() const
get the EnhancedTabBar unique window id
OpenMS::TOPPASBase::openOnlinePipelineRepository
void openOnlinePipelineRepository()
opens the OpenMS Homepage to download example workflows
Definition: TOPPASBase.cpp:398
OpenMS::TOPPASScene::setDescription
void setDescription(const QString &desc)
when description is updated by user, use this to update the description for later storage in file
OpenMS::TOPPASScene::connectToolVertexSignals
void connectToolVertexSignals(TOPPASToolVertex *ttv)
Connects the signals to slots.
OpenMS::TOPPASVertex
The base class of the different vertex classes.
Definition: TOPPASVertex.h:100
OpenMS::Logger::LogStream
Log Stream Class.
Definition: LogStream.h:311
QMainWindow
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::TOPPASBase::updateTabBar
void updateTabBar(QMdiSubWindow *w)
brings the tab corresponding to the active window in front
Definition: TOPPASBase.cpp:996
OpenMS::StopWatch
This class is used to determine the current process' CPU (user and/or kernel) and wall time.
Definition: StopWatch.h:65
OpenMS::TOPPASWidget::getScene
TOPPASScene * getScene()
Returns the scene.
OpenMS::TOPPASMergerVertex
A special vertex that allows to merge several inputs.
Definition: TOPPASMergerVertex.h:58
OpenMS::TOPPASBase::closeFile
void closeFile()
closes the active window
Definition: TOPPASBase.cpp:963
OpenMS::ParamValue::toString
std::string toString(bool full_precision=true) const
Convert ParamValue to string.
OpenMS::TOPPASBase::focusByTab
void focusByTab(int id)
Raises the window corresponding to the data of the tab with identifier id.
Definition: TOPPASBase.cpp:944
OpenMS::TOPPASBase::preferencesDialog
void preferencesDialog()
shows the preferences dialog
Definition: TOPPASBase.cpp:832
main
int main(int argc, const char **argv)
Definition: TOPPAS.cpp:116
OpenMS::TOPPASBase::downloadTOPPASfromHomepage_
void downloadTOPPASfromHomepage_(const QUrl &url)
triggered when user clicks a link - if it ends in .TOPPAS we're done
Definition: TOPPASBase.cpp:370
OpenMS::TOPPASScene::updateEdgeColors
void updateEdgeColors()
Updates all edge colors (color of green and yellow edges can change when edges are added/removed)
OpenMS::TOPPASBase::loadFiles
void loadFiles(const std::vector< String > &list, QSplashScreen *splash_screen)
loads the files and updates the splash screen
Definition: TOPPASBase.cpp:517
OpenMS::ToolHandler::getTypes
static StringList getTypes(const String &toolname)
get all types of a tool (empty if none)
OpenMS::ToolListType
std::map< String, Internal::ToolDescription > ToolListType
Handles lists of TOPP and UTILS tools and their categories (for TOPPAS)
Definition: ToolHandler.h:74
OpenMS::OpenMS_Log_error
Logger::LogStream OpenMS_Log_error
Global static instance of a LogStream to capture messages classified as errors. By default it is boun...
OpenMS::Param::removeAll
void removeAll(const std::string &prefix)
Remove all entries that start with prefix.
OpenMS::EnhancedTabBarWidgetInterface::getFirstWindowID
static Int getFirstWindowID()
the first object to be created will get this ID
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::OpenMS_Log_debug
Logger::LogStream OpenMS_Log_debug
Global static instance of a LogStream to capture messages classified as debug output....
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::TOPPASScene::addVertex
void addVertex(TOPPASVertex *tv)
Adds a vertex.
OpenMS::TOPPASBase::toolCrashed
void toolCrashed()
Called when a tool crashes.
Definition: TOPPASBase.cpp:1347
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::TOPPASBase::clipboard_scene_
TOPPASScene * clipboard_scene_
The clipboard.
Definition: TOPPASBase.h:275
OpenMS::EnhancedTabBarWidgetInterface::addToTabBar
void addToTabBar(EnhancedTabBar *const parent, const String &caption, const bool make_active_tab=true)
OpenMS::TOPPASBase::tools_tree_view_
QTreeWidget * tools_tree_view_
Tree view of all available TOPP tools.
Definition: TOPPASBase.h:237
TOPPASBase.h
OpenMS::TOPPASBase::TOPPASreadyRead
void TOPPASreadyRead()
debug...
Definition: TOPPASBase.cpp:362
OpenMS::TOPPASBase::showStatusMessage
void showStatusMessage(std::string msg, OpenMS::UInt time)
Shows a status message in the status bar.
Definition: TOPPASBase.cpp:972
OpenMS::TOPPASBase::toolStarted
void toolStarted()
Called when a tool is started.
Definition: TOPPASBase.cpp:1311
print_usage
void print_usage(Logger::LogStream &stream=OpenMS_Log_info)
Definition: TOPPAS.cpp:101
OpenMS::File::getOpenMSDataPath
static String getOpenMSDataPath()
Returns the OpenMS data path (environment variable overwrites the default installation path)
OpenMS::TOPPASOutputFileListVertex
A vertex representing an output file list.
Definition: TOPPASOutputFileListVertex.h:49
OpenMS::OpenMS_Log_info
Logger::LogStream OpenMS_Log_info
Global static instance of a LogStream to capture messages classified as information....
tool_name
const char * tool_name
Definition: SwathWizard.cpp:145
OpenMS::TOPPASBase::insertNewVertex_
void insertNewVertex_(double x, double y, QTreeWidgetItem *item=nullptr)
Inserts a new TOPP tool in the current window at (x,y)
Definition: TOPPASBase.cpp:1205
OpenMS::TOPPASBase::network_reply_
QNetworkReply * network_reply_
the content of the network request
Definition: TOPPASBase.h:231
OpenMS::DefaultParamHandler::defaults_
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!
Definition: DefaultParamHandler.h:173
OpenMS::TOPPASBase::savePipelineResourceFile
void savePipelineResourceFile()
shows a file dialog for selecting the resource file to write to
Definition: TOPPASBase.cpp:803
OpenMS::Exception::BaseException::getFile
const char * getFile() const noexcept
Returns the file where it occurred.
OpenMS::RecentFilesMenu::getMenu
QMenu * getMenu()
get a menu-pointer to an internal member which always contains the up-to-date recent items
OpenMS::TOPPASBase::openToppasFile
void openToppasFile(QString filename)
Opens a toppas file.
Definition: TOPPASBase.cpp:1532
OpenMS::DefaultParamHandler::defaultsToParam_
void defaultsToParam_()
Updates the parameters after the defaults have been set in the constructor.
OpenMS::TOPPASBase::keyPressEvent
void keyPressEvent(QKeyEvent *e) override
Definition: TOPPASBase.cpp:1173
TOPPASSplitterVertex.h
OpenMS::StringUtils::substitute
static String & substitute(String &this_s, char from, char to)
Definition: StringUtilsSimple.h:578
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::File::getTempDirectory
static String getTempDirectory()
QTreeWidget
OpenMS::TOPPASBase::activeSubWindow_
TOPPASWidget * activeSubWindow_() const
returns a pointer to the active TOPPASWidget (0 if none is active)
Definition: TOPPASBase.cpp:923
OpenMS::TOPPASScene::ST_REFRESH_REMAINSINVALID
pipeline was not valid before and is invalid afterwards
Definition: TOPPASScene.h:128
OpenMS::ParamXMLFile::store
void store(const String &filename, const Param &param) const
Write XML file.
OpenMS::TOPPASBase::refreshPipelineParameters
static QString refreshPipelineParameters(TOPPASWidget *tw, QString current_path)
Refreshes the TOPP tools parameters of the pipeline.
Definition: TOPPASBase.cpp:1450
TOPPASInputFileListVertex.h
OpenMS::TOPPASScene::connectVertexSignals
void connectVertexSignals(TOPPASVertex *tv)
Connects the signals to slots.
OpenMS::TOPPASBase::tool_bar_
QToolBar * tool_bar_
Definition: TOPPASBase.h:217
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::TOPPASScene::load
void load(const String &file)
Loads the pipeline from file.
TOPPASMergerVertex.h
QApplicationTOPP.h
OpenMS::File::removeDirRecursively
static bool removeDirRecursively(const String &dir_name)
Removes the subdirectories of the specified directory (absolute path). Returns true if successful.
OpenMS::Exception::FileEmpty
File is empty.
Definition: Exception.h:594
OpenMS::EnhancedTabBar::removeId
void removeId(int id)
Remove the tab with identifier id.
OpenMS::ParamXMLFile::load
void load(const String &filename, Param &param)
Read XML file.
OpenMS::TOPPASBase::tab_bar_
EnhancedTabBar * tab_bar_
Tab bar. The address of the corresponding window to a tab is stored as an int in tabData()
Definition: TOPPASBase.h:234
OpenMS::TOPPASBase::desc_
QTextEdit * desc_
Workflow Description window.
Definition: TOPPASBase.h:212
OpenMS::Param::getValue
const ParamValue & getValue(const std::string &key) const
Returns a value of a parameter.
OpenMS::DefaultParamHandler::subsections_
std::vector< String > subsections_
Container for registered subsections. This member should be filled in the constructor of derived clas...
Definition: DefaultParamHandler.h:180
OpenMS::TOPPASScene::getDescription
QString getDescription() const
workflow description (to be displayed in TOPPAS window)
OpenMS::TOPPASBase::savePipeline
void savePipeline()
saves the pipeline (determined by Qt's sender mechanism)
Definition: TOPPASBase.cpp:628
OpenMS::TOPPASBase::refreshParameters
void refreshParameters()
Refreshes the parameters of the TOPP tools of the current workflow and stores an updated workflow inc...
Definition: TOPPASBase.cpp:1439
OpenMS::Exception::FileNotReadable
File not readable exception.
Definition: Exception.h:523
OpenMS::Param::setValidStrings
void setValidStrings(const std::string &key, const std::vector< std::string > &strings)
Sets the valid strings for the parameter key.
OpenMS::TOPPASScene::setChanged
void setChanged(bool b)
Sets the changed flag.
OpenMS::TOPPASScene::ST_REFRESH_CHANGEINVALID
updating made pipeline invalid
Definition: TOPPASScene.h:127
File.h
OpenMS::LogWindow::setMaxLength
void setMaxLength(int max_length)
set max_length
TOPPBase.h
EnhancedWorkspace.h
OpenMS::RecentFilesMenu::getAsParam
Param getAsParam() const
Convert current file list to Param. Their names are just numbers, starting at "0"....
OpenMS::TOPPASResources::store
void store(const QString &file_name)
Writes the dictionary to file file_name.
OpenMS::TOPPASBase::toolFinished
void toolFinished()
Called when a tool is finished.
Definition: TOPPASBase.cpp:1329
OpenMS::DefaultParamHandler::param_
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:166
ToolHandler.h
OpenMS::TOPPASBase::abortPipeline
void abortPipeline()
Terminates the current pipeline.
Definition: TOPPASBase.cpp:1301
OpenMS::TOPPASBase::showPipelineFinishedLogMessage
void showPipelineFinishedLogMessage()
Called by the scene if the pipeline execution finishes successfully.
Definition: TOPPASBase.cpp:1403
TOPPASWidget.h
OpenMS::Exception::BaseException::getLine
int getLine() const noexcept
Returns the line number where it occurred.
OpenMS::EnhancedTabBar::setTabText
void setTabText(const QString &text)
sets the text of the current tab
EnhancedTabBar.h