TOPPViewBase Class Reference

Main window of TOPPView tool. More...

#include <OpenMS/VISUAL/APPLICATIONS/TOPPViewBase.h>

Inheritance diagram for TOPPViewBase:

Public Types
Type definitions
typedef LayerData::FeatureMapType	FeatureMapType
typedef LayerData::FeatureMapSharedPtrType	FeatureMapSharedPtrType
typedef LayerData::ConsensusMapType	ConsensusMapType
typedef LayerData::ConsensusMapSharedPtrType	ConsensusMapSharedPtrType
typedef LayerData::ExperimentType	ExperimentType
typedef LayerData::ExperimentSharedPtrType	ExperimentSharedPtrType
typedef LayerData::ODExperimentSharedPtrType	ODExperimentSharedPtrType
typedef ExperimentType::SpectrumType	SpectrumType
	Peak spectrum type. More...

Public Slots
void	updateCurrentPath ()
	changes the current path according to the currently active window/layer More...
void	showURL ()
	shows the URL stored in the data of the sender QAction More...
void	openFileDialog ()
	shows the file dialog for opening files More...
void	openExampleDialog ()
	shows the file dialog for opening example files More...
void	showGoToDialog ()
	shows the DB dialog for opening files More...
void	preferencesDialog ()
	shows the preferences dialog More...
void	layerStatistics ()
	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	layerZoomChanged ()
	gets called when a layer changes in zoom More...
void	linkZoom ()
	link the zoom of individual windows More...
void	layerDeactivated ()
	gets called if a layer got deactivated More...
void	closeFile ()
	closes the active window 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	viewChanged (int)
	changes the behavior according to the selected view in the spectra view bar and calls updateSpectraViewBar() More...
void	viewTabwidgetDoubleClicked (int)
	adds empty ID structure to allow manual annotations More...
void	updateFilterBar ()
	adapts the filter bar to the active window More...
void	updateMenu ()
	enabled/disabled menu entries depending on the current state More...
void	updateTabBar (QMdiSubWindow *w)
	brings the tab corresponding to the active window in front More...
void	tileVertical ()
	tile the open windows vertically More...
void	tileHorizontal ()
	tile the open windows horizontally More...
void	showStatusMessage (std::string msg, OpenMS::UInt time)
	Shows a status message in the status bar. More...
void	showCursorStatus (double mz, double rt)
	shows m/z and rt in the status bar More...
void	showCursorStatusInvert (double mz, double rt)
	shows m/z and rt in the status bar (inverting RT and m/z) More...
void	showTOPPDialog ()
	Apply TOPP tool. More...
void	annotateWithID ()
	Annotates current layer with ID data. More...
void	showSpectrumGenerationDialog ()
	Shows the theoretical spectrum generation dialog. More...
void	showSpectrumAlignmentDialog ()
	Shows the spectrum alignment dialog. More...
void	showSpectrumAs1D (int index)
	Shows the spectrum with index index of the active layer in 1D. More...
void	showSpectrumAs1D (std::vector< int, std::allocator< int > > indices)
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 ()
	Shows the current peak data of the active layer as ion mobility. More...
void	showCurrentPeaksAsDIA ()
	Shows the current peak data of the active layer as DIA data. More...
void	showAboutDialog ()
	Shows the 'About' dialog. More...
void	saveLayerAll ()
	Saves the whole current layer data. More...
void	saveLayerVisible ()
	Saves the visible layer data. More...
void	toggleGridLines ()
	Toggles the grid lines. More...
void	toggleAxisLegends ()
	Toggles the axis legends. More...
void	showPreferences ()
	Shows current layer preferences. More...
void	metadataFileDialog ()
	dialog for inspecting database meta data More...
void	loadFile (QString)
	Loads a file given by the passed string. More...
Toolbar slots
void	setDrawMode1D (int)
void	setIntensityMode (int)
void	changeLayerFlag (bool)
void	changeLabel (QAction *)
void	changeUnassigned (QAction *)
void	resetZoom ()
void	toggleProjections ()

Public Member Functions
	TOPPViewBase (QWidget *parent=nullptr)
	Constructor. More...
	~TOPPViewBase () override
	Destructor. More...
void	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 (FeatureMapSharedPtrType feature_map, ConsensusMapSharedPtrType consensus_map, std::vector< PeptideIdentification > &peptides, ExperimentSharedPtrType peak_map, ODExperimentSharedPtrType on_disc_peak_map, LayerData::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	getSpectrumParameters (UInt dim)
	Returns the parameters for a SpectrumCanvas of dimension dim. More...
const LayerData *	getCurrentLayer () const
	Returns the active Layer data (0 if no layer is active) More...
SpectrumCanvas *	getActiveCanvas () const
	returns a pointer to the active SpectrumCanvas (0 if none is active) More...
SpectraIdentificationViewWidget *	getSpectraIdentificationViewWidget ()
	returns a pointer to the SpectraIdentificationViewWidget More...
void	showSpectrumWidgetInWindow (SpectrumWidget *sw, const String &caption)
	Opens the provided spectrum widget in a new window. More...
float	estimateNoiseFromRandomMS1Scans (const ExperimentType &exp, UInt n_scans=10)
	Estimates the noise by evaluating n_scans random scans of MS level 1. Assumes that 4/5 of intensities is noise. More...
EnhancedWorkspace *	getWorkspace () const
	returns a pointer to the EnhancedWorkspace containing SpectrumWidgets More...
SpectrumWidget *	getActiveSpectrumWidget () const
	returns a pointer to the active SpectrumWidget (0 if none is active) More...
Spectrum1DWidget *	getActive1DWidget () const
	returns a pointer to the active Spectrum1DWidget (0 the active window is no Spectrum1DWidget or there is no active window) More...
Spectrum2DWidget *	getActive2DWidget () const
	returns a pointer to the active Spectrum2DWidget (0 the active window is no Spectrum2DWidget or there is no active window) More...
Spectrum3DWidget *	getActive3DWidget () const
	returns a pointer to the active Spectrum3DWidget (0 the active window is no Spectrum2DWidget or there is no active window) More...
Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...
	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...
virtual	~DefaultParamHandler ()
	Destructor. More...
virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...
virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...
void	setParameters (const Param &param)
	Sets the parameters. More...
const Param &	getParameters () const
	Non-mutable access to the parameters. More...
const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...
const String &	getName () const
	Non-mutable access to the name. More...
void	setName (const String &name)
	Mutable access to the name. More...
const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Static Public Member Functions
static bool	containsMS1Scans (const ExperimentType &exp)
	Returns true if contains at least one MS1 spectrum. More...
static bool	containsIMData (const MSSpectrum &s)
	Returns true if contains ion mobility data. More...
static bool	hasMS1Zeros (const ExperimentType &exp)
	Returns true of experiment has at least one exact zero valued peak in any of its MS1 spectra. More...
static bool	hasPeptideIdentifications (const ExperimentType &map)
	Returns true if the experiment map contains peptide identifications. More...

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

Protected Slots
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	rerunTOPPTool ()
	returns the last invoked TOPP tool with the same parameters More...
void	showSpectrumBrowser ()
	shows the spectrum browser and updates it More...
void	showSpectrumMetaData (int spectrum_index)
	shows the spectrum metadata More...
void	updateProcessLog ()
	Appends process output to log window. More...
void	fileChanged_ (const String &)
	Called if a data file has been externally changed. More...
Layer manager and filter manager slots
void	layerSelectionChange (int)
	slot for layer manager selection change More...
void	layerFilterVisibilityChange (bool)
	Enables/disables the data filters for the current layer. More...
void	layerContextMenu (const QPoint &pos)
	slot for layer manager context menu More...
void	logContextMenu (const QPoint &pos)
	slot for log window context menu More...
void	layerVisibilityChange (QListWidgetItem *item)
	slot for layer manager visibility change (check box) More...
void	filterContextMenu (const QPoint &pos)
	slot for filter manager context menu More...
void	filterEdit (QListWidgetItem *item)
	slot for editing a filter More...
void	layerEdit (QListWidgetItem *)
	slot for editing the preferences of the current layer More...
Tabbar slots
void	closeByTab (int id)
	Closes the window corresponding to the data of the tab with identifier id. More...
void	enhancedWorkspaceWindowChanged (int id)
	Raises the window corresponding to the data of the tab with identifier id. More...
void	openRecentFile ()
	Opens a file from the recent files menu. More...
void	copyLayer (const QMimeData *data, QWidget *source, int id=-1)
	Slot for drag-and-drop of layer manager to tabbar. More...

Protected Member Functions
void	initializeDefaultParameters_ ()
	Initializes the default parameters on TOPPView construction. More...
bool	annotateMS1FromMassFingerprinting_ (const FeatureMap &identifications)
std::set< String >	getFilenamesOfOpenFiles_ ()
	unique list of files referenced by all layers More...
QStringList	getFileList_ (const String &path_overwrite="")
	Shows a dialog where the user can select files. More...
EnhancedTabBarWidgetInterface *	window_ (int id) const
	Returns the enhanced tabbar widget with id id. 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...
void	showLogMessage_ (LogState state, const String &heading, const String &body)
	Shows a log message in the log_ window. More...
void	showTOPPDialog_ (bool visible)
	Apply TOPP tool. If visible is true, only the visible data is used, otherwise the whole layer is used. More...
reimplemented Qt events
void	closeEvent (QCloseEvent *event) 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
QListWidget *	layer_manager_
	Layer management widget. More...
FileWatcher *	watcher_
	Watcher that tracks file changes (in order to update the data in the different views) More...
bool	watcher_msgbox_
	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_
	Stores whether the individual windows should zoom together (be linked) or not. More...
QAction *	linkZoom_action_
QTextEdit *	log_
	Log output window. More...
EnhancedWorkspace *	ws_
	Main workspace. More...
EnhancedTabBar *	tab_bar_
	Tab bar. The address of the corresponding window to a tab is stored as an int in tabData() More...
QMenu *	add_2d_context_
	Additional context menu for 2D layers. More...
String	current_path_
QTabWidget *	views_tabwidget_
	Tabwidget that hold the different views on the loaded data. More...
TOPPViewIdentificationViewBehavior *	identificationview_behavior_
	TOPPView behavior for the identification view. More...
TOPPViewSpectraViewBehavior *	spectraview_behavior_
	TOPPView behavior for the spectra view. More...
dock widgets
QDockWidget *	layer_dock_widget_
QDockWidget *	views_dockwidget_
QDockWidget *	filter_dock_widget_
Spectrum selection widgets
SpectraViewWidget *	spectra_view_widget_
SpectraIdentificationViewWidget *	spectra_identification_view_widget_
Filter widgets
QListWidget *	filters_
QCheckBox *	filters_check_box_
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_
Status bar
QLabel *	message_label_
	Label for messages in the status bar. More...
QLabel *	mz_label_
	m/z label for messages in the status bar More...
QLabel *	rt_label_
	RT 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 Private Attributes
static const String	CAPTION_3D_SUFFIX_ = " (3D)"
	Suffix appended to caption of tabs when layer is shown in 3D. More...

Friends
class	TestTOPPView

Recent files
QStringList	recent_files_
	list of the recently opened files More...
std::vector< QAction * >	recent_actions_
	list of the recently opened files actions (menu entries) More...
void	addRecentFile_ (const String &filename)
	adds a Filename to the recent files More...
void	updateRecentMenu_ ()
	update the recent files menu More...

TOPP tool execution
struct {
Param   param
String   tool
String   in
String   out
String   file_name
String   layer_name
UInt   window_id
Size   spectrum_id
QProcess *   process
QTime   timer
bool   visible
}	topp_
	Information needed for execution of TOPP tools. More...
void	runTOPPTool_ ()
	Runs the TOPP tool according to the information in topp_. More...

Detailed Description

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

• Central Widget:
  • EnhancedTabBar: tab_bar_
  • EnhancedWorkspace: ws_
• Docked to the right:
  • layer_dock_widget_
  • views_dockwidget_
  • filter_dock_widget_
• Docked to the bottom:
  • log_bar (only connected through slots)

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 identificationview_behavior_ and spectraview_behavior_.

Improvement:

Use DataRepository singleton to share data between TOPPView and the canvas classes (Hiwi)

Improvement:

For painting single mass traces with no width we currently paint each line twice (once going down, and then coming back up). This could be more efficient...

Improvement:

Keep spectrum browser widgets of all layers in memory in order to avoid rebuilding the entire tree view every time the active layer changes (Hiwi, Johannes)

Member Typedef Documentation

ConsensusMapSharedPtrType

typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

ConsensusMapType

typedef LayerData::ConsensusMapType ConsensusMapType

ExperimentSharedPtrType

typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType

ExperimentType

typedef LayerData::ExperimentType ExperimentType

FeatureMapSharedPtrType

typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType

FeatureMapType

typedef LayerData::FeatureMapType FeatureMapType

ODExperimentSharedPtrType

typedef LayerData::ODExperimentSharedPtrType ODExperimentSharedPtrType

SpectrumType

typedef ExperimentType::SpectrumType SpectrumType

Peak spectrum type.

Member Enumeration Documentation

LogState

enum LogState

protected

Log message states.

Enumerator
LS_NOTICE	Notice.
LS_WARNING	Warning.
LS_ERROR	Fatal error.

Constructor & Destructor Documentation

TOPPViewBase()

TOPPViewBase

(

QWidget *

parent = nullptr

)

Constructor.

References EnhancedTabBar::addTab(), TOPPViewBase::annotateWithID(), TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::closeByTab(), TOPPViewBase::closeFile(), TOPPViewBase::copyLayer(), TOPPViewBase::current_path_, DefaultParamHandler::defaultsToParam_(), Spectrum1DCanvas::DM_CONNECTEDLINES, TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_label_2d_, Spectrum1DCanvas::DM_PEAKS, TOPPViewBase::dm_precursors_2d_, TOPPViewBase::dm_unassigned_2d_, TOPPViewBase::draw_group_1d_, TOPPViewBase::editMetadata(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::fileChanged_(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::filters_, TOPPViewBase::filters_check_box_, Param::getValue(), TOPPViewBase::group_label_2d_, TOPPViewBase::group_unassigned_2d_, TOPPViewBase::identificationview_behavior_, SpectrumCanvas::IM_LOG, SpectrumCanvas::IM_NONE, SpectrumCanvas::IM_PERCENTAGE, SpectrumCanvas::IM_SNAP, TOPPViewBase::initializeDefaultParameters_(), TOPPViewBase::intensity_button_group_, TOPPViewBase::layer_dock_widget_, TOPPViewBase::layer_manager_, TOPPViewBase::layerContextMenu(), TOPPViewBase::layerEdit(), TOPPViewBase::layerFilterVisibilityChange(), TOPPViewBase::layerSelectionChange(), TOPPViewBase::layerStatistics(), TOPPViewBase::layerVisibilityChange(), TOPPViewBase::linkZoom(), TOPPViewBase::linkZoom_action_, TOPPViewBase::loadPreferences(), TOPPViewBase::log_, TOPPViewBase::logContextMenu(), TOPPViewBase::message_label_, TOPPViewBase::metadataFileDialog(), TOPPViewBase::mz_label_, LayerData::NamesOfLabelType, TOPPViewBase::openExampleDialog(), TOPPViewBase::openFileDialog(), TOPPViewBase::openRecentFile(), DefaultParamHandler::param_, TOPPViewBase::preferencesDialog(), TOPPViewBase::projections_2d_, TOPPViewBase::recent_actions_, EnhancedTabBar::removeId(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::resetZoom(), TOPPViewBase::rt_label_, TOPPViewBase::saveLayerAll(), TOPPViewBase::saveLayerVisible(), TOPPViewBase::setDrawMode1D(), TOPPViewBase::setIntensityMode(), TOPPViewBase::showAboutDialog(), TOPPViewBase::showGoToDialog(), TOPPViewBase::showPreferences(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::showSpectrumGenerationDialog(), TOPPViewBase::showSpectrumMetaData(), TOPPViewBase::showTOPPDialog(), TOPPViewBase::showURL(), LayerData::SIZE_OF_LABEL_TYPE, TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, TOPPViewBase::spectraview_behavior_, TOPPViewBase::tab_bar_, TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::toggleAxisLegends(), TOPPViewBase::toggleGridLines(), 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::topp_, TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateTabBar(), TOPPViewBase::updateToolBar(), TOPPViewBase::updateViewBar(), TOPPViewBase::viewChanged(), TOPPViewBase::views_dockwidget_, TOPPViewBase::views_tabwidget_, TOPPViewBase::viewTabwidgetDoubleClicked(), TOPPViewBase::watcher_, TOPPViewBase::ws_, and TOPPViewBase::zoom_together_.

~TOPPViewBase()

~TOPPViewBase ( )

override

Destructor.

References TOPPViewBase::abortTOPPTool(), TOPPViewBase::identificationview_behavior_, TOPPViewBase::savePreferences(), and TOPPViewBase::spectraview_behavior_.

Member Function Documentation

abortTOPPTool

void abortTOPPTool ( )

protectedslot

aborts the execution of a TOPP tool

References TOPPViewBase::log_, TOPPViewBase::topp_, and TOPPViewBase::updateMenu().

Referenced by TOPPViewBase::~TOPPViewBase().

addData()

void addData	(	FeatureMapSharedPtrType	feature_map,
		ConsensusMapSharedPtrType	consensus_map,
		std::vector< PeptideIdentification > &	peptides,
		ExperimentSharedPtrType	peak_map,
		ODExperimentSharedPtrType	on_disc_peak_map,
		LayerData::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.

Parameters

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)
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 or default equals current
spectrum_id	determines the spectrum to show in 1D view.

add filter

References Spectrum1DCanvas::activateSpectrum(), SpectrumCanvas::activeLayerIndex(), DataFilters::add(), SpectrumCanvas::addLayer(), Spectrum1DWidget::canvas(), SpectrumWidget::canvas(), TOPPViewOpenDialog::disableCutoff(), TOPPViewOpenDialog::disableDimension(), TOPPViewOpenDialog::disableLocation(), LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_IDENT, TOPPViewBase::estimateNoiseFromRandomMS1Scans(), DataFilters::DataFilter::field, TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), TOPPViewOpenDialog::getMergeLayer(), LayerData::getPeakData(), TOPPViewBase::getSpectrumParameters(), Param::getValue(), DataFilters::GREATER_EQUAL, TOPPViewBase::hasMS1Zeros(), DataFilters::INTENSITY, TOPPViewOpenDialog::isCutoffEnabled(), TOPPViewOpenDialog::isDataDIA(), Spectrum2DCanvas::mergeIntoLayer(), LayerData::name, DataFilters::DataFilter::op, TOPPViewOpenDialog::openAsNewWindow(), DefaultParamHandler::param_, SpectrumCanvas::setFilters(), SpectrumCanvas::setLayerName(), TOPPViewOpenDialog::setMergeLayers(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::spectrum_id, LayerData::type, TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), DataFilters::DataFilter::value, TOPPViewOpenDialog::viewMapAs1D(), TOPPViewOpenDialog::viewMapAs2D(), TOPPViewBase::views_tabwidget_, TOPPViewBase::window_(), TOPPViewBase::window_id, and TOPPViewBase::ws_.

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::copyLayer(), and TOPPViewBase::showSpectrumGenerationDialog().

addDataFile()

void 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.

Loads the data and adds it to the application by calling addData_()

Parameters

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_(), File::basename(), FileTypes::CONSENSUSXML, TOPPViewBase::containsMS1Scans(), LayerData::DT_CHROMATOGRAM, LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_IDENT, LayerData::DT_PEAK, File::exists(), FileTypes::FEATUREXML, IndexedMzMLHandler::getNrChromatograms(), IndexedMzMLHandler::getNrSpectra(), IndexedMzMLHandler::getParsingSuccess(), FileHandler::getType(), Param::getValue(), ProgressLogger::GUI, FileTypes::IDXML, FileTypes::INI, OpenMS::Constants::k, ConsensusXMLFile::load(), MzIdentMLFile::load(), IdXMLFile::load(), FeatureXMLFile::load(), FileHandler::loadExperiment(), LOG_INFO, TOPPViewBase::LS_ERROR, TOPPViewBase::LS_WARNING, FileTypes::MZIDENTML, FileTypes::MZML, IndexedMzMLHandler::openFile(), DefaultParamHandler::param_, TOPPViewBase::showLogMessage_(), TOPPViewBase::spectrum_id, FileTypes::typeToName(), FileTypes::UNKNOWN, TOPPViewBase::watcher_, BaseException::what(), and TOPPViewBase::window_id.

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::loadFile(), TOPPViewBase::loadFiles(), TOPPViewBase::openExampleDialog(), TOPPViewBase::openFileDialog(), and TOPPViewBase::openRecentFile().

addRecentFile_()

void addRecentFile_ ( const String &  filename )

protected

adds a Filename to the recent files

References File::absolutePath(), Param::getValue(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, String::toQString(), and TOPPViewBase::updateRecentMenu_().

Referenced by TOPPViewBase::addDataFile().

annotateMS1FromMassFingerprinting_()

bool annotateMS1FromMassFingerprinting_ ( const FeatureMap &  identifications )

protected

add annotations from an AccurateMassSearch to an MS1 spectrum

Returns

true on success, otherwise false

References IDMapper::annotate(), LayerData::DT_PEAK, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), DefaultParamHandler::getParameters(), LayerData::getPeakDataMuteable(), TOPPViewBase::LS_NOTICE, DefaultParamHandler::setParameters(), Param::setValue(), TOPPViewBase::showLogMessage_(), and LayerData::type.

Referenced by TOPPViewBase::annotateWithID().

annotateWithID

void annotateWithID ( )

slot

Annotates current layer with ID data.

References IDMapper::annotate(), TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::current_path_, LayerData::DT_FEATURE, LayerData::DT_PEAK, FileTypes::FEATUREXML, TOPPViewBase::getActiveCanvas(), LayerData::getConsensusMap(), SpectrumCanvas::getCurrentLayer(), DefaultParamHandler::getDefaults(), LayerData::getFeatureMap(), LayerData::getPeakDataMuteable(), FeatureMap::getProteinIdentifications(), FileHandler::getType(), FileTypes::IDXML, MzIdentMLFile::load(), IdXMLFile::load(), FeatureXMLFile::load(), TOPPViewBase::LS_NOTICE, FileTypes::MZIDENTML, DefaultParamHandler::setParameters(), Param::setValue(), TOPPViewBase::showLogMessage_(), String::toQString(), LayerData::type, TOPPViewBase::updateViewBar(), TOPPViewBase::views_tabwidget_, LayerData::visible, and BaseException::what().

Referenced by TOPPViewBase::TOPPViewBase().

changeLabel

void changeLabel ( QAction *  action )

slot

References Spectrum2DWidget::canvas(), TOPPViewBase::dm_label_2d_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::getCurrentLayer(), LayerData::L_INDEX, LayerData::L_NONE, LayerData::NamesOfLabelType, SpectrumCanvas::setLabel(), LayerData::SIZE_OF_LABEL_TYPE, and TOPPViewBase::updateToolBar().

Referenced by TOPPViewBase::TOPPViewBase().

changeLayerFlag

void changeLayerFlag ( bool  on )

slot

References LayerData::C_ELEMENTS, TOPPViewBase::dm_elements_2d_, TOPPViewBase::dm_hull_2d_, TOPPViewBase::dm_hulls_2d_, TOPPViewBase::dm_ident_2d_, TOPPViewBase::dm_precursors_2d_, LayerData::F_HULL, LayerData::F_HULLS, TOPPViewBase::getActive2DWidget(), LayerData::I_PEPTIDEMZ, and LayerData::P_PRECURSORS.

Referenced by TOPPViewBase::TOPPViewBase().

changeUnassigned

void changeUnassigned ( QAction *  action )

slot

References Spectrum2DWidget::canvas(), TOPPViewBase::dm_unassigned_2d_, LayerData::F_UNASSIGNED, TOPPViewBase::getActive2DWidget(), SpectrumCanvas::getLayerFlag(), LayerData::I_PEPTIDEMZ, SpectrumCanvas::setLayerFlag(), and TOPPViewBase::updateToolBar().

Referenced by TOPPViewBase::TOPPViewBase().

checkPreferences_()

void checkPreferences_ ( )

protected

check if all available preferences get set by the .ini file. If there are some missing entries fill them with default values.

closeByTab

void closeByTab ( int  id )

protectedslot

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

References TOPPViewBase::updateMenu(), and TOPPViewBase::window_().

Referenced by TOPPViewBase::TOPPViewBase().

closeEvent()

void closeEvent ( QCloseEvent *  event )

overrideprotected

References TOPPViewBase::ws_.

closeFile

void closeFile ( )

slot

closes the active window

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

Referenced by TOPPViewBase::TOPPViewBase().

containsIMData()

bool containsIMData ( const MSSpectrum &  s )

static

Returns true if contains ion mobility data.

References MSSpectrum::getFloatDataArrays().

Referenced by TOPPViewBase::showCurrentPeaksAsIonMobility().

containsMS1Scans()

bool containsMS1Scans ( const ExperimentType &  exp )

static

Returns true if contains at least one MS1 spectrum.

References MSExperiment::size().

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::estimateNoiseFromRandomMS1Scans(), and TOPPViewBase::hasMS1Zeros().

copyLayer

void copyLayer ( const QMimeData *  data, QWidget *  source, int  id = -1  )

protectedslot

Slot for drag-and-drop of layer manager to tabbar.

References TOPPViewBase::addData(), TOPPViewBase::addDataFile(), MSExperiment::addSpectrum(), LayerData::DT_CHROMATOGRAM, LayerData::filename, TOPPViewBase::getActiveCanvas(), LayerData::getConsensusMap(), SpectrumCanvas::getCurrentLayer(), LayerData::getFeatureMap(), LayerData::getOnDiscPeakData(), LayerData::getPeakData(), LayerData::getPeakDataMuteable(), SpectraViewWidget::getTreeWidget(), TOPPViewBase::layer_manager_, TOPPViewBase::LS_ERROR, LayerData::name, LayerData::peptides, TOPPViewBase::showLogMessage_(), TOPPViewBase::spectra_view_widget_, LayerData::type, and BaseException::what().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow(), and TOPPViewBase::TOPPViewBase().

editMetadata

void editMetadata ( )

slot

lets the user edit the meta data of a layer

References TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), TOPPViewBase::LS_NOTICE, TOPPViewBase::showLogMessage_(), SpectrumCanvas::showMetaData(), and LayerData::visible.

Referenced by TOPPViewBase::TOPPViewBase().

enhancedWorkspaceWindowChanged

void enhancedWorkspaceWindowChanged ( int  id )

protectedslot

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

References SpectrumWidget::canvas(), SpectrumCanvas::getCurrentLayer(), SpectrumCanvas::getLayerCount(), LayerData::getPeakData(), TOPPViewBase::hasPeptideIdentifications(), TOPPViewBase::views_tabwidget_, and TOPPViewBase::window_().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow(), and TOPPViewBase::TOPPViewBase().

estimateNoiseFromRandomMS1Scans()

float estimateNoiseFromRandomMS1Scans	(	const ExperimentType &	exp,
		UInt	n_scans = 10
	)

Estimates the noise by evaluating n_scans random scans of MS level 1. Assumes that 4/5 of intensities is noise.

References TOPPViewBase::containsMS1Scans(), MSExperiment::end(), and MSExperiment::size().

Referenced by TOPPViewBase::addData().

fileChanged_

void fileChanged_ ( const String &  filename )

protectedslot

Called if a data file has been externally changed.

References FileWatcher::addFile(), SpectrumWidget::canvas(), LayerData::DT_CHROMATOGRAM, LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_PEAK, LayerData::filename, LayerData::getConsensusMap(), LayerData::getFeatureMap(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), LayerData::getPeakDataMuteable(), Param::getValue(), ConsensusXMLFile::load(), FileHandler::loadExperiment(), FileHandler::loadFeatures(), DefaultParamHandler::param_, FileWatcher::removeFile(), String::toQString(), LayerData::type, TOPPViewBase::updateFilterBar(), SpectrumCanvas::updateLayer(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), TOPPViewBase::watcher_, TOPPViewBase::watcher_msgbox_, BaseException::what(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

filterContextMenu

void filterContextMenu ( const QPoint &  pos )

protectedslot

slot for filter manager context menu

References DataFilters::add(), TOPPViewBase::filterEdit(), LayerData::filters, TOPPViewBase::filters_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), SpectrumCanvas::getCurrentLayer(), TOPPViewBase::layer_name, LayerData::name, DataFilters::remove(), SpectrumCanvas::setFilters(), String::toQString(), TOPPViewBase::updateFilterBar(), and TOPPViewBase::visible.

Referenced by TOPPViewBase::TOPPViewBase().

filterEdit

void filterEdit ( QListWidgetItem *  item )

protectedslot

slot for editing a filter

References LayerData::filters, TOPPViewBase::filters_, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), DataFilters::replace(), SpectrumCanvas::setFilters(), and TOPPViewBase::updateFilterBar().

Referenced by TOPPViewBase::filterContextMenu(), and TOPPViewBase::TOPPViewBase().

finishTOPPToolExecution

void finishTOPPToolExecution ( int  exitCode, QProcess::ExitStatus  exitStatus  )

protectedslot

slot for the finished signal of the TOPP tools execution

References TOPPViewBase::addDataFile(), Param::getValue(), TOPPViewBase::log_, TOPPViewBase::LS_ERROR, TOPPViewBase::LS_NOTICE, DefaultParamHandler::param_, File::readable(), File::remove(), TOPPViewBase::showLogMessage_(), TOPPViewBase::topp_, String::toQString(), DataValue::toString(), and TOPPViewBase::updateMenu().

Referenced by TOPPViewBase::runTOPPTool_().

getActive1DWidget()

Spectrum1DWidget * getActive1DWidget

(

)

const

returns a pointer to the active Spectrum1DWidget (0 the active window is no Spectrum1DWidget or there is no active window)

References TOPPViewBase::getActiveSpectrumWidget().

Referenced by TOPPViewBase::layerContextMenu(), TOPPViewBase::setDrawMode1D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateToolBar().

getActive2DWidget()

Spectrum2DWidget * getActive2DWidget

(

)

const

returns a pointer to the active Spectrum2DWidget (0 the active window is no Spectrum2DWidget or there is no active window)

References TOPPViewBase::getActiveSpectrumWidget().

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::changeLayerFlag(), TOPPViewBase::changeUnassigned(), TOPPViewBase::loadFiles(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::toggleProjections(), TOPPViewBase::updateToolBar(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

getActive3DWidget()

Spectrum3DWidget * getActive3DWidget

(

)

const

returns a pointer to the active Spectrum3DWidget (0 the active window is no Spectrum2DWidget or there is no active window)

References TOPPViewBase::getActiveSpectrumWidget().

Referenced by TOPPViewBase::loadFiles(), and TOPPViewBase::updateToolBar().

getActiveCanvas()

SpectrumCanvas * getActiveCanvas

(

)

const

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

References SpectrumWidget::canvas(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::getCurrentLayer(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerEdit(), TOPPViewBase::layerFilterVisibilityChange(), TOPPViewBase::layerSelectionChange(), TOPPViewBase::layerVisibilityChange(), TOPPViewBase::layerZoomChanged(), 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::updateCurrentPath(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateViewBar().

getActiveSpectrumWidget()

SpectrumWidget * getActiveSpectrumWidget

(

)

const

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

References TOPPViewBase::ws_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerStatistics(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::loadFiles(), TOPPViewBase::resetZoom(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::setIntensityMode(), TOPPViewBase::showGoToDialog(), TOPPViewBase::toggleAxisLegends(), TOPPViewBase::updateToolBar(), and TOPPViewBase::viewTabwidgetDoubleClicked().

getCurrentLayer()

const LayerData * getCurrentLayer

(

)

const

Returns the active Layer data (0 if no layer is active)

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::getCurrentLayer().

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::filterContextMenu(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::updateCurrentPath(), and TOPPViewBase::updateFilterBar().

getFileList_()

QStringList getFileList_ ( const String &  path_overwrite = "" )

protected

Shows a dialog where the user can select files.

References TOPPViewBase::current_path_, and String::toQString().

Referenced by TOPPViewBase::metadataFileDialog(), TOPPViewBase::openExampleDialog(), and TOPPViewBase::openFileDialog().

getFilenamesOfOpenFiles_()

std::set< String > getFilenamesOfOpenFiles_ ( )

protected

unique list of files referenced by all layers

References SpectrumWidget::canvas(), LayerData::filename, SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), and TOPPViewBase::ws_.

getSpectraIdentificationViewWidget()

SpectraIdentificationViewWidget * getSpectraIdentificationViewWidget

(

)

returns a pointer to the SpectraIdentificationViewWidget

References TOPPViewBase::spectra_identification_view_widget_.

getSpectrumParameters()

Param getSpectrumParameters

(

UInt

dim

)

Returns the parameters for a SpectrumCanvas of dimension dim.

References Param::copy(), Param::getValue(), TOPPViewBase::out, DefaultParamHandler::param_, and DataValue::toString().

Referenced by TOPPViewBase::addData(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

getWorkspace()

EnhancedWorkspace * getWorkspace

(

)

const

returns a pointer to the EnhancedWorkspace containing SpectrumWidgets

References TOPPViewBase::ws_.

hasMS1Zeros()

bool hasMS1Zeros ( const ExperimentType &  exp )

static

Returns true of experiment has at least one exact zero valued peak in any of its MS1 spectra.

References TOPPViewBase::containsMS1Scans(), and MSExperiment::size().

Referenced by TOPPViewBase::addData().

hasPeptideIdentifications()

bool hasPeptideIdentifications ( const ExperimentType &  map )

static

Returns true if the experiment map contains peptide identifications.

References MSExperiment::empty(), and MSExperiment::size().

Referenced by TOPPViewBase::enhancedWorkspaceWindowChanged().

initializeDefaultParameters_()

void initializeDefaultParameters_ ( )

protected

Initializes the default parameters on TOPPView construction.

References DefaultParamHandler::defaults_, DefaultParamHandler::getDefaults(), Param::insert(), Param::setMaxInt(), Param::setMinInt(), Param::setSectionDescription(), Param::setValidStrings(), Param::setValue(), and DefaultParamHandler::subsections_.

Referenced by TOPPViewBase::TOPPViewBase().

layerActivated

void layerActivated ( )

slot

gets called if a layer got activated

References TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateToolBar(), and TOPPViewBase::updateViewBar().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

layerContextMenu

void layerContextMenu ( const QPoint &  pos )

protectedslot

slot for layer manager context menu

References Spectrum1DWidget::canvas(), Spectrum1DCanvas::flipLayer(), Spectrum1DCanvas::flippedLayersExist(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getLayer(), TOPPViewBase::layer_manager_, LayerData::name, SpectrumCanvas::removeLayer(), SpectrumCanvas::setLayerName(), Spectrum1DCanvas::setMirrorModeActive(), SpectrumCanvas::showCurrentLayerPreferences(), TOPPViewBase::tab_bar_, String::toQString(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateViewBar().

Referenced by TOPPViewBase::TOPPViewBase().

layerDeactivated

void layerDeactivated ( )

slot

gets called if a layer got deactivated

layerEdit

void layerEdit ( QListWidgetItem *  )

protectedslot

slot for editing the preferences of the current layer

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showCurrentLayerPreferences().

Referenced by TOPPViewBase::TOPPViewBase().

layerFilterVisibilityChange

void layerFilterVisibilityChange ( bool  on )

protectedslot

Enables/disables the data filters for the current layer.

References SpectrumCanvas::changeLayerFilterState(), and TOPPViewBase::getActiveCanvas().

Referenced by TOPPViewBase::TOPPViewBase().

layerSelectionChange

void layerSelectionChange ( int  i )

protectedslot

slot for layer manager selection change

References SpectrumCanvas::activateLayer(), TOPPViewBase::getActiveCanvas(), and TOPPViewBase::updateFilterBar().

Referenced by TOPPViewBase::TOPPViewBase().

layerStatistics

void layerStatistics ( )

slot

Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data.

References TOPPViewBase::getActiveSpectrumWidget(), SpectrumWidget::showStatistics(), and TOPPViewBase::updateFilterBar().

Referenced by TOPPViewBase::TOPPViewBase().

layerVisibilityChange

void layerVisibilityChange ( QListWidgetItem *  item )

protectedslot

slot for layer manager visibility change (check box)

References SpectrumCanvas::changeVisibility(), TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getLayer(), TOPPViewBase::layer_manager_, LayerData::visible, and TOPPViewBase::visible.

Referenced by TOPPViewBase::TOPPViewBase().

layerZoomChanged

void layerZoomChanged ( )

slot

gets called when a layer changes in zoom

References Spectrum1DWidget::canvas(), SpectrumWidget::canvas(), LayerData::DT_CHROMATOGRAM, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), LayerData::getPeakData(), SpectrumCanvas::getVisibleArea(), DIntervalBase< D >::maxX(), DIntervalBase< D >::minX(), DIntervalBase< D >::setMaxX(), DIntervalBase< D >::setMinX(), SpectrumCanvas::setVisibleArea(), LayerData::type, TOPPViewBase::ws_, and TOPPViewBase::zoom_together_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

linkZoom

void linkZoom ( )

slot

link the zoom of individual windows

References TOPPViewBase::linkZoom_action_, and TOPPViewBase::zoom_together_.

Referenced by TOPPViewBase::TOPPViewBase().

loadFile

void loadFile ( QString  filename )

slot

Loads a file given by the passed string.

References TOPPViewBase::addDataFile().

loadFiles()

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

Opens all the files in the string list.

References TOPPViewBase::addDataFile(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), LayerData::param, SpectrumCanvas::setCurrentLayerParameters(), and Param::setValue().

Referenced by main().

loadPreferences()

void loadPreferences

(

String

filename = ""

)

Loads the preferences from the filename given.

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

References Param::begin(), Param::copy(), Param::end(), File::exists(), Param::exists(), Param::getValue(), VersionInfo::getVersion(), ParamXMLFile::load(), DefaultParamHandler::param_, TOPPViewBase::recent_files_, DefaultParamHandler::setParameters(), Param::setValue(), Param::size(), String::toQString(), DataValue::toString(), and TOPPViewBase::updateRecentMenu_().

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

logContextMenu

void logContextMenu ( const QPoint &  pos )

protectedslot

slot for log window context menu

References TOPPViewBase::log_.

Referenced by TOPPViewBase::TOPPViewBase().

metadataFileDialog

void metadataFileDialog ( )

slot

dialog for inspecting database meta data

References MetaDataBrowser::add(), TOPPViewBase::getFileList_(), FileHandler::getOptions(), FileHandler::loadExperiment(), PeakFileOptions::setMetadataOnly(), and BaseException::what().

Referenced by TOPPViewBase::TOPPViewBase().

openExampleDialog

void openExampleDialog ( )

slot

shows the file dialog for opening example files

References TOPPViewBase::addDataFile(), TOPPViewBase::getFileList_(), and File::getOpenMSDataPath().

Referenced by TOPPViewBase::TOPPViewBase().

openFileDialog

void openFileDialog ( )

slot

shows the file dialog for opening files

References TOPPViewBase::addDataFile(), and TOPPViewBase::getFileList_().

Referenced by TOPPViewBase::TOPPViewBase().

openRecentFile

void openRecentFile ( )

protectedslot

Opens a file from the recent files menu.

References TOPPViewBase::addDataFile().

Referenced by TOPPViewBase::TOPPViewBase().

preferencesDialog

void preferencesDialog ( )

slot

shows the preferences dialog

References Param::getValue(), TOPPViewBase::LS_ERROR, DefaultParamHandler::param_, TOPPViewBase::savePreferences(), Param::setValue(), TOPPViewBase::showLogMessage_(), DataValue::toBool(), and DataValue::toQString().

Referenced by TOPPViewBase::TOPPViewBase().

rerunTOPPTool

void rerunTOPPTool ( )

protectedslot

returns the last invoked TOPP tool with the same parameters

References TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), TOPPViewBase::LS_NOTICE, File::remove(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showLogMessage_(), TOPPViewBase::topp_, and LayerData::visible.

Referenced by TOPPViewBase::TOPPViewBase().

resetZoom

void resetZoom ( )

slot

References SpectrumWidget::canvas(), TOPPViewBase::getActiveSpectrumWidget(), and SpectrumCanvas::resetZoom().

Referenced by TOPPViewBase::TOPPViewBase().

runTOPPTool_()

void runTOPPTool_ ( )

protected

Runs the TOPP tool according to the information in topp_.

References LayerData::chromatogram_flag_set(), LayerData::DT_CHROMATOGRAM, LayerData::DT_FEATURE, LayerData::DT_PEAK, File::findExecutable(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), LayerData::getConsensusMap(), SpectrumCanvas::getCurrentLayer(), LayerData::getCurrentSpectrumIndex(), LayerData::getFeatureMap(), LayerData::getPeakData(), SpectrumCanvas::getVisibleConsensusData(), SpectrumCanvas::getVisibleFeatureData(), SpectrumCanvas::getVisiblePeakData(), SpectrumWidget::getWindowId(), ProgressLogger::GUI, TOPPViewBase::LS_ERROR, TOPPViewBase::LS_NOTICE, LayerData::name, LayerData::remove_chromatogram_flag(), ProgressLogger::setLogType(), TOPPViewBase::showLogMessage_(), ConsensusXMLFile::store(), FeatureXMLFile::store(), MzMLFile::store(), TOPPViewBase::topp_, String::toQString(), LayerData::type, TOPPViewBase::updateMenu(), TOPPViewBase::updateProcessLog(), and File::writable().

Referenced by TOPPViewBase::rerunTOPPTool(), and TOPPViewBase::showTOPPDialog_().

saveLayerAll

void saveLayerAll ( )

slot

Saves the whole current layer data.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::saveCurrentLayer().

Referenced by TOPPViewBase::TOPPViewBase().

saveLayerVisible

void saveLayerVisible ( )

slot

Saves the visible layer data.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::saveCurrentLayer().

Referenced by TOPPViewBase::TOPPViewBase().

savePreferences()

void savePreferences

(

)

Stores the preferences (used when this window is closed)

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

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

setDrawMode1D

void setDrawMode1D ( int  index )

slot

References Spectrum1DWidget::canvas(), TOPPViewBase::getActive1DWidget(), and Spectrum1DCanvas::setDrawMode().

Referenced by TOPPViewBase::showSpectrumGenerationDialog(), and TOPPViewBase::TOPPViewBase().

setIntensityMode

void setIntensityMode ( int  index )

slot

References TOPPViewBase::getActiveSpectrumWidget(), TOPPViewBase::intensity_button_group_, and SpectrumWidget::setIntensityMode().

Referenced by TOPPViewBase::showCurrentPeaksAs3D(), and TOPPViewBase::TOPPViewBase().

showAboutDialog

void showAboutDialog ( )

slot

Shows the 'About' dialog.

References QApplicationTOPP::showAboutDialog().

Referenced by TOPPViewBase::TOPPViewBase().

showCurrentPeaksAs2D

void showCurrentPeaksAs2D ( )

slot

Shows the current peak data of the active layer in 2D.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum2DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, LayerData::filename, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), LayerData::getOnDiscPeakData(), LayerData::getPeakDataMuteable(), TOPPViewBase::getSpectrumParameters(), String::hasSuffix(), LayerData::name, String::prefix(), SpectrumCanvas::setLayerName(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

showCurrentPeaksAs3D

void showCurrentPeaksAs3D ( )

slot

Shows the current peak data of the active layer in 3D.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum3DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, LayerData::DT_PEAK, LayerData::filename, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayerIndex(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), LayerData::getPeakDataMuteable(), TOPPViewBase::getSpectrumParameters(), SpectrumCanvas::IM_SNAP, LayerData::isIonMobilityData(), TOPPViewBase::LS_NOTICE, LayerData::name, Spectrum3DCanvas::openglwidget(), TOPPViewBase::setIntensityMode(), SpectrumCanvas::setLayerName(), SpectrumCanvas::setVisibleArea(), Spectrum3DOpenGLCanvas::setYLabel(), TOPPViewBase::showLogMessage_(), TOPPViewBase::showSpectrumWidgetInWindow(), LayerData::type, TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

showCurrentPeaksAsDIA

void showCurrentPeaksAsDIA ( )

slot

Shows the current peak data of the active layer as DIA data.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum2DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, LayerData::filename, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), LayerData::getCurrentSpectrum(), LayerData::getOnDiscPeakData(), LayerData::getPeakData(), SpectrumSettings::getPrecursors(), TOPPViewBase::getSpectrumParameters(), String::hasSuffix(), LayerData::isDIAData(), OpenMS::Constants::k, LayerData::name, String::prefix(), SpectrumCanvas::setLayerName(), MSSpectrum::setMSLevel(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

showCurrentPeaksAsIonMobility

void showCurrentPeaksAsIonMobility ( )

slot

Shows the current peak data of the active layer as ion mobility.

References SpectrumCanvas::activeLayerIndex(), SpectrumCanvas::addLayer(), Spectrum2DWidget::canvas(), TOPPViewBase::CAPTION_3D_SUFFIX_, TOPPViewBase::containsIMData(), LayerData::filename, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getCurrentLayer(), LayerData::getCurrentSpectrum(), LayerData::getCurrentSpectrumIndex(), MSSpectrum::getFloatDataArrays(), TOPPViewBase::getSpectrumParameters(), String::hasSuffix(), OpenMS::Constants::k, LayerData::name, String::prefix(), SpectrumCanvas::setLayerName(), AxisWidget::setLegend(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), TOPPViewBase::ws_, and SpectrumWidget::xAxis().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

showCursorStatus

void showCursorStatus ( double  mz, double  rt  )

slot

shows m/z and rt in the status bar

References TOPPViewBase::message_label_, TOPPViewBase::mz_label_, String::number(), and TOPPViewBase::rt_label_.

Referenced by TOPPViewBase::showCursorStatusInvert(), and TOPPViewBase::showSpectrumWidgetInWindow().

showCursorStatusInvert

void showCursorStatusInvert ( double  mz, double  rt  )

slot

shows m/z and rt in the status bar (inverting RT and m/z)

References TOPPViewBase::showCursorStatus().

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

showGoToDialog

void showGoToDialog ( )

slot

shows the DB dialog for opening files

References TOPPViewBase::getActiveSpectrumWidget(), and SpectrumWidget::showGoToDialog().

Referenced by TOPPViewBase::TOPPViewBase().

showLogMessage_()

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

protected

Shows a log message in the log_ window.

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

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::annotateMS1FromMassFingerprinting_(), TOPPViewBase::annotateWithID(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::preferencesDialog(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showTOPPDialog_(), and TOPPViewBase::updateToolBar().

showPreferences

void showPreferences ( )

slot

Shows current layer preferences.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showCurrentLayerPreferences().

Referenced by TOPPViewBase::TOPPViewBase().

showSpectrumAlignmentDialog

void showSpectrumAlignmentDialog ( )

slot

Shows the spectrum alignment dialog.

References Spectrum1DWidget::canvas(), SpectrumAlignmentDialog::get1stLayerIndex(), SpectrumAlignmentDialog::get2ndLayerIndex(), TOPPViewBase::getActive1DWidget(), Spectrum1DCanvas::getAlignmentScore(), Spectrum1DCanvas::getAlignmentSize(), SpectrumAlignmentDialog::getTolerance(), SpectrumAlignmentDialog::isPPM(), Spectrum1DCanvas::mirrorModeActive(), TOPPViewBase::param, Spectrum1DWidget::performAlignment(), and Param::setValue().

Referenced by TOPPViewBase::TOPPViewBase().

showSpectrumAs1D [1/2]

void showSpectrumAs1D ( int  index )

slot

Shows the spectrum with index index of the active layer in 1D.

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::identificationview_behavior_, TOPPViewSpectraViewBehavior::showSpectrumAs1D(), TOPPViewIdentificationViewBehavior::showSpectrumAs1D(), TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, and TOPPViewBase::spectraview_behavior_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

showSpectrumAs1D [2/2]

void showSpectrumAs1D ( std::vector< int, std::allocator< int > >  indices )

slot

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewSpectraViewBehavior::showSpectrumAs1D(), TOPPViewBase::spectra_view_widget_, and TOPPViewBase::spectraview_behavior_.

showSpectrumBrowser

void showSpectrumBrowser ( )

protectedslot

shows the spectrum browser and updates it

References TOPPViewBase::updateViewBar(), and TOPPViewBase::views_dockwidget_.

showSpectrumGenerationDialog

void showSpectrumGenerationDialog ( )

slot

Shows the theoretical spectrum generation dialog.

References TOPPViewBase::addData(), MSExperiment::addSpectrum(), Spectrum1DCanvas::DM_PEAKS, TOPPViewBase::draw_group_1d_, LayerData::DT_CHROMATOGRAM, AASequence::fromString(), AASequence::getMonoWeight(), TheoreticalSpectrumGenerationDialog::getParam(), TheoreticalSpectrumGenerationDialog::getSequence(), TheoreticalSpectrumGenerator::getSpectrum(), Param::getValue(), Precursor::setCharge(), TOPPViewBase::setDrawMode1D(), MSSpectrum::setMSLevel(), Peak1D::setMZ(), DefaultParamHandler::setParameters(), SpectrumSettings::setPrecursors(), Param::setValue(), DataValue::toBool(), and BaseException::what().

Referenced by TOPPViewBase::TOPPViewBase().

showSpectrumMetaData

void showSpectrumMetaData ( int  spectrum_index )

protectedslot

shows the spectrum metadata

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showMetaData().

Referenced by TOPPViewBase::TOPPViewBase().

showSpectrumWidgetInWindow()

void showSpectrumWidgetInWindow	(	SpectrumWidget *	sw,
		const String &	caption
	)

Opens the provided spectrum widget in a new window.

References EnhancedTabBar::addTab(), SpectrumWidget::canvas(), TOPPViewBase::copyLayer(), TOPPViewBase::enhancedWorkspaceWindowChanged(), Spectrum2DWidget::getHorizontalProjection(), Spectrum2DWidget::getVerticalProjection(), SpectrumWidget::getWindowId(), TOPPViewBase::layerActivated(), TOPPViewBase::layerZoomChanged(), EnhancedTabBar::setCurrentId(), SpectrumWidget::setWindowId(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showCursorStatus(), TOPPViewBase::showCursorStatusInvert(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::showStatusMessage(), TOPPViewBase::tab_bar_, String::toQString(), TOPPViewBase::updateLayerBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

showStatusMessage

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

slot

Shows a status message in the status bar.

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

References TOPPViewBase::message_label_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

showTOPPDialog

void showTOPPDialog ( )

slot

Apply TOPP tool.

References TOPPViewBase::showTOPPDialog_().

Referenced by TOPPViewBase::TOPPViewBase().

showTOPPDialog_()

void showTOPPDialog_ ( bool  visible )

protected

Apply TOPP tool. If visible is true, only the visible data is used, otherwise the whole layer is used.

References TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), SpectrumCanvas::getCurrentLayer(), ToolsDialog::getInput(), ToolsDialog::getOutput(), ToolsDialog::getTool(), File::getUniqueName(), Param::getValue(), TOPPViewBase::LS_ERROR, TOPPViewBase::LS_NOTICE, DefaultParamHandler::param_, TOPPViewBase::runTOPPTool_(), TOPPViewBase::showLogMessage_(), TOPPViewBase::topp_, DataValue::toString(), LayerData::visible, TOPPViewBase::visible, and File::writable().

Referenced by TOPPViewBase::showTOPPDialog().

showURL

void showURL ( )

slot

shows the URL stored in the data of the sender QAction

References GUIHelpers::openURL().

Referenced by TOPPViewBase::TOPPViewBase().

tileHorizontal

void tileHorizontal ( )

slot

tile the open windows horizontally

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

tileVertical

void tileVertical ( )

slot

tile the open windows vertically

References TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

toggleAxisLegends

void toggleAxisLegends ( )

slot

Toggles the axis legends.

References TOPPViewBase::getActiveSpectrumWidget(), and SpectrumWidget::showLegend().

Referenced by TOPPViewBase::TOPPViewBase().

toggleGridLines

void toggleGridLines ( )

slot

Toggles the grid lines.

References TOPPViewBase::getActiveCanvas(), and SpectrumCanvas::showGridLines().

Referenced by TOPPViewBase::TOPPViewBase().

toggleProjections

void toggleProjections ( )

slot

References TOPPViewBase::getActive2DWidget(), Spectrum2DWidget::projectionsVisible(), and Spectrum2DWidget::toggleProjections().

Referenced by TOPPViewBase::TOPPViewBase().

updateCurrentPath

void updateCurrentPath ( )

slot

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

References TOPPViewBase::current_path_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), Param::getValue(), DefaultParamHandler::param_, and File::path().

Referenced by TOPPViewBase::layerActivated(), and TOPPViewBase::TOPPViewBase().

updateFilterBar

void updateFilterBar ( )

slot

adapts the filter bar to the active window

References LayerData::filters, TOPPViewBase::filters_, TOPPViewBase::filters_check_box_, TOPPViewBase::getActiveCanvas(), TOPPViewBase::getCurrentLayer(), SpectrumCanvas::getCurrentLayer(), SpectrumCanvas::getLayerCount(), DataFilters::isActive(), DataFilters::size(), and OpenMS::StringConversions::toString().

Referenced by TOPPViewBase::addData(), TOPPViewBase::fileChanged_(), TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerSelectionChange(), TOPPViewBase::layerStatistics(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), and TOPPViewBase::TOPPViewBase().

updateLayerBar

void updateLayerBar ( )

slot

adapts the layer bar to the active window

References SpectrumCanvas::activeLayerIndex(), LayerData::filename, LayerData::flipped, TOPPViewBase::getActiveCanvas(), SpectrumCanvas::getLayer(), SpectrumCanvas::getLayerCount(), Param::getValue(), TOPPViewBase::layer_manager_, LayerData::modified, LayerData::name, LayerData::param, String::toQString(), DataValue::toQString(), and LayerData::visible.

Referenced by TOPPViewBase::addData(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerContextMenu(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showSpectrumWidgetInWindow(), and TOPPViewBase::TOPPViewBase().

updateMenu

void updateMenu ( )

slot

enabled/disabled menu entries depending on the current state

References Spectrum1DWidget::canvas(), TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActiveCanvas(), Spectrum1DCanvas::mirrorModeActive(), and TOPPViewBase::topp_.

Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::addData(), TOPPViewBase::closeByTab(), TOPPViewBase::closeFile(), TOPPViewBase::fileChanged_(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::layerContextMenu(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), and TOPPViewBase::TOPPViewBase().

updateProcessLog

void updateProcessLog ( )

protectedslot

Appends process output to log window.

References TOPPViewBase::log_, and TOPPViewBase::topp_.

Referenced by TOPPViewBase::runTOPPTool_().

updateRecentMenu_()

void updateRecentMenu_ ( )

protected

update the recent files menu

References Param::getValue(), DefaultParamHandler::param_, TOPPViewBase::recent_actions_, TOPPViewBase::recent_files_, and Param::setValue().

Referenced by TOPPViewBase::addRecentFile_(), and TOPPViewBase::loadPreferences().

updateTabBar

void updateTabBar ( QMdiSubWindow *  w )

slot

brings the tab corresponding to the active window in front

References EnhancedTabBarWidgetInterface::getWindowId(), EnhancedTabBar::setCurrentId(), TOPPViewBase::tab_bar_, and TOPPViewBase::window_id.

Referenced by TOPPViewBase::TOPPViewBase().

updateToolBar

void updateToolBar ( )

slot

updates the toolbar

References LayerData::C_ELEMENTS, Spectrum1DWidget::canvas(), Spectrum2DWidget::canvas(), SpectrumWidget::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_, LayerData::DT_CONSENSUS, LayerData::DT_FEATURE, LayerData::DT_IDENT, LayerData::DT_PEAK, LayerData::F_HULL, LayerData::F_HULLS, LayerData::F_UNASSIGNED, TOPPViewBase::getActive1DWidget(), TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActive3DWidget(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), Spectrum1DCanvas::getDrawMode(), SpectrumCanvas::getIntensityMode(), SpectrumCanvas::getLayerCount(), SpectrumCanvas::getLayerFlag(), LayerData::I_PEPTIDEMZ, TOPPViewBase::intensity_button_group_, LayerData::L_NONE, LayerData::label, TOPPViewBase::LS_ERROR, LayerData::P_PRECURSORS, TOPPViewBase::showLogMessage_(), 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 LayerData::type.

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::changeUnassigned(), TOPPViewBase::layerActivated(), and TOPPViewBase::TOPPViewBase().

updateViewBar

void updateViewBar ( )

slot

adapts view bar to the active window

References TOPPViewBase::getActiveCanvas(), SpectraViewWidget::getComboBox(), SpectrumCanvas::getCurrentLayer(), SpectraIdentificationViewWidget::getLayer(), SpectraIdentificationViewWidget::getTableWidget(), SpectraViewWidget::getTreeWidget(), TOPPViewBase::layer_manager_, SpectraIdentificationViewWidget::setLayer(), TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, SpectraViewWidget::updateEntries(), and TOPPViewBase::views_tabwidget_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateWithID(), TOPPViewBase::fileChanged_(), TOPPViewBase::layerActivated(), TOPPViewBase::layerContextMenu(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showSpectrumBrowser(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

viewChanged

void viewChanged ( int  tab_index )

slot

changes the behavior according to the selected view in the spectra view bar and calls updateSpectraViewBar()

References TOPPViewSpectraViewBehavior::activateBehavior(), TOPPViewIdentificationViewBehavior::activateBehavior(), TOPPViewSpectraViewBehavior::deactivateBehavior(), TOPPViewIdentificationViewBehavior::deactivateBehavior(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::identificationview_behavior_, TOPPViewBase::layer_dock_widget_, TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::spectraview_behavior_, TOPPViewBase::updateViewBar(), and TOPPViewBase::views_tabwidget_.

Referenced by TOPPViewBase::TOPPViewBase().

viewTabwidgetDoubleClicked

void viewTabwidgetDoubleClicked ( int  tab_index )

slot

adds empty ID structure to allow manual annotations

References TOPPViewIdentificationViewBehavior::activateBehavior(), TOPPViewSpectraViewBehavior::deactivateBehavior(), TOPPViewBase::filter_dock_widget_, TOPPViewBase::getActive2DWidget(), TOPPViewBase::getActiveSpectrumWidget(), TOPPViewBase::identificationview_behavior_, TOPPViewBase::layer_dock_widget_, TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::spectraview_behavior_, TOPPViewBase::updateViewBar(), and TOPPViewBase::views_tabwidget_.

Referenced by TOPPViewBase::TOPPViewBase().

window_()

EnhancedTabBarWidgetInterface * window_ ( int  id ) const

protected

Returns the enhanced tabbar widget with id id.

References EnhancedTabBarWidgetInterface::getWindowId(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::addData(), TOPPViewBase::closeByTab(), and TOPPViewBase::enhancedWorkspaceWindowChanged().

Friends And Related Function Documentation

TestTOPPView

friend class TestTOPPView

friend

Member Data Documentation

add_2d_context_

QMenu* add_2d_context_

protected

Additional context menu for 2D layers.

CAPTION_3D_SUFFIX_

const String CAPTION_3D_SUFFIX_ = " (3D)"

staticprivate

Suffix appended to caption of tabs when layer is shown in 3D.

Referenced by TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

current_path_

String current_path_

protected

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

Referenced by TOPPViewBase::annotateWithID(), TOPPViewBase::getFileList_(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateCurrentPath().

dm_elements_2d_

QAction* dm_elements_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

dm_hull_2d_

QAction* dm_hull_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

dm_hulls_2d_

QAction* dm_hulls_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

dm_ident_2d_

QAction* dm_ident_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

dm_label_2d_

QToolButton* dm_label_2d_

protected

Referenced by TOPPViewBase::changeLabel(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

dm_precursors_2d_

QAction* dm_precursors_2d_

protected

Referenced by TOPPViewBase::changeLayerFlag(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

dm_unassigned_2d_

QToolButton* dm_unassigned_2d_

protected

Referenced by TOPPViewBase::changeUnassigned(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

draw_group_1d_

QButtonGroup* draw_group_1d_

protected

Referenced by TOPPViewBase::showSpectrumGenerationDialog(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

file_name

String file_name

filter_dock_widget_

QDockWidget* filter_dock_widget_

protected

Referenced by TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

filters_

QListWidget* filters_

protected

Referenced by TOPPViewBase::filterContextMenu(), TOPPViewBase::filterEdit(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateFilterBar().

filters_check_box_

QCheckBox* filters_check_box_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateFilterBar().

group_label_2d_

QActionGroup* group_label_2d_

protected

Referenced by TOPPViewBase::TOPPViewBase().

group_unassigned_2d_

QActionGroup* group_unassigned_2d_

protected

Referenced by TOPPViewBase::TOPPViewBase().

identificationview_behavior_

TOPPViewIdentificationViewBehavior* identificationview_behavior_

protected

TOPPView behavior for the identification view.

Referenced by TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), TOPPViewBase::viewTabwidgetDoubleClicked(), and TOPPViewBase::~TOPPViewBase().

in

String in

intensity_button_group_

QButtonGroup* intensity_button_group_

protected

Referenced by TOPPViewBase::setIntensityMode(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

layer_dock_widget_

QDockWidget* layer_dock_widget_

protected

Referenced by TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

layer_manager_

QListWidget* layer_manager_

protected

Layer management widget.

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::layerContextMenu(), TOPPViewBase::layerVisibilityChange(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateLayerBar(), and TOPPViewBase::updateViewBar().

layer_name

String layer_name

Referenced by TOPPViewBase::filterContextMenu().

linkZoom_action_

QAction* linkZoom_action_

protected

Referenced by TOPPViewBase::linkZoom(), and TOPPViewBase::TOPPViewBase().

log_

QTextEdit* log_

protected

Log output window.

Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::logContextMenu(), TOPPViewBase::showLogMessage_(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateProcessLog().

message_label_

QLabel* message_label_

protected

Label for messages in the status bar.

Referenced by TOPPViewBase::showCursorStatus(), TOPPViewBase::showStatusMessage(), and TOPPViewBase::TOPPViewBase().

mz_label_

QLabel* mz_label_

protected

m/z label for messages in the status bar

Referenced by TOPPViewBase::showCursorStatus(), and TOPPViewBase::TOPPViewBase().

out

String out

Referenced by TOPPViewBase::getSpectrumParameters().

param

Param param

Referenced by TOPPViewBase::showSpectrumAlignmentDialog().

process

QProcess* process

projections_2d_

QAction* projections_2d_

protected

Referenced by TOPPViewBase::TOPPViewBase().

recent_actions_

std::vector<QAction*> recent_actions_

protected

list of the recently opened files actions (menu entries)

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateRecentMenu_().

recent_files_

QStringList recent_files_

protected

list of the recently opened files

Referenced by TOPPViewBase::addRecentFile_(), TOPPViewBase::loadPreferences(), TOPPViewBase::savePreferences(), and TOPPViewBase::updateRecentMenu_().

rt_label_

QLabel* rt_label_

protected

RT label for messages in the status bar.

Referenced by TOPPViewBase::showCursorStatus(), and TOPPViewBase::TOPPViewBase().

spectra_identification_view_widget_

SpectraIdentificationViewWidget* spectra_identification_view_widget_

protected

Referenced by TOPPViewBase::getSpectraIdentificationViewWidget(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateViewBar().

spectra_view_widget_

SpectraViewWidget* spectra_view_widget_

protected

Referenced by TOPPViewBase::copyLayer(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateViewBar().

spectraview_behavior_

TOPPViewSpectraViewBehavior* spectraview_behavior_

protected

TOPPView behavior for the spectra view.

Referenced by TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::viewChanged(), TOPPViewBase::viewTabwidgetDoubleClicked(), and TOPPViewBase::~TOPPViewBase().

spectrum_id

Size spectrum_id

Referenced by TOPPViewBase::addData(), and TOPPViewBase::addDataFile().

tab_bar_

EnhancedTabBar* tab_bar_

protected

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

Referenced by TOPPViewBase::layerContextMenu(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateTabBar().

timer

QTime timer

tool

String tool

tool_bar_

QToolBar* tool_bar_

protected

Referenced by TOPPViewBase::TOPPViewBase().

tool_bar_1d_

QToolBar* tool_bar_1d_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

tool_bar_2d_cons_

QToolBar* tool_bar_2d_cons_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

tool_bar_2d_feat_

QToolBar* tool_bar_2d_feat_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

tool_bar_2d_ident_

QToolBar* tool_bar_2d_ident_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

tool_bar_2d_peak_

QToolBar* tool_bar_2d_peak_

protected

Referenced by TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

topp_

struct { ... } topp_

Information needed for execution of TOPP tools.

Referenced by TOPPViewBase::abortTOPPTool(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateProcessLog().

views_dockwidget_

QDockWidget* views_dockwidget_

protected

Referenced by TOPPViewBase::showSpectrumBrowser(), and TOPPViewBase::TOPPViewBase().

views_tabwidget_

QTabWidget* views_tabwidget_

protected

Tabwidget that hold the different views on the loaded data.

Referenced by TOPPViewBase::addData(), TOPPViewBase::annotateWithID(), TOPPViewBase::enhancedWorkspaceWindowChanged(), TOPPViewBase::TOPPViewBase(), TOPPViewBase::updateViewBar(), TOPPViewBase::viewChanged(), and TOPPViewBase::viewTabwidgetDoubleClicked().

visible

bool visible

Referenced by TOPPViewBase::filterContextMenu(), TOPPViewBase::layerVisibilityChange(), and TOPPViewBase::showTOPPDialog_().

watcher_

FileWatcher* watcher_

protected

Watcher that tracks file changes (in order to update the data in the different views)

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::fileChanged_(), and TOPPViewBase::TOPPViewBase().

watcher_msgbox_

bool watcher_msgbox_

protected

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_().

window_id

UInt window_id

Referenced by TOPPViewBase::addData(), TOPPViewBase::addDataFile(), and TOPPViewBase::updateTabBar().

ws_

EnhancedWorkspace* ws_

protected

Main workspace.

Referenced by TOPPViewBase::addData(), TOPPViewBase::closeEvent(), TOPPViewBase::closeFile(), TOPPViewBase::fileChanged_(), TOPPViewBase::getActiveCanvas(), TOPPViewBase::getActiveSpectrumWidget(), TOPPViewBase::getFilenamesOfOpenFiles_(), TOPPViewBase::getWorkspace(), TOPPViewBase::layerZoomChanged(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showCurrentPeaksAsDIA(), TOPPViewBase::showCurrentPeaksAsIonMobility(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::window_().

zoom_together_

bool zoom_together_

protected

Stores whether the individual windows should zoom together (be linked) or not.

Referenced by TOPPViewBase::layerZoomChanged(), TOPPViewBase::linkZoom(), and TOPPViewBase::TOPPViewBase().