OpenMS
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Main window of TOPPView tool. More...
#include <OpenMS/VISUAL/APPLICATIONS/TOPPViewBase.h>
Protected Member Functions | |
Recent files | |
void | addRecentFile_ (const String &filename) |
adds a Filename to the recent files More... | |
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 | |
dock widgets | |
QDockWidget * | layer_dock_widget_ |
QDockWidget * | views_dockwidget_ |
QDockWidget * | filter_dock_widget_ |
LayerListView * | layers_view_ |
Layer management widget. More... | |
DataSelectionTabs * | selection_view_ |
Filter widget | |
FilterList * | filter_list_ |
FileWatcher * | watcher_ = nullptr |
Watcher that tracks file changes (in order to update the data in the different views) More... | |
bool | watcher_msgbox_ = false |
Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again, if file changes again before the messagebox is closed) More... | |
bool | zoom_together_ = false |
Stores whether the individual windows should zoom together (be linked) or not. More... | |
LogWindow * | log_ |
Log output window. More... | |
TOOL_SCAN | scan_mode_ |
Determines TVToolDiscovery scans for tools and generates new params. More... | |
TVToolDiscovery | tool_scanner_ |
Scans for tools and generates a param for each. More... | |
VERBOSITY | verbosity_ |
Verbosity of TV. More... | |
Toolbar | |
QToolBar * | tool_bar_ |
QButtonGroup * | intensity_button_group_ |
QToolBar * | tool_bar_1d_ |
QButtonGroup * | draw_group_1d_ |
QToolBar * | tool_bar_2d_peak_ |
QToolBar * | tool_bar_2d_feat_ |
QToolBar * | tool_bar_2d_cons_ |
QToolBar * | tool_bar_2d_ident_ |
QAction * | dm_precursors_2d_ |
QAction * | dm_hull_2d_ |
QAction * | dm_hulls_2d_ |
QToolButton * | dm_label_2d_ |
QActionGroup * | group_label_2d_ |
QToolButton * | dm_unassigned_2d_ |
QActionGroup * | group_unassigned_2d_ |
QAction * | dm_elements_2d_ |
QAction * | projections_2d_ |
QAction * | dm_ident_2d_ |
EnhancedWorkspace | ws_ |
Main workspace. More... | |
QMdiSubWindow * | lastActiveSubwindow_ = nullptr |
EnhancedTabBar | tab_bar_ |
Tab bar. The address of the corresponding window to a tab is stored as an int in tabData() More... | |
RecentFilesMenu | recent_files_ |
manages recent list of filenames and the menu that goes with it More... | |
TOPPViewMenu | menu_ |
manages the menu items (active/inactive) and recent files etc More... | |
Status bar | |
QLabel * | message_label_ |
Label for messages in the status bar. More... | |
QLabel * | x_label_ |
x-axis label for messages in the status bar More... | |
QLabel * | y_label_ |
y-axis 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... | |
Friends | |
class | TestTOPPView |
Type definitions | |
enum class | TOOL_SCAN { SKIP_SCAN , SCAN_IF_NEWER_VERSION , FORCE_SCAN } |
Used for deciding whether new tool/util params should be generated or reused from TOPPView's ini file. More... | |
enum class | VERBOSITY { DEFAULT , VERBOSE } |
enum class | LOAD_RESULT { OK , FILE_NOT_FOUND , FILETYPE_UNKNOWN , FILETYPE_UNSUPPORTED , LOAD_ERROR } |
typedef LayerDataBase::FeatureMapType | FeatureMapType |
typedef LayerDataBase::FeatureMapSharedPtrType | FeatureMapSharedPtrType |
typedef LayerDataBase::ConsensusMapType | ConsensusMapType |
typedef LayerDataBase::ConsensusMapSharedPtrType | ConsensusMapSharedPtrType |
typedef LayerDataBase::ExperimentType | ExperimentType |
typedef LayerDataBase::ExperimentSharedPtrType | ExperimentSharedPtrType |
typedef LayerDataBase::ODExperimentSharedPtrType | ODExperimentSharedPtrType |
typedef ExperimentType::SpectrumType | SpectrumType |
Peak spectrum type. More... | |
TOPPViewBase (TOOL_SCAN scan_mode=TOOL_SCAN::SCAN_IF_NEWER_VERSION, VERBOSITY verbosity=VERBOSITY::DEFAULT, QWidget *parent=nullptr) | |
Constructor. More... | |
~TOPPViewBase () override | |
Destructor. More... | |
LOAD_RESULT | addDataFile (const String &filename, bool show_options, bool add_to_recent, String caption="", UInt window_id=0, Size spectrum_id=0) |
Opens and displays data from a file. More... | |
void | addData (const FeatureMapSharedPtrType &feature_map, const ConsensusMapSharedPtrType &consensus_map, std::vector< PeptideIdentification > &peptides, const ExperimentSharedPtrType &peak_map, const ODExperimentSharedPtrType &on_disc_peak_map, LayerDataBase::DataType data_type, bool show_as_1d, bool show_options, bool as_new_window=true, const String &filename="", const String &caption="", UInt window_id=0, Size spectrum_id=0) |
Adds a peak or feature map to the viewer. More... | |
void | loadFiles (const StringList &list, QSplashScreen *splash_screen) |
Opens all the files in the string list. 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... | |
Param | getCanvasParameters (UInt dim) const |
Returns the parameters for a PlotCanvas of dimension dim . More... | |
const LayerDataBase * | getCurrentLayer () const |
Returns the active Layer data (0 if no layer is active) More... | |
LayerDataBase * | getCurrentLayer () |
Returns the active Layer data (0 if no layer is active) More... | |
EnhancedWorkspace * | getWorkspace () |
returns a pointer to the EnhancedWorkspace containing PlotWidgets More... | |
PlotWidget * | getActivePlotWidget () const |
returns a pointer to the active PlotWidget (0 if none is active) More... | |
Plot1DWidget * | getActive1DWidget () const |
returns a pointer to the active Plot1DWidget (0 the active window is no Plot1DWidget or there is no active window) More... | |
Plot2DWidget * | getActive2DWidget () const |
returns a pointer to the active Plot2DWidget (0 the active window is no Plot2DWidget or there is no active window) More... | |
Plot3DWidget * | getActive3DWidget () const |
returns a pointer to the active Plot3DWidget (0 the active window is no Plot2DWidget or there is no active window) More... | |
PlotCanvas * | getActiveCanvas () const |
returns a pointer to the active PlotCanvas (0 if none is active) More... | |
void | showPlotWidgetInWindow (PlotWidget *sw) |
Opens the provided spectrum widget in a new window. More... | |
void | updateCurrentPath () |
changes the current path according to the currently active window/layer More... | |
void | openFilesByDialog (const String &initial_directory="") |
shows the file dialog for opening files (a starting directory, e.g. for the example files can be provided; otherwise, uses the current_path_) More... | |
void | showGoToDialog () const |
shows the DB dialog for opening files More... | |
void | preferencesDialog () |
shows the preferences dialog More... | |
void | layerStatistics () const |
Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data. More... | |
void | editMetadata () |
lets the user edit the meta data of a layer More... | |
void | layerActivated () |
gets called if a layer got activated More... | |
void | zoomOtherWindows () const |
gets called when a layer changes in zoom; will apply the same zoom to other windows (if linked) More... | |
void | linkZoom () |
link the zoom of individual windows More... | |
void | layerDeactivated () |
gets called if a layer got deactivated More... | |
void | closeTab () |
closes the active window More... | |
void | rerunTOPPTool () |
returns the last invoked TOPP tool with the same parameters More... | |
void | updateBarsAndMenus () |
calls update*Bar and updateMenu_() to make sure the interface matches the current data More... | |
void | updateToolBar () |
updates the toolbar More... | |
void | updateLayerBar () |
adapts the layer bar to the active window More... | |
void | updateViewBar () |
adapts view bar to the active window More... | |
void | updateMenu () |
activates/deactivates menu entries More... | |
void | updateFilterBar () |
adapts the filter bar to the active window More... | |
void | showStatusMessage (const std::string &msg, OpenMS::UInt time) |
Shows a status message in the status bar. More... | |
void | showCursorStatus (const String &x, const String &y) |
shows X/Y axis mouse values in the status bar More... | |
void | showTOPPDialog () |
Apply TOPP tool. More... | |
void | annotateWithAMS () |
Annotates current layer with ID data from AccurateMassSearch. More... | |
void | annotateWithID () |
Annotates current layer with ID data. More... | |
void | annotateWithOSW () |
Annotates current chromatogram layer with ID data. More... | |
void | showSpectrumGenerationDialog () |
Shows the theoretical spectrum generation dialog. More... | |
void | showSpectrumAlignmentDialog () |
Shows the spectrum alignment dialog. More... | |
void | showCurrentPeaksAs2D () |
Shows the current peak data of the active layer in 2D. More... | |
void | showCurrentPeaksAs3D () |
Shows the current peak data of the active layer in 3D. More... | |
void | showCurrentPeaksAsIonMobility (const MSSpectrum &spec) |
Shows the current peak data of the active layer as ion mobility. More... | |
void | showCurrentPeaksAsDIA (const Precursor &pc, const MSExperiment &exp) |
Shows the current peak data of the active layer as DIA data. More... | |
void | saveLayerAll () const |
Saves the whole current layer data. More... | |
void | saveLayerVisible () const |
Saves the visible layer data. More... | |
void | toggleGridLines () const |
Toggles the grid lines. More... | |
void | toggleAxisLegends () const |
Toggles the axis legends. More... | |
void | toggleInterestingMZs () const |
Toggles drawing of interesting MZs. More... | |
void | showPreferences () const |
Shows current layer preferences. More... | |
void | metadataFileDialog () |
dialog for inspecting database meta data More... | |
TOPP tool execution | |
struct { | |
Param | param |
String | tool |
String | in |
String | out |
String | file_name |
String | file_name_in |
String | file_name_out |
String | layer_name |
UInt | window_id |
Size | spectrum_id |
QProcess * | process = nullptr |
QElapsedTimer | timer |
bool | visible_area_only |
} | topp_ |
Information needed for execution of TOPP tools. More... | |
void | runTOPPTool_ () |
Runs the TOPP tool according to the information in topp_. More... | |
void | checkPreferences_ () |
check if all available preferences get set by the .ini file. If there are some missing entries fill them with default values. More... | |
reimplemented Qt events | |
QMenu * | add_2d_context_ |
Additional context menu for 2D layers. More... | |
String | current_path_ |
static const String | CAPTION_3D_SUFFIX_ |
Suffix appended to caption of tabs when layer is shown in 3D. More... | |
TheoreticalSpectrumGenerationDialog | spec_gen_dialog_ |
This dialog is a member so that its settings can be perserved upon closing. More... | |
void | closeEvent (QCloseEvent *event) override |
void | showTOPPDialog_ (bool visible) |
Apply TOPP tool. If visible is true, only the visible data is used, otherwise the whole layer is used. More... | |
Toolbar slots | |
void | setDrawMode1D (int) const |
void | setIntensityMode (int) |
void | changeLayerFlag (bool) |
void | changeLabel (QAction *) |
void | changeUnassigned (QAction *) |
void | resetZoom () const |
void | toggleProjections () |
void | openFile (const String &filename) |
void | layerFilterVisibilityChange (bool) const |
Enables/disables the data filters for the current layer. More... | |
void | showSpectrumMetaData (int spectrum_index) const |
shows a spectrum's metadata with index spectrum_index from the currently active canvas More... | |
void | finishTOPPToolExecution (int exitCode, QProcess::ExitStatus exitStatus) |
slot for the finished signal of the TOPP tools execution More... | |
void | abortTOPPTool () |
aborts the execution of a TOPP tool More... | |
void | showSpectrumBrowser () |
shows the spectrum browser and updates it More... | |
Tabbar slots | |
void | closeByTab (int id) |
Closes the window corresponding to the data of the tab with identifier id . More... | |
void | showWindow (int id) |
Raises the window corresponding to the data of the tab with identifier id . More... | |
void | copyLayer (const QMimeData *data, QWidget *source, int id=-1) |
Slot for drag-and-drop of layer manager to tabbar. More... | |
void | updateProcessLog () |
Appends process output to log window. More... | |
void | fileChanged_ (const String &) |
Called if a data file has been externally changed. More... | |
void | initializeDefaultParameters_ () |
Initializes the default parameters on TOPPView construction. More... | |
QStringList | chooseFilesDialog_ (const String &path_overwrite="") |
Shows a dialog where the user can select files. More... | |
Additional Inherited Members | |
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... | |
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 inherited from DefaultParamHandler | |
static void | writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="") |
Writes all parameters to meta values. More... | |
Main window of TOPPView tool.
Uses the default QMainWindow layout (see Qt documentation) with a central widget in the middle (consistent of a EnhancedTabBar and an EnhancedWorkspace) and multiple docked widgets around it (to the right and below) and multiple tool bars. On top and bottom are a menu bar and a status bar.
The main layout is using
The views_dockwidget_ internally holds a tab widget views_tabwidget_ which holds the two different views on the data (spectra and identification view) which are implemented using idview_behaviour_ and spectraview_behavior_.
Peak spectrum type.
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Used for deciding whether new tool/util params should be generated or reused from TOPPView's ini file.
Enumerator | |
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SKIP_SCAN | TVToolDiscovery does not generate params for each tool/util unless they are absolutely needed and could not be extracted from TOPPView's ini file. This may be useful for testing. |
SCAN_IF_NEWER_VERSION | Only generate params for each tool/util if TOPPView's last ini file has an older version. (Default behaviour) |
FORCE_SCAN | Forces TVToolDiscovery to generate params and using them instead of the params in TOPPView's ini file. |
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Constructor.
References EnhancedTabBar::addTab(), TOPPViewMenu::addWindowToggle(), TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::closeByTab(), EnhancedTabBar::closeRequested(), CONNECTCAST, TOPPViewBase::copyLayer(), TOPPViewBase::current_path_, EnhancedTabBar::currentIdChanged(), DefaultParamHandler::defaultsToParam_(), Plot1DCanvas::DM_CONNECTEDLINES, TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_label_2d_, Plot1DCanvas::DM_PEAKS, TOPPViewBase::dm_precursors_2d_, TOPPViewBase::dm_unassigned_2d_, TOPPViewBase::draw_group_1d_, EnhancedTabBar::dropOnTab(), EnhancedTabBar::dropOnWidget(), EnhancedWorkspace::dropReceived(), FileWatcher::fileChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::filter_list_, FilterList::filterChanged(), TOPPViewBase::getActiveCanvas(), Param::getValue(), TOPPViewBase::group_label_2d_, TOPPViewBase::group_unassigned_2d_, PlotCanvas::IM_LOG, PlotCanvas::IM_NONE, PlotCanvas::IM_PERCENTAGE, PlotCanvas::IM_SNAP, TOPPViewBase::initializeDefaultParameters_(), TOPPViewBase::intensity_button_group_, TOPPViewBase::lastActiveSubwindow_, TOPPViewBase::layer_dock_widget_, LayerListView::layerDataChanged(), TOPPViewBase::layers_view_, TOPPViewBase::loadPreferences(), TOPPViewBase::log_, TOPPViewBase::menu_, TOPPViewBase::message_label_, LayerDataDefs::NamesOfLabelType, TOPPViewBase::openFile(), DefaultParamHandler::param_, TOPPViewBase::projections_2d_, TOPPViewBase::recent_files_, RecentFilesMenu::recentFileClicked(), EnhancedTabBar::removeId(), TOPPViewBase::resetZoom(), TOPPViewBase::selection_view_, TOPPViewBase::setDrawMode1D(), PlotCanvas::setFilters(), TOPPViewBase::setIntensityMode(), TVToolDiscovery::setPluginPath(), TVToolDiscovery::setVerbose(), TOPPViewBase::showWindow(), LayerDataDefs::SIZE_OF_LABEL_TYPE, TOPPViewBase::tab_bar_, TOPPViewBase::toggleProjections(), TOPPViewBase::tool_bar_, TOPPViewBase::tool_bar_1d_, TOPPViewBase::tool_bar_2d_cons_, TOPPViewBase::tool_bar_2d_feat_, TOPPViewBase::tool_bar_2d_ident_, TOPPViewBase::tool_bar_2d_peak_, TOPPViewBase::tool_scanner_, ParamValue::toString(), TOPPViewBase::updateBarsAndMenus(), TOPPViewBase::updateMenu(), OpenMS::user_section, TOPPViewBase::VERBOSE, TOPPViewBase::verbosity_, TOPPViewBase::views_dockwidget_, TOPPViewBase::watcher_, TOPPViewBase::ws_, TOPPViewBase::x_label_, and TOPPViewBase::y_label_.
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Destructor.
References TOPPViewBase::abortTOPPTool(), and TOPPViewBase::savePreferences().
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protectedslot |
aborts the execution of a TOPP tool
References LogWindow::addNewline(), TOPPViewBase::log_, TOPPViewBase::topp_, and TOPPViewBase::updateMenu().
Referenced by TOPPViewBase::~TOPPViewBase().
void addData | ( | const FeatureMapSharedPtrType & | feature_map, |
const ConsensusMapSharedPtrType & | consensus_map, | ||
std::vector< PeptideIdentification > & | peptides, | ||
const ExperimentSharedPtrType & | peak_map, | ||
const ODExperimentSharedPtrType & | on_disc_peak_map, | ||
LayerDataBase::DataType | data_type, | ||
bool | show_as_1d, | ||
bool | show_options, | ||
bool | as_new_window = true , |
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const String & | filename = "" , |
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const String & | caption = "" , |
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UInt | window_id = 0 , |
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Size | spectrum_id = 0 |
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) |
Adds a peak or feature map to the viewer.
feature_map | The feature data (empty if not feature data) |
consensus_map | The consensus feature data (empty if not consensus feature data) |
peptides | The peptide identifications (empty if not ID data) |
peak_map | The peak data (empty if not peak data) |
on_disc_peak_map | The peak data managed on disc (empty if not peak data) |
data_type | Type of the data |
show_as_1d | Force dataset to be opened in 1D mode (even if it contains several spectra) |
show_options | If the options dialog should be shown (otherwise the defaults are used) |
as_new_window | Open the layer in a new window within TOPPView (ignored if 'window_id' is set) |
filename | source file name (if the data came from a file) |
caption | Sets the layer name and window caption of the data. If unset the file name is used. If set, the file is not monitored for changes. |
window_id | in which window the file is opened if opened as a new layer (0 will open a new window). |
spectrum_id | determines the spectrum to show in 1D view. |
References Plot1DCanvas::activateSpectrum(), PlotCanvas::addChromLayer(), PlotCanvas::addLayer(), PlotCanvas::addPeakLayer(), PlotWidget::canvas(), Plot1DWidget::canvas(), TOPPViewOpenDialog::disableCutoff(), TOPPViewOpenDialog::disableDimension(), TOPPViewOpenDialog::disableLocation(), LayerDataDefs::DT_CHROMATOGRAM, LayerDataDefs::DT_CONSENSUS, LayerDataDefs::DT_FEATURE, LayerDataDefs::DT_IDENT, LayerDataDefs::DT_PEAK, TOPPViewBase::getActivePlotWidget(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getLayer(), PlotCanvas::getLayerCount(), PlotCanvas::getLayerName(), TOPPViewOpenDialog::getMergeLayer(), LayerDataBase::getName(), Param::getValue(), EnhancedWorkspace::getWidget(), TOPPViewOpenDialog::isCutoffEnabled(), TOPPViewOpenDialog::isDataDIA(), Plot2DCanvas::mergeIntoLayer(), TOPPViewOpenDialog::openAsNewWindow(), DefaultParamHandler::param_, PlotCanvas::setLayerName(), TOPPViewOpenDialog::setMergeLayers(), TOPPViewBase::showPlotWidgetInWindow(), LayerDataBase::type, OpenMS::user_section, TOPPViewOpenDialog::viewMapAs1D(), TOPPViewOpenDialog::viewMapAs2D(), TOPPViewBase::ws_, and OpenMS::Y.
Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::copyLayer(), and TOPPViewBase::showSpectrumGenerationDialog().
TOPPViewBase::LOAD_RESULT addDataFile | ( | const String & | filename, |
bool | show_options, | ||
bool | add_to_recent, | ||
String | caption = "" , |
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UInt | window_id = 0 , |
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Size | spectrum_id = 0 |
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) |
Opens and displays data from a file.
Loads the data and adds it to the application by calling addData_()
filename | The file to open |
show_options | If the options dialog should be shown (otherwise the defaults are used) |
caption | Sets the layer name and window caption of the data. If unset the file name is used. |
add_to_recent | If the file should be added to the recent files after opening |
window_id | in which window the file is opened if opened as a new layer (0 or default equals current window). |
spectrum_id | determines the spectrum to show in 1D view. |
References File::absolutePath(), TOPPViewBase::addData(), FileWatcher::addFile(), TOPPViewBase::addRecentFile_(), LogWindow::appendNewHeader(), File::basename(), FileTypes::CONSENSUSXML, FileTypeList::contains(), LayerDataDefs::DT_CHROMATOGRAM, LayerDataDefs::DT_CONSENSUS, LayerDataDefs::DT_FEATURE, LayerDataDefs::DT_IDENT, LayerDataDefs::DT_PEAK, LayerDataDefs::DT_UNKNOWN, File::exists(), FileTypes::FEATUREXML, TOPPViewBase::FILE_NOT_FOUND, TOPPViewBase::FILETYPE_UNKNOWN, TOPPViewBase::FILETYPE_UNSUPPORTED, TOPPViewBase::getActivePlotWidget(), TOPPViewBase::getCurrentLayer(), IndexedMzMLHandler::getNrChromatograms(), IndexedMzMLHandler::getNrSpectra(), IndexedMzMLHandler::getParsingSuccess(), FileHandler::getType(), Param::getValue(), EnhancedTabBarWidgetInterface::getWindowId(), ProgressLogger::GUI, FileTypes::IDXML, OpenMS::Constants::k, TOPPViewBase::LOAD_ERROR, FileHandler::loadConsensusFeatures(), FileHandler::loadExperiment(), FileHandler::loadFeatures(), FileHandler::loadIdentifications(), TOPPViewBase::log_, FileTypes::MZIDENTML, FileTypes::MZML, TOPPViewBase::OK, IndexedMzMLHandler::openFile(), OPENMS_LOG_INFO, OPENMS_LOG_WARN, DefaultParamHandler::param_, FileHandler::stripExtension(), OpenMS::supported_types, FileHandler::swapExtension(), OpenMS::StringUtils::toQString(), FileTypes::typeToName(), FileTypes::UNKNOWN, GUILock::unlock(), OpenMS::user_section, and TOPPViewBase::watcher_.
Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::loadFiles(), TOPPViewBase::openFile(), and TOPPViewBase::openFilesByDialog().
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adds a Filename to the recent files
References RecentFilesMenu::add(), and TOPPViewBase::recent_files_.
Referenced by TOPPViewBase::addDataFile().
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Annotates current layer with ID data from AccurateMassSearch.
References LayerAnnotatorBase::annotateWithFileDialog(), TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), and TOPPViewBase::log_.
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Annotates current layer with ID data.
References LayerAnnotatorBase::annotateWithFileDialog(), TOPPViewBase::current_path_, DataSelectionTabs::currentTabChanged(), TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), DataSelectionTabs::IDENT_IDX, TOPPViewBase::log_, and TOPPViewBase::selection_view_.
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Annotates current chromatogram layer with ID data.
References LayerAnnotatorBase::annotateWithFileDialog(), TOPPViewBase::current_path_, DataSelectionTabs::currentTabChanged(), DataSelectionTabs::DIAOSW_IDX, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), TOPPViewBase::log_, and TOPPViewBase::selection_view_.
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References Plot2DWidget::canvas(), TOPPViewBase::dm_label_2d_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::getCurrentLayer(), LayerDataDefs::L_INDEX, LayerDataDefs::L_NONE, LayerDataDefs::NamesOfLabelType, PlotCanvas::setLabel(), LayerDataDefs::SIZE_OF_LABEL_TYPE, and TOPPViewBase::updateToolBar().
Referenced by TOPPViewBase::TOPPViewBase().
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References LayerDataDefs::C_ELEMENTS, TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_precursors_2d_, LayerDataDefs::F_HULL, LayerDataDefs::F_HULLS, TOPPViewBase::getActive2DWidget(), LayerDataDefs::I_PEPTIDEMZ, and LayerDataDefs::P_PRECURSORS.
Referenced by TOPPViewBase::TOPPViewBase().
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References Plot2DWidget::canvas(), TOPPViewBase::dm_unassigned_2d_, LayerDataDefs::F_UNASSIGNED, TOPPViewBase::getActive2DWidget(), PlotCanvas::getLayerFlag(), LayerDataDefs::I_LABELS, LayerDataDefs::I_PEPTIDEMZ, PlotCanvas::setLayerFlag(), and TOPPViewBase::updateToolBar().
Referenced by TOPPViewBase::TOPPViewBase().
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check if all available preferences get set by the .ini file. If there are some missing entries fill them with default values.
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Shows a dialog where the user can select files.
References OpenMS::BOTH, TOPPViewBase::current_path_, OpenMS::supported_types, FileTypeList::toFileDialogFilter(), and String::toQString().
Referenced by TOPPViewBase::metadataFileDialog(), and TOPPViewBase::openFilesByDialog().
|
protectedslot |
Closes the window corresponding to the data of the tab with identifier id
.
References EnhancedWorkspace::getWidget(), TOPPViewBase::updateBarsAndMenus(), and TOPPViewBase::ws_.
Referenced by TOPPViewBase::TOPPViewBase().
|
overrideprotected |
References TOPPViewBase::ws_.
|
slot |
closes the active window
References TOPPViewBase::ws_.
|
protectedslot |
Slot for drag-and-drop of layer manager to tabbar.
References TOPPViewBase::addData(), TOPPViewBase::addDataFile(), LogWindow::appendNewHeader(), LayerDataBase::filename, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), LayerDataBase::getName(), SpectraTreeTab::getSelectedScan(), TOPPViewBase::layers_view_, TOPPViewBase::log_, and LayerDataBase::type.
Referenced by TOPPViewBase::showPlotWidgetInWindow(), and TOPPViewBase::TOPPViewBase().
|
slot |
lets the user edit the meta data of a layer
References LogWindow::appendNewHeader(), TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), TOPPViewBase::log_, PlotCanvas::showMetaData(), and LayerDataBase::visible.
|
protectedslot |
Called if a data file has been externally changed.
References FileWatcher::addFile(), PlotWidget::canvas(), LayerDataBase::filename, PlotCanvas::getLayer(), PlotCanvas::getLayerCount(), Param::getValue(), TOPPViewBase::layerActivated(), FileHandler::loadConsensusFeatures(), FileHandler::loadExperiment(), FileHandler::loadFeatures(), ProgressLogger::NONE, DefaultParamHandler::param_, FileWatcher::removeFile(), String::toQString(), OpenMS::StringUtils::toQString(), PlotCanvas::updateLayer(), OpenMS::user_section, TOPPViewBase::watcher_, TOPPViewBase::watcher_msgbox_, and TOPPViewBase::ws_.
Referenced by TOPPViewBase::TOPPViewBase().
|
protectedslot |
slot for the finished signal of the TOPP tools execution
References TOPPViewBase::addDataFile(), LogWindow::addNewline(), LogWindow::appendNewHeader(), File::getTempDirectory(), Param::getValue(), TOPPViewBase::log_, DefaultParamHandler::param_, File::readable(), File::remove(), TOPPViewBase::topp_, OpenMS::StringUtils::toQString(), and TOPPViewBase::updateMenu().
Referenced by TOPPViewBase::runTOPPTool_().
Plot1DWidget * getActive1DWidget | ( | ) | const |
returns a pointer to the active Plot1DWidget (0 the active window is no Plot1DWidget or there is no active window)
References TOPPViewBase::getActivePlotWidget().
Referenced by TOPPViewBase::setDrawMode1D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::toggleInterestingMZs(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateToolBar().
Plot2DWidget * getActive2DWidget | ( | ) | const |
returns a pointer to the active Plot2DWidget (0 the active window is no Plot2DWidget or there is no active window)
References TOPPViewBase::getActivePlotWidget().
Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::loadFiles(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::toggleProjections(), and TOPPViewBase::updateToolBar().
Plot3DWidget * getActive3DWidget | ( | ) | const |
returns a pointer to the active Plot3DWidget (0 the active window is no Plot2DWidget or there is no active window)
References TOPPViewBase::getActivePlotWidget().
Referenced by TOPPViewBase::loadFiles(), and TOPPViewBase::updateToolBar().
PlotCanvas * getActiveCanvas | ( | ) | const |
returns a pointer to the active PlotCanvas (0 if none is active)
References PlotWidget::canvas(), and TOPPViewBase::getActivePlotWidget().
Referenced by TOPPViewBase::annotateWithAMS(), TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::getCurrentLayer(), TOPPViewBase::layerFilterVisibilityChange(), TOPPViewBase::loadFiles(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::saveLayerAll(), TOPPViewBase::saveLayerVisible(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showPreferences(), TOPPViewBase::showSpectrumMetaData(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::toggleGridLines(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), and TOPPViewBase::updateMenu().
PlotWidget * getActivePlotWidget | ( | ) | const |
returns a pointer to the active PlotWidget (0 if none is active)
References TOPPViewBase::tab_bar_, and TOPPViewBase::ws_.
Referenced by TOPPViewBase::addData(), TOPPViewBase::addDataFile(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::layerStatistics(), TOPPViewBase::loadFiles(), TOPPViewBase::resetZoom(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::setIntensityMode(), TOPPViewBase::showGoToDialog(), TOPPViewBase::toggleAxisLegends(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateToolBar(), and TOPPViewBase::zoomOtherWindows().
Returns the parameters for a PlotCanvas of dimension dim
.
References Param::copy(), Param::getValue(), DefaultParamHandler::param_, Param::setValue(), ParamValue::toString(), and OpenMS::user_section.
Referenced by TOPPViewBase::addData(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().
LayerDataBase * getCurrentLayer | ( | ) |
Returns the active Layer data (0 if no layer is active)
References TOPPViewBase::getActiveCanvas(), and PlotCanvas::getCurrentLayer().
const LayerDataBase * getCurrentLayer | ( | ) | const |
Returns the active Layer data (0 if no layer is active)
References TOPPViewBase::getActiveCanvas(), and PlotCanvas::getCurrentLayer().
Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::changeLabel(), TOPPViewBase::loadFiles(), TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), and TOPPViewBase::updateMenu().
EnhancedWorkspace * getWorkspace | ( | ) |
returns a pointer to the EnhancedWorkspace containing PlotWidgets
References TOPPViewBase::ws_.
|
protected |
Initializes the default parameters on TOPPView construction.
References DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), DefaultParamHandler::getDefaults(), File::getUserDirectory(), Param::insert(), Param::setSectionDescription(), Param::setValidStrings(), Param::setValue(), DefaultParamHandler::subsections_, and OpenMS::user_section.
Referenced by TOPPViewBase::TOPPViewBase().
|
slot |
gets called if a layer got activated
References TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateToolBar(), and TOPPViewBase::updateViewBar().
Referenced by TOPPViewBase::fileChanged_(), TOPPViewBase::showPlotWidgetInWindow(), and TOPPViewBase::updateBarsAndMenus().
|
slot |
gets called if a layer got deactivated
|
slot |
Enables/disables the data filters for the current layer.
References PlotCanvas::changeLayerFilterState(), and TOPPViewBase::getActiveCanvas().
|
slot |
Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data.
References TOPPViewBase::getActivePlotWidget(), and PlotWidget::showStatistics().
|
slot |
link the zoom of individual windows
References TOPPViewBase::zoom_together_.
void loadFiles | ( | const StringList & | list, |
QSplashScreen * | splash_screen | ||
) |
Opens all the files in the string list.
References TOPPViewBase::addDataFile(), LogWindow::appendNewHeader(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActivePlotWidget(), LayerAnnotatorBase::getAnnotatorWhichSupports(), TOPPViewBase::getCurrentLayer(), PlotCanvas::getCurrentLayer(), OpenMS::Helpers::indexOf(), TOPPViewBase::log_, LayerDataBase::param, PlotCanvas::setCurrentLayerParameters(), Param::setValue(), and OpenMS::StringUtils::toQString().
Referenced by main().
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 Param::copy(), Param::exists(), File::exists(), TOPPViewBase::FORCE_SCAN, File::getUserDirectory(), Param::getValue(), VersionInfo::getVersion(), Param::hasSection(), Param::insert(), ParamXMLFile::load(), TVToolDiscovery::loadToolParams(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, TOPPViewBase::scan_mode_, RecentFilesMenu::setFromParam(), DefaultParamHandler::setParameters(), TVToolDiscovery::setPluginPath(), Param::setValue(), TOPPViewBase::SKIP_SCAN, TOPPViewBase::tool_scanner_, ParamValue::toString(), and OpenMS::user_section.
Referenced by main(), and TOPPViewBase::TOPPViewBase().
|
slot |
dialog for inspecting database meta data
References MetaDataBrowser::add(), TOPPViewBase::chooseFilesDialog_(), FileHandler::getOptions(), and PeakFileOptions::setMetadataOnly().
|
slot |
list of the recently opened files called when RecentFileMenu items is clicked
References TOPPViewBase::addDataFile().
Referenced by main(), and TOPPViewBase::TOPPViewBase().
|
slot |
shows the file dialog for opening files (a starting directory, e.g. for the example files can be provided; otherwise, uses the current_path_)
References TOPPViewBase::addDataFile(), and TOPPViewBase::chooseFilesDialog_().
|
slot |
shows the preferences dialog
References Param::copy(), TOPPViewPrefDialog::getParam(), Param::insert(), DefaultParamHandler::param_, Param::remove(), TOPPViewBase::savePreferences(), TOPPViewPrefDialog::setParam(), and OpenMS::user_section.
|
slot |
returns the last invoked TOPP tool with the same parameters
References LogWindow::appendNewHeader(), TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), TOPPViewBase::log_, TOPPViewBase::runTOPPTool_(), TOPPViewBase::topp_, and LayerDataBase::visible.
|
slot |
References PlotWidget::canvas(), TOPPViewBase::getActivePlotWidget(), and PlotCanvas::resetZoom().
Referenced by TOPPViewBase::TOPPViewBase().
|
protected |
Runs the TOPP tool according to the information in topp_.
References LogWindow::appendNewHeader(), CONNECTCAST, LayerDataBase::filters, TVToolDiscovery::findPluginExecutable(), File::findSiblingTOPPExecutable(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActivePlotWidget(), PlotCanvas::getCurrentLayer(), LayerDataBase::getName(), EnhancedTabBarWidgetInterface::getWindowId(), ProgressLogger::GUI, TOPPViewBase::log_, File::remove(), LayerDataBase::storeFullData(), LayerDataBase::storeVisibleData(), TOPPViewBase::tool_scanner_, TOPPViewBase::topp_, String::toQString(), OpenMS::StringUtils::toQString(), TOPPViewBase::updateMenu(), TOPPViewBase::updateProcessLog(), and File::writable().
Referenced by TOPPViewBase::rerunTOPPTool(), and TOPPViewBase::showTOPPDialog_().
|
slot |
Saves the whole current layer data.
References TOPPViewBase::getActiveCanvas(), and PlotCanvas::saveCurrentLayer().
|
slot |
Saves the visible layer data.
References TOPPViewBase::getActiveCanvas(), and PlotCanvas::saveCurrentLayer().
void savePreferences | ( | ) |
Stores the preferences (used when this window is closed)
References Param::copy(), RecentFilesMenu::getAsParam(), TVToolDiscovery::getPluginPath(), TVToolDiscovery::getToolParams(), Param::getValue(), VersionInfo::getVersion(), Param::hasSection(), Param::insert(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, Param::removeAll(), TOPPViewBase::scan_mode_, TVToolDiscovery::setPluginPath(), Param::setValue(), TOPPViewBase::SKIP_SCAN, ParamXMLFile::store(), TOPPViewBase::tool_scanner_, ParamValue::toString(), OpenMS::user_section, and TVToolDiscovery::waitForToolParams().
Referenced by TOPPViewBase::preferencesDialog(), and TOPPViewBase::~TOPPViewBase().
|
slot |
References Plot1DWidget::canvas(), TOPPViewBase::getActive1DWidget(), and Plot1DCanvas::setDrawMode().
Referenced by TOPPViewBase::showSpectrumGenerationDialog(), and TOPPViewBase::TOPPViewBase().
|
slot |
References TOPPViewBase::getActivePlotWidget(), TOPPViewBase::intensity_button_group_, and PlotWidget::setIntensityMode().
Referenced by TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::TOPPViewBase().
|
slot |
Shows the current peak data of the active layer in 2D.
References PlotCanvas::addPeakLayer(), Plot2DWidget::canvas(), LayerDataBase::filename, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getCurrentLayer(), LayerDataPeak::getPeakDataMuteable(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.
Referenced by TOPPViewBase::showPlotWidgetInWindow().
|
slot |
Shows the current peak data of the active layer in 3D.
References PlotCanvas::addPeakLayer(), LogWindow::appendNewHeader(), Plot3DWidget::canvas(), LayerDataDefs::DT_PEAK, LayerDataBase::filename, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getCurrentLayerIndex(), PlotCanvas::getLayer(), PlotCanvas::getLayerCount(), PlotCanvas::IM_SNAP, TOPPViewBase::log_, Plot3DCanvas::openglwidget(), TOPPViewBase::setIntensityMode(), PlotCanvas::setVisibleArea(), Plot3DOpenGLCanvas::setYLabel(), TOPPViewBase::showPlotWidgetInWindow(), LayerDataBase::type, TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.
Referenced by TOPPViewBase::showPlotWidgetInWindow().
|
slot |
Shows the current peak data of the active layer as DIA data.
References PlotCanvas::addPeakLayer(), Plot2DWidget::canvas(), LayerDataBase::filename, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getCurrentLayer(), PlotCanvas::getCurrentLayerIndex(), Precursor::getIsolationWindowLowerOffset(), Precursor::getIsolationWindowUpperOffset(), Peak1D::getMZ(), LayerDataBase::getName(), OpenMS::Constants::k, PlotCanvas::setLayerName(), MSSpectrum::setMSLevel(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.
Referenced by TOPPViewBase::showPlotWidgetInWindow().
|
slot |
Shows the current peak data of the active layer as ion mobility.
References PlotCanvas::addPeakLayer(), Plot2DWidget::canvas(), LayerDataBase::filename, IMTypes::fromIMUnit(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCanvasParameters(), PlotCanvas::getCurrentLayer(), OpenMS::MZ, IMDataConverter::reshapeIMFrameToMany(), Plot2DWidget::setMapper(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::updateMenu(), and TOPPViewBase::ws_.
Referenced by TOPPViewBase::showPlotWidgetInWindow().
shows X/Y axis mouse values in the status bar
References TOPPViewBase::message_label_, String::toQString(), TOPPViewBase::x_label_, and TOPPViewBase::y_label_.
Referenced by TOPPViewBase::showPlotWidgetInWindow().
|
slot |
shows the DB dialog for opening files
References TOPPViewBase::getActivePlotWidget(), and PlotWidget::showGoToDialog().
void showPlotWidgetInWindow | ( | PlotWidget * | sw | ) |
Opens the provided spectrum widget in a new window.
References EnhancedWorkspace::addSubWindow(), EnhancedTabBarWidgetInterface::addToTabBar(), PlotWidget::canvas(), TOPPViewBase::copyLayer(), PlotWidget::dropReceived(), PlotCanvas::getCurrentLayer(), LayerDataBase::getDecoratedName(), Plot2DWidget::getProjectionOntoX(), Plot2DWidget::getProjectionOntoY(), EnhancedTabBarWidgetInterface::getWindowId(), TOPPViewBase::layerActivated(), PlotCanvas::layerActivated(), PlotCanvas::layerModficationChange(), PlotCanvas::layerZoomChanged(), PlotCanvas::preferencesChange(), TOPPViewBase::selection_view_, PlotWidget::sendCursorStatus(), PlotWidget::sendStatusMessage(), TOPPViewBase::showCurrentPeaksAs2D(), Plot1DWidget::showCurrentPeaksAs2D(), Plot3DWidget::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), Plot1DWidget::showCurrentPeaksAs3D(), Plot2DWidget::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), Plot1DWidget::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), Plot1DWidget::showCurrentPeaksAsIonMobility(), Plot2DWidget::showCurrentPeaksAsIonMobility(), TOPPViewBase::showCursorStatus(), DataSelectionTabs::showSpectrumAsNew1D(), Plot2DWidget::showSpectrumAsNew1D(), TOPPViewBase::showStatusMessage(), TOPPViewBase::showWindow(), TOPPViewBase::tab_bar_, TOPPViewBase::updateLayerBar(), TOPPViewBase::ws_, and TOPPViewBase::zoomOtherWindows().
Referenced by TOPPViewBase::addData(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().
|
slot |
Shows current layer preferences.
References TOPPViewBase::getActiveCanvas(), and PlotCanvas::showCurrentLayerPreferences().
|
slot |
Shows the spectrum alignment dialog.
References Plot1DWidget::canvas(), SpectrumAlignmentDialog::get1stLayerIndex(), SpectrumAlignmentDialog::get2ndLayerIndex(), TOPPViewBase::getActive1DWidget(), Plot1DCanvas::getAlignmentScore(), Plot1DCanvas::getAlignmentSize(), SpectrumAlignmentDialog::getTolerance(), SpectrumAlignmentDialog::isPPM(), Plot1DCanvas::mirrorModeActive(), Plot1DWidget::performAlignment(), and Param::setValue().
|
protectedslot |
shows the spectrum browser and updates it
References TOPPViewBase::updateViewBar(), and TOPPViewBase::views_dockwidget_.
|
slot |
Shows the theoretical spectrum generation dialog.
References TOPPViewBase::addData(), MSExperiment::addSpectrum(), Plot1DCanvas::DM_PEAKS, TOPPViewBase::draw_group_1d_, LayerDataDefs::DT_PEAK, TheoreticalSpectrumGenerationDialog::getSequence(), TheoreticalSpectrumGenerationDialog::getSpectrum(), TOPPViewBase::setDrawMode1D(), and TOPPViewBase::spec_gen_dialog_.
|
slot |
shows a spectrum's metadata with index spectrum_index
from the currently active canvas
References TOPPViewBase::getActiveCanvas(), and PlotCanvas::showMetaData().
|
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 TOPPViewBase::message_label_.
Referenced by TOPPViewBase::showPlotWidgetInWindow().
|
slot |
Apply TOPP tool.
References TOPPViewBase::showTOPPDialog_().
|
protected |
Apply TOPP tool. If visible
is true, only the visible data is used, otherwise the whole layer is used.
References LogWindow::appendNewHeader(), FileTypes::CONSENSUSXML, TOPPViewBase::current_path_, FileTypes::FEATUREXML, TOPPViewBase::getActiveCanvas(), PlotCanvas::getCurrentLayer(), ToolsDialog::getExtension(), ToolsDialog::getInput(), LayerDataBase::getName(), ToolsDialog::getOutput(), File::getTempDirectory(), ToolsDialog::getTool(), TVToolDiscovery::getToolParams(), File::getUniqueName(), Param::hasSection(), FileTypes::IDXML, Param::insert(), TOPPViewBase::log_, FileTypes::MZML, DefaultParamHandler::param_, TOPPViewBase::runTOPPTool_(), TOPPViewBase::tool_scanner_, TOPPViewBase::topp_, LayerDataBase::type, FileTypes::typeToName(), FileTypes::UNKNOWN, LayerDataBase::visible, TVToolDiscovery::waitForToolParams(), and File::writable().
Referenced by TOPPViewBase::showTOPPDialog().
|
protectedslot |
Raises the window corresponding to the data of the tab with identifier id
.
References EnhancedWorkspace::getWidget(), and TOPPViewBase::ws_.
Referenced by TOPPViewBase::showPlotWidgetInWindow(), and TOPPViewBase::TOPPViewBase().
|
slot |
Toggles the axis legends.
References TOPPViewBase::getActivePlotWidget(), and PlotWidget::showLegend().
|
slot |
Toggles the grid lines.
References TOPPViewBase::getActiveCanvas(), and PlotCanvas::showGridLines().
|
slot |
Toggles drawing of interesting MZs.
References TOPPViewBase::getActive1DWidget().
|
slot |
References TOPPViewBase::getActive2DWidget(), Plot2DWidget::projectionsVisible(), and Plot2DWidget::toggleProjections().
Referenced by TOPPViewBase::TOPPViewBase().
|
slot |
calls update*Bar and updateMenu_() to make sure the interface matches the current data
References TOPPViewBase::layerActivated(), and TOPPViewBase::updateMenu().
Referenced by TOPPViewBase::closeByTab(), and TOPPViewBase::TOPPViewBase().
|
slot |
changes the current path according to the currently active window/layer
References TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), Param::getValue(), DefaultParamHandler::param_, File::path(), ParamValue::toString(), and OpenMS::user_section.
Referenced by TOPPViewBase::layerActivated().
|
slot |
adapts the filter bar to the active window
References TOPPViewBase::filter_list_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), PlotCanvas::getLayerCount(), and FilterList::set().
Referenced by TOPPViewBase::layerActivated().
|
slot |
adapts the layer bar to the active window
References TOPPViewBase::getActivePlotWidget(), TOPPViewBase::layers_view_, and LayerListView::update().
Referenced by TOPPViewBase::layerActivated(), and TOPPViewBase::showPlotWidgetInWindow().
|
slot |
activates/deactivates menu entries
References LayerDataDefs::DT_UNKNOWN, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), OpenMS::HAS_CANVAS, OpenMS::HAS_LAYER, OpenMS::HAS_MIRROR_MODE, OpenMS::IS_1D_VIEW, TOPPViewBase::menu_, TOPPViewBase::topp_, OpenMS::TOPP_IDLE, LayerDataBase::type, and TOPPViewMenu::update().
Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateBarsAndMenus().
|
protectedslot |
Appends process output to log window.
References LogWindow::appendText(), TOPPViewBase::log_, and TOPPViewBase::topp_.
Referenced by TOPPViewBase::runTOPPTool_().
|
slot |
updates the toolbar
References LogWindow::appendNewHeader(), LayerDataDefs::C_ELEMENTS, PlotWidget::canvas(), Plot1DWidget::canvas(), Plot2DWidget::canvas(), TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_label_2d_, TOPPViewBase::dm_precursors_2d_, TOPPViewBase::dm_unassigned_2d_, TOPPViewBase::draw_group_1d_, LayerDataDefs::DT_CONSENSUS, LayerDataDefs::DT_FEATURE, LayerDataDefs::DT_IDENT, LayerDataDefs::DT_PEAK, LayerDataDefs::F_HULL, LayerDataDefs::F_HULLS, LayerDataDefs::F_UNASSIGNED, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActivePlotWidget(), PlotCanvas::getCurrentLayer(), Plot1DCanvas::getDrawMode(), PlotCanvas::getIntensityMode(), PlotCanvas::getLayerCount(), PlotCanvas::getLayerFlag(), LayerDataDefs::I_PEPTIDEMZ, TOPPViewBase::intensity_button_group_, LayerDataDefs::L_NONE, LayerDataBase::label, TOPPViewBase::log_, LayerDataDefs::P_PRECURSORS, TOPPViewBase::tool_bar_1d_, TOPPViewBase::tool_bar_2d_cons_, TOPPViewBase::tool_bar_2d_feat_, TOPPViewBase::tool_bar_2d_ident_, TOPPViewBase::tool_bar_2d_peak_, and LayerDataBase::type.
Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::changeUnassigned(), and TOPPViewBase::layerActivated().
|
slot |
adapts view bar to the active window
References DataSelectionTabs::callUpdateEntries(), and TOPPViewBase::selection_view_.
Referenced by TOPPViewBase::layerActivated(), and TOPPViewBase::showSpectrumBrowser().
|
slot |
gets called when a layer changes in zoom; will apply the same zoom to other windows (if linked)
References PlotWidget::canvas(), LayerDataDefs::DT_CHROMATOGRAM, TOPPViewBase::getActivePlotWidget(), PlotCanvas::getCurrentLayer(), DefaultParamHandler::getName(), PlotCanvas::getVisibleArea(), PlotCanvas::setVisibleArea(), LayerDataBase::type, TOPPViewBase::ws_, and TOPPViewBase::zoom_together_.
Referenced by TOPPViewBase::showPlotWidgetInWindow().
|
friend |
|
protected |
Additional context menu for 2D layers.
|
staticprivate |
Suffix appended to caption of tabs when layer is shown in 3D.
|
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 TOPPViewBase::annotateWithAMS(), TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::chooseFilesDialog_(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateCurrentPath().
|
protected |
Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
Referenced by TOPPViewBase::changeUnassigned(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
|
protected |
Referenced by TOPPViewBase::TOPPViewBase().
|
protected |
Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateFilterBar().
|
protected |
Referenced by TOPPViewBase::TOPPViewBase().
|
protected |
Referenced by TOPPViewBase::TOPPViewBase().
|
protected |
Referenced by TOPPViewBase::setIntensityMode(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
|
protected |
LAST active subwindow (~ corresponding to tab) in the MDI container. Since subwindows can lose focus, we want to make sure that things like the ID tables only update when a NEW window is activated. (Actually, we should check for the underlying data but this might be a
Referenced by TOPPViewBase::TOPPViewBase().
|
protected |
Referenced by TOPPViewBase::TOPPViewBase().
|
protected |
Layer management widget.
Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateLayerBar().
|
protected |
Log output window.
Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::addDataFile(), TOPPViewBase::annotateWithAMS(), TOPPViewBase::annotateWithID(), TOPPViewBase::annotateWithOSW(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::loadFiles(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateProcessLog(), and TOPPViewBase::updateToolBar().
|
protected |
manages the menu items (active/inactive) and recent files etc
Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateMenu().
|
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Label for messages in the status bar.
Referenced by TOPPViewBase::showCursorStatus(), TOPPViewBase::showStatusMessage(), and TOPPViewBase::TOPPViewBase().
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Referenced by TOPPViewBase::TOPPViewBase().
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manages recent list of filenames and the menu that goes with it
Referenced by TOPPViewBase::addRecentFile_(), TOPPViewBase::loadPreferences(), TOPPViewBase::savePreferences(), and TOPPViewBase::TOPPViewBase().
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Determines TVToolDiscovery scans for tools and generates new params.
Referenced by TOPPViewBase::loadPreferences(), and TOPPViewBase::savePreferences().
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This dialog is a member so that its settings can be perserved upon closing.
Referenced by TOPPViewBase::showSpectrumGenerationDialog().
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Tab bar. The address of the corresponding window to a tab is stored as an int in tabData()
Referenced by TOPPViewBase::getActivePlotWidget(), TOPPViewBase::showPlotWidgetInWindow(), and TOPPViewBase::TOPPViewBase().
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Referenced by TOPPViewBase::TOPPViewBase().
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Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
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Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
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Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
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Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
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Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().
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Scans for tools and generates a param for each.
Referenced by TOPPViewBase::loadPreferences(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::savePreferences(), TOPPViewBase::showTOPPDialog_(), and TOPPViewBase::TOPPViewBase().
struct { ... } topp_ |
Information needed for execution of TOPP tools.
Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateProcessLog().
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Verbosity of TV.
Referenced by TOPPViewBase::TOPPViewBase().
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Referenced by TOPPViewBase::showSpectrumBrowser(), and TOPPViewBase::TOPPViewBase().
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Watcher that tracks file changes (in order to update the data in the different views)
Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), and TOPPViewBase::TOPPViewBase().
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Holds the messageboxes for each layer that are currently popped up (to avoid popping them up again, if file changes again before the messagebox is closed)
Referenced by TOPPViewBase::fileChanged_().
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Main workspace.
Referenced by TOPPViewBase::addData(), TOPPViewBase::closeByTab(), TOPPViewBase::closeEvent(), TOPPViewBase::closeTab(), TOPPViewBase::fileChanged_(), TOPPViewBase::getActivePlotWidget(), TOPPViewBase::getWorkspace(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showPlotWidgetInWindow(), TOPPViewBase::showWindow(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::zoomOtherWindows().
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x-axis label for messages in the status bar
Referenced by TOPPViewBase::showCursorStatus(), and TOPPViewBase::TOPPViewBase().
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y-axis label for messages in the status bar
Referenced by TOPPViewBase::showCursorStatus(), and TOPPViewBase::TOPPViewBase().
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Stores whether the individual windows should zoom together (be linked) or not.
Referenced by TOPPViewBase::linkZoom(), and TOPPViewBase::zoomOtherWindows().