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 ExperimentType::SpectrumType	SpectrumType
	Peak spectrum type.
Public Slots
void	updateCurrentPath ()
	changes the current path according to the currently active window/layer
void	showURL ()
	shows the URL stored in the data of the sender QAction
void	openFileDialog ()
	shows the file dialog for opening files
void	openExampleDialog ()
	shows the file dialog for opening example files
void	openDatabaseDialog ()
	shows the DB dialog for opening files
void	showGoToDialog ()
	shows the goto dialog
void	preferencesDialog ()
	shows the preferences dialog
void	layerStatistics ()
	Shows statistics (count,min,max,avg) about Intensity, Quality, Charge and meta data.
void	editMetadata ()
	lets the user edit the meta data of a layer
void	layerActivated ()
	get's called if a layer got activated
void	layerZoomChanged ()
	gets called when a layer changes in zoom
void	linkZoom ()
	link the zoom of individual windows
void	layerDeactivated ()
	get's called if a layer got deactivated
void	activate1DSpectrum (int index)
	Activation of 1D spectrum.
void	activate1DSpectrum (std::vector< int, std::allocator< int > > indices)
	Activation of 1D with multiple entries (e.g. chromatograms).
void	deactivate1DSpectrum (int index)
	Deactivation of 1D spectrum.
void	closeFile ()
	closes the active window
void	updateToolBar ()
	updates the toolbar
void	updateLayerBar ()
	adapts the layer bar to the active window
void	updateViewBar ()
	adapts view bar to the active window
void	viewChanged (int)
	changes the behavior according to the selected view in the spectra view bar and calls updateSpectraViewBar()
void	updateFilterBar ()
	adapts the filter bar to the active window
void	updateMenu ()
	enabled/disabled menu entries depending on the current state
void	updateTabBar (QWidget *w)
	brings the tab corresponding to the active window in front
void	tileVertical ()
	tile the open windows vertically
void	tileHorizontal ()
	tile the open windows horizontally
void	showStatusMessage (std::string msg, OpenMS::UInt time)
	Shows a status message in the status bar.
void	showCursorStatus (double mz, double rt)
	shows m/z and rt in the status bar
void	showCursorStatusInvert (double mz, double rt)
	shows m/z and rt in the status bar (inverting RT and m/z)
void	showTOPPDialog ()
	Apply TOPP tool.
void	annotateWithID ()
	Annotates current layer with ID data.
void	showSpectrumGenerationDialog ()
	Shows the theoretical spectrum generation dialog.
void	showSpectrumAlignmentDialog ()
	Shows the spectrum alignment dialog.
void	showSpectrumAs1D (int index)
	Shows the spectrum with index `index` of the active layer in 1D.
void	showSpectrumAs1D (std::vector< int, std::allocator< int > > indices)
void	showCurrentPeaksAs2D ()
	Shows the current peak data of the active layer in 2D.
void	showCurrentPeaksAs3D ()
	Shows the current peak data of the active layer in 3D.
void	showAboutDialog ()
	Shows the 'About' dialog.
void	saveLayerAll ()
	Saves the whole current layer data.
void	saveLayerVisible ()
	Saves the visible layer data.
void	toggleGridLines ()
	Toggles the grid lines.
void	toggleAxisLegends ()
	Toggles the axis legends.
void	showPreferences ()
	Shows current layer preferences.
void	metadataDatabaseDialog ()
	dialog for inspecting database meta data
void	metadataFileDialog ()
	dialog for inspecting file meta data
void	loadFile (QString)
	Loads a file given by the passed string.
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=0)
	Constructor.
	~TOPPViewBase ()
	Destructor.
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.
void	addDataDB (UInt db_id, bool show_options, String caption="", UInt window_id=0)
	Opens and displays a data from a database.
void	addData (FeatureMapSharedPtrType feature_map, ConsensusMapSharedPtrType consensus_map, std::vector< PeptideIdentification > &peptides, ExperimentSharedPtrType 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.
void	loadFiles (const StringList &list, QSplashScreen *splash_screen)
	Opens all the files in the string list.
void	loadPreferences (String filename="")
	Loads the preferences from the filename given.
void	savePreferences ()
	Stores the preferences (used when this window is closed).
Param	getSpectrumParameters (UInt dim)
	Returns the parameters for a SpectrumCanvas of dimension `dim`.
const LayerData *	getCurrentLayer () const
	Returns the active Layer data (0 if no layer is active).
SpectrumCanvas *	getActiveCanvas () const
	returns a pointer to the active SpectrumCanvas (0 if none is active)
SpectraIdentificationViewWidget *	getSpectraIdentificationViewWidget ()
	returns a pointer to the SpectraIdentificationViewWidget
void	showSpectrumWidgetInWindow (SpectrumWidget *sw, const String &caption)
	Opens the provided spectrum widget in a new window.
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.


EnhancedWorkspace *	getWorkspace () const
	returns a pointer to the EnhancedWorkspace containing SpectrumWidgets
SpectrumWidget *	getActiveSpectrumWidget () const
	returns a pointer to the active SpectrumWidget (0 if none is active)
Spectrum1DWidget *	getActive1DWidget () const
	returns a pointer to the active Spectrum1DWidget (0 the active window is no Spectrum1DWidget or there is no active window)
Spectrum2DWidget *	getActive2DWidget () const
	returns a pointer to the active Spectrum2DWidget (0 the active window is no Spectrum2DWidget or there is no active window)
Spectrum3DWidget *	getActive3DWidget () const
	returns a pointer to the active Spectrum3DWidget (0 the active window is no Spectrum2DWidget or there is no active window)
Static Public Member Functions
static bool	containsMS1Scans (const ExperimentType &exp)
	Returns true if `contains` at least one MS1 spectrum.
static UInt	countMS1Zeros (const ExperimentType &exp)
	Counts the number of exact zero valued intensities in all MS1 spectra.
static bool	hasPeptideIdentifications (const ExperimentType &map)
	Returns true if the experiment map contains peptide identifications.
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
void	abortTOPPTool ()
	aborts the execution of a TOPP tool
void	rerunTOPPTool ()
	retuns the last invoked TOPP tool with the same parameters
void	showSpectrumBrowser ()
	shows the spectrum browser and updates it
void	showSpectrumMetaData (int spectrum_index)
	shows the spectrum metadata
void	updateProcessLog ()
	Appends process output to log window.
void	fileChanged_ (const String &)
	Called if a data file has been externally changed.
Layer manager and filter manager slots

void	layerSelectionChange (int)
	slot for layer manager selection change
void	layerFilterVisibilityChange (bool)
	Enables/disables the data filters for the current layer.
void	layerContextMenu (const QPoint &pos)
	slot for layer manager context menu
void	logContextMenu (const QPoint &pos)
	slot for log window context menu
void	layerVisibilityChange (QListWidgetItem *item)
	slot for layer manager visibility change (check box)
void	filterContextMenu (const QPoint &pos)
	slot for filter manager context menu
void	filterEdit (QListWidgetItem *item)
	slot for editing a filter
void	layerEdit (QListWidgetItem *)
	slot for editing the preferences of the current layer
Tabbar slots

void	closeByTab (int id)
	Closes the window corresponding to the data of the tab with identifier `id`.
void	enhancedWorkspaceWindowChanged (int id)
	Raises the window corresponding to the data of the tab with identifier `id`.
void	openRecentFile ()
	Opens a file from the recent files menu.
void	copyLayer (const QMimeData data, QWidget source, int id=-1)
	Slot for drag-and-drop of layer manager to tabbar.
Protected Member Functions
void	initializeDefaultParameters_ ()
	Initializes the default parameters on TOPPView construction.
std::set< String >	getFilenamesOfOpenFiles_ ()
	unique list of files referenced by all layers
void	connectToDB_ (DBConnection &db)
	Tries to open a db connection (queries the user for the DB password).
QStringList	getFileList_ (const String &path_overwrite="")
	Shows a dialog where the user can select files.
EnhancedTabBarWidgetInterface *	window_ (int id) const
	Returns the enhanced tabbar widget with id `id`.
void	checkPreferences_ ()
	check if all available preferences get set by the .ini file. If there are some missing entries fill them with default values.
void	showLogMessage_ (LogState state, const String &heading, const String &body)
	Shows a log message in the log_ window.
void	showTOPPDialog_ (bool visible)
	Apply TOPP tool. If `visible` is true, only the visible data is used, otherwise the whole layer is used.
reimplemented Qt events

void	closeEvent (QCloseEvent *event)
Protected Attributes
QListWidget *	layer_manager_
	Layer management widget.
FileWatcher *	watcher_
	Watcher that tracks file changes (in order to update the data in the different views).
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).
bool	zoom_together_
	Stores whether the individual windows should zoom together (be linked) or not.
QAction *	linkZoom_action_
QTextEdit *	log_
	Log output window.
EnhancedWorkspace *	ws_
	Main workspace.
EnhancedTabBar *	tab_bar_
	Tab bar. The address of the corresponding window to a tab is stored as an int in tabData().
QMenu *	add_2d_context_
	Additional context menu for 2D layers.
String	current_path_
QTabWidget *	views_tabwidget_
	Tabwidget that hold the different views on the loaded data.
TOPPViewBehaviorInterface *	view_behavior_
	The current TOPPView view behavior.
TOPPViewIdentificationViewBehavior *	identificationview_behavior_
	TOPPView behavior for the identification view.
TOPPViewSpectraViewBehavior *	spectraview_behavior_
	TOPPView behavior for the spectra view.
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.
QLabel *	mz_label_
	m/z label for messages in the status bar
QLabel *	rt_label_
	RT label for messages in the status bar.
Static Private Attributes
static const String	CAPTION_3D_SUFFIX_ = " (3D)"
	Suffix appended to caption of tabs when layer is shown in 3D.
Friends
class	TestTOPPView
Recent files

QStringList	recent_files_
	list of the recently opened files
std::vector< QAction * >	recent_actions_
	list of the recently opened files actions (menu entries)
void	addRecentFile_ (const String &filename)
	adds a Filename to the recent files
void	updateRecentMenu_ ()
	update the recent files menu
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.
void	runTOPPTool_ ()
	Runs the TOPP tool according to the information in topp_.

Detailed Description

Main window of TOPPView tool.

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)

Todo:: Add TOPPView live-tutorial (Stephan, Marc)

Member Typedef Documentation

typedef LayerData::ConsensusMapSharedPtrType ConsensusMapSharedPtrType

typedef LayerData::ConsensusMapType ConsensusMapType

typedef LayerData::ExperimentSharedPtrType ExperimentSharedPtrType

typedef LayerData::ExperimentType ExperimentType

typedef LayerData::FeatureMapSharedPtrType FeatureMapSharedPtrType

typedef LayerData::FeatureMapType FeatureMapType

typedef ExperimentType::SpectrumType SpectrumType

Peak spectrum type.

Member Enumeration Documentation

enum LogState [protected]

Log message states.

Enumerator:

LS_NOTICE	Notice.
LS_WARNING	Warning.
LS_ERROR	Fatal error.

Constructor & Destructor Documentation

TOPPViewBase ( QWidget * parent = 0 )

Constructor.

~TOPPViewBase ( )

Destructor.

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

Member Function Documentation

void abortTOPPTool ( ) [protected, slot]

aborts the execution of a TOPP tool

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

Referenced by TOPPViewBase::~TOPPViewBase().

void activate1DSpectrum ( int index ) [slot]

Activation of 1D spectrum.

References TOPPViewBehaviorInterface::activate1DSpectrum(), TOPPViewBase::getActive1DWidget(), and TOPPViewBase::view_behavior_.

Referenced by TOPPViewBase::TOPPViewBase().

void activate1DSpectrum ( std::vector< int, std::allocator< int > > indices ) [slot]

Activation of 1D with multiple entries (e.g. chromatograms).

References TOPPViewBehaviorInterface::activate1DSpectrum(), TOPPViewBase::getActive1DWidget(), and TOPPViewBase::view_behavior_.

void addData	(	FeatureMapSharedPtrType	feature_map,
		ConsensusMapSharedPtrType	consensus_map,
		std::vector< PeptideIdentification > &	peptides,
		ExperimentSharedPtrType	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)
	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 foro 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(), TOPPViewBase::countMS1Zeros(), 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(), TOPPViewOpenDialog::isCutoffEnabled(), Spectrum2DCanvas::mergeIntoLayer(), LayerData::name, DataFilters::DataFilter::op, TOPPViewOpenDialog::openAsNewWindow(), DefaultParamHandler::param_, SpectrumCanvas::setFilters(), SpectrumCanvas::setLayerName(), TOPPViewOpenDialog::setMergeLayers(), TOPPViewBase::showSpectrumWidgetInWindow(), LayerData::type, TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), DataFilters::DataFilter::value, TOPPViewOpenDialog::viewMapAs1D(), TOPPViewOpenDialog::viewMapAs2D(), TOPPViewBase::views_tabwidget_, TOPPViewBase::window_(), and TOPPViewBase::ws_.

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

void addDataDB	(	UInt	db_id,
		bool	show_options,
		String	caption = `""`,
		UInt	window_id = `0`
	)

Opens and displays a data from a database.

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

Parameters:

	db_id	The id in the database
	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.
	window_id	in which window the file is opened if opened as a new layer (0 or default equals current window).

References TOPPViewBase::addData(), TOPPViewBase::connectToDB_(), LayerData::DT_CHROMATOGRAM, LayerData::DT_PEAK, DBConnection::executeQuery(), DBConnection::isConnected(), DBAdapter::loadExperiment(), and BaseException::what().

Referenced by TOPPViewBase::openDatabaseDialog().

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(), File::exists(), FileTypes::FEATUREXML, FileHandler::getType(), ProgressLogger::GUI, FileTypes::IDXML, FileTypes::INI, FileHandler::loadExperiment(), TOPPViewBase::LS_ERROR, TOPPViewBase::showLogMessage_(), FileTypes::typeToName(), FileTypes::UNKNOWN, TOPPViewBase::watcher_, and BaseException::what().

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

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().

void annotateWithID ( ) [slot]

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(), and TOPPViewBase::updateToolBar().

Referenced by TOPPViewBase::TOPPViewBase().

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().

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().

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.

void closeByTab ( int id ) [protected, slot]

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

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

Referenced by TOPPViewBase::TOPPViewBase().

void closeEvent ( QCloseEvent * event ) [protected]

References TOPPViewBase::ws_.

void closeFile ( ) [slot]

closes the active window

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

Referenced by TOPPViewBase::TOPPViewBase().

void connectToDB_ ( DBConnection & db ) [protected]

Tries to open a db connection (queries the user for the DB password).

References DBConnection::connect(), Param::exists(), Param::getValue(), TOPPViewBase::LS_ERROR, DefaultParamHandler::param_, Param::remove(), Param::setValue(), TOPPViewBase::showLogMessage_(), and BaseException::what().

Referenced by TOPPViewBase::addDataDB(), TOPPViewBase::metadataDatabaseDialog(), and TOPPViewBase::openDatabaseDialog().

bool containsMS1Scans ( const ExperimentType & exp ) [static]

Returns true if contains at least one MS1 spectrum.

Referenced by TOPPViewBase::addDataFile(), TOPPViewBase::countMS1Zeros(), and TOPPViewBase::estimateNoiseFromRandomMS1Scans().

void copyLayer	(	const QMimeData *	data,
		QWidget *	source,
		int	id = `-1`
	)			`[protected, slot]`

UInt countMS1Zeros ( const ExperimentType & exp ) [static]

Counts the number of exact zero valued intensities in all MS1 spectra.

References TOPPViewBase::containsMS1Scans().

Referenced by TOPPViewBase::addData().

void deactivate1DSpectrum ( int index ) [slot]

Deactivation of 1D spectrum.

References TOPPViewBehaviorInterface::deactivate1DSpectrum(), TOPPViewBase::getActive1DWidget(), and TOPPViewBase::view_behavior_.

Referenced by TOPPViewBase::TOPPViewBase().

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().

void enhancedWorkspaceWindowChanged ( int id ) [protected, slot]

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().

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().

Referenced by TOPPViewBase::addData().

void fileChanged_ ( const String & filename ) [protected, slot]

void filterContextMenu ( const QPoint & pos ) [protected, slot]

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().

void filterEdit ( QListWidgetItem * item ) [protected, slot]

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().

void finishTOPPToolExecution	(	int	exitCode,
		QProcess::ExitStatus	exitStatus
	)			`[protected, slot]`

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_().

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::activate1DSpectrum(), TOPPViewBase::deactivate1DSpectrum(), TOPPViewBase::layerContextMenu(), TOPPViewBase::setDrawMode1D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumAlignmentDialog(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateToolBar().

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(), and TOPPViewBase::viewChanged().

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().

SpectrumCanvas * getActiveCanvas ( ) const

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

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

Referenced by 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::showPreferences(), TOPPViewBase::showSpectrumMetaData(), TOPPViewBase::showTOPPDialog_(), TOPPViewBase::toggleGridLines(), TOPPViewBase::updateCurrentPath(), TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), and TOPPViewBase::updateViewBar().

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(), and TOPPViewBase::updateToolBar().

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().

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().

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_.

SpectraIdentificationViewWidget * getSpectraIdentificationViewWidget ( )

returns a pointer to the SpectraIdentificationViewWidget

References TOPPViewBase::spectra_identification_view_widget_.

Param getSpectrumParameters ( UInt dim )

Returns the parameters for a SpectrumCanvas of dimension dim.

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

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

EnhancedWorkspace * getWorkspace ( ) const

returns a pointer to the EnhancedWorkspace containing SpectrumWidgets

References TOPPViewBase::ws_.

bool hasPeptideIdentifications ( const ExperimentType & map ) [static]

Returns true if the experiment map contains peptide identifications.

Referenced by TOPPViewBase::enhancedWorkspaceWindowChanged().

void initializeDefaultParameters_ ( ) [protected]

Initializes the default parameters on TOPPView construction.

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

Referenced by TOPPViewBase::TOPPViewBase().

void layerActivated ( ) [slot]

get's called if a layer got activated

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

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

void layerContextMenu ( const QPoint & pos ) [protected, slot]

void layerDeactivated ( ) [slot]

get's called if a layer got deactivated

void layerEdit ( QListWidgetItem * ) [protected, slot]

slot for editing the preferences of the current layer

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

Referenced by TOPPViewBase::TOPPViewBase().

void layerFilterVisibilityChange ( bool on ) [protected, slot]

Enables/disables the data filters for the current layer.

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

Referenced by TOPPViewBase::TOPPViewBase().

void layerSelectionChange ( int i ) [protected, slot]

slot for layer manager selection change

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

Referenced by TOPPViewBase::TOPPViewBase().

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().

void layerVisibilityChange ( QListWidgetItem * item ) [protected, slot]

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().

void layerZoomChanged ( ) [slot]

gets called when a layer changes in zoom

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

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

void linkZoom ( ) [slot]

link the zoom of individual windows

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

Referenced by TOPPViewBase::TOPPViewBase().

void loadFile ( QString filename ) [slot]

Loads a file given by the passed string.

References TOPPViewBase::addDataFile().

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().

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(), Param::exists(), File::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().

void logContextMenu ( const QPoint & pos ) [protected, slot]

slot for log window context menu

References TOPPViewBase::log_.

Referenced by TOPPViewBase::TOPPViewBase().

void metadataDatabaseDialog ( ) [slot]

dialog for inspecting database meta data

References MetaDataBrowser::add(), TOPPViewBase::connectToDB_(), DBAdapter::getOptions(), DBConnection::isConnected(), DBAdapter::loadExperiment(), PeakFileOptions::setMetadataOnly(), BaseException::what(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::TOPPViewBase().

void metadataFileDialog ( ) [slot]

dialog for inspecting file meta data

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

Referenced by TOPPViewBase::TOPPViewBase().

void openDatabaseDialog ( ) [slot]

shows the DB dialog for opening files

References TOPPViewBase::addDataDB(), TOPPViewBase::connectToDB_(), DBConnection::disconnect(), and DBConnection::isConnected().

Referenced by TOPPViewBase::TOPPViewBase().

void openExampleDialog ( ) [slot]

shows the file dialog for opening example files

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

Referenced by TOPPViewBase::TOPPViewBase().

void openFileDialog ( ) [slot]

shows the file dialog for opening files

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

Referenced by TOPPViewBase::TOPPViewBase().

void openRecentFile ( ) [protected, slot]

Opens a file from the recent files menu.

References TOPPViewBase::addDataFile().

Referenced by TOPPViewBase::TOPPViewBase().

void preferencesDialog ( ) [slot]

shows the preferences dialog

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

Referenced by TOPPViewBase::TOPPViewBase().

void rerunTOPPTool ( ) [protected, slot]

retuns 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().

void resetZoom ( ) [slot]

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

Referenced by TOPPViewBase::TOPPViewBase().

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, 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_(), MzMLFile::store(), TOPPViewBase::topp_, LayerData::type, TOPPViewBase::updateMenu(), TOPPViewBase::updateProcessLog(), and File::writable().

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

void saveLayerAll ( ) [slot]

Saves the whole current layer data.

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

Referenced by TOPPViewBase::TOPPViewBase().

void saveLayerVisible ( ) [slot]

Saves the visible layer data.

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

Referenced by TOPPViewBase::TOPPViewBase().

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().

void setDrawMode1D ( int index ) [slot]

References Spectrum1DWidget::canvas(), Spectrum1DCanvas::DM_PEAKS, TOPPViewBase::draw_group_1d_, TOPPViewBase::getActive1DWidget(), and Spectrum1DCanvas::setDrawMode().

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

void setIntensityMode ( int index ) [slot]

References Spectrum2DWidget::canvas(), TOPPViewBase::getActiveSpectrumWidget(), SpectrumCanvas::getCurrentLayer(), MultiGradient::getDefaultGradientLinearIntensityMode(), MultiGradient::getDefaultGradientLogarithmicIntensityMode(), SpectrumCanvas::getIntensityMode(), SpectrumCanvas::IM_LOG, TOPPViewBase::intensity_button_group_, LayerData::param, Spectrum2DCanvas::recalculateCurrentLayerDotGradient(), SpectrumWidget::setIntensityMode(), and Param::setValue().

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

void showAboutDialog ( ) [slot]

Shows the 'About' dialog.

References VersionInfo::getVersion().

Referenced by TOPPViewBase::TOPPViewBase().

void showCurrentPeaksAs2D ( ) [slot]

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::getCurrentLayer(), LayerData::getPeakData(), TOPPViewBase::getSpectrumParameters(), SpectrumCanvas::IM_SNAP, TOPPViewBase::LS_NOTICE, LayerData::name, TOPPViewBase::setIntensityMode(), SpectrumCanvas::setLayerName(), SpectrumCanvas::setVisibleArea(), TOPPViewBase::showLogMessage_(), TOPPViewBase::showSpectrumWidgetInWindow(), LayerData::type, TOPPViewBase::updateFilterBar(), TOPPViewBase::updateLayerBar(), TOPPViewBase::updateMenu(), TOPPViewBase::updateViewBar(), and TOPPViewBase::ws_.

Referenced by TOPPViewBase::showSpectrumWidgetInWindow().

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().

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().

void showGoToDialog ( ) [slot]

shows the goto dialog

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

Referenced by TOPPViewBase::TOPPViewBase().

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::annotateWithID(), TOPPViewBase::connectToDB_(), TOPPViewBase::copyLayer(), TOPPViewBase::editMetadata(), TOPPViewBase::finishTOPPToolExecution(), TOPPViewBase::preferencesDialog(), TOPPViewBase::rerunTOPPTool(), TOPPViewBase::runTOPPTool_(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showTOPPDialog_(), and TOPPViewBase::updateToolBar().

void showPreferences ( ) [slot]

Shows current layer preferences.

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

Referenced by TOPPViewBase::TOPPViewBase().

void showSpectrumAlignmentDialog ( ) [slot]

Shows the spectrum alignment dialog.

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

Referenced by TOPPViewBase::TOPPViewBase().

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_.

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_, TOPPViewIdentificationViewBehavior::showSpectrumAs1D(), TOPPViewSpectraViewBehavior::showSpectrumAs1D(), TOPPViewBase::spectra_identification_view_widget_, TOPPViewBase::spectra_view_widget_, and TOPPViewBase::spectraview_behavior_.

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

void showSpectrumBrowser ( ) [protected, slot]

shows the spectrum browser and updates it

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

void showSpectrumGenerationDialog ( ) [slot]

void showSpectrumMetaData ( int spectrum_index ) [protected, slot]

shows the spectrum metadata

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

Referenced by TOPPViewBase::TOPPViewBase().

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::showCursorStatus(), TOPPViewBase::showCursorStatusInvert(), TOPPViewBase::showSpectrumAs1D(), TOPPViewBase::showStatusMessage(), TOPPViewBase::tab_bar_, String::toQString(), TOPPViewBase::updateLayerBar(), and TOPPViewBase::ws_.

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

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().

void showTOPPDialog ( ) [slot]

Apply TOPP tool.

References TOPPViewBase::showTOPPDialog_().

Referenced by TOPPViewBase::TOPPViewBase().

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, and File::writable().

Referenced by TOPPViewBase::showTOPPDialog().

void showURL ( ) [slot]

shows the URL stored in the data of the sender QAction

Referenced by TOPPViewBase::TOPPViewBase().

void tileHorizontal ( ) [slot]

tile the open windows horizontally

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

Referenced by TOPPViewBase::TOPPViewBase().

void tileVertical ( ) [slot]

tile the open windows vertically

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

Referenced by TOPPViewBase::TOPPViewBase().

void toggleAxisLegends ( ) [slot]

Toggles the axis legends.

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

Referenced by TOPPViewBase::TOPPViewBase().

void toggleGridLines ( ) [slot]

Toggles the grid lines.

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

Referenced by TOPPViewBase::TOPPViewBase().

void toggleProjections ( ) [slot]

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

Referenced by TOPPViewBase::TOPPViewBase().

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().

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(), and DataFilters::size().

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

void updateLayerBar ( ) [slot]

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(), and TOPPViewBase::TOPPViewBase().

void updateProcessLog ( ) [protected, slot]

Appends process output to log window.

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

Referenced by TOPPViewBase::runTOPPTool_().

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().

void updateTabBar ( QWidget * 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().

void updateToolBar ( ) [slot]

updates the toolbar

References LayerData::C_ELEMENTS, Spectrum2DWidget::canvas(), Spectrum1DWidget::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::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::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().

void updateViewBar ( ) [slot]

adapts view bar to the active window

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

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

void viewChanged ( int tab_index ) [slot]

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

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

Referenced by TOPPViewBase::TOPPViewBase().

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

friend class TestTOPPView [friend]

Member Data Documentation

QMenu* add_2d_context_ [protected]

Additional context menu for 2D layers.

const String CAPTION_3D_SUFFIX_ = " (3D)" [static, private]

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

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

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().

QAction* dm_elements_2d_ [protected]

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

QAction* dm_hull_2d_ [protected]

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

QAction* dm_hulls_2d_ [protected]

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

QAction* dm_ident_2d_ [protected]

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

QToolButton* dm_label_2d_ [protected]

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

QAction* dm_precursors_2d_ [protected]

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

QToolButton* dm_unassigned_2d_ [protected]

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

QButtonGroup* draw_group_1d_ [protected]

Referenced by TOPPViewBase::setDrawMode1D(), TOPPViewBase::showSpectrumGenerationDialog(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::updateToolBar().

String file_name

QDockWidget* filter_dock_widget_ [protected]

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

QListWidget* filters_ [protected]

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

QCheckBox* filters_check_box_ [protected]

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

QActionGroup* group_label_2d_ [protected]

Referenced by TOPPViewBase::TOPPViewBase().

QActionGroup* group_unassigned_2d_ [protected]

Referenced by TOPPViewBase::TOPPViewBase().

TOPPViewIdentificationViewBehavior* identificationview_behavior_ [protected]

TOPPView behavior for the identification view.

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

String in

QButtonGroup* intensity_button_group_ [protected]

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

QDockWidget* layer_dock_widget_ [protected]

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

QListWidget* layer_manager_ [protected]

Layer management widget.

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

String layer_name

Referenced by TOPPViewBase::filterContextMenu().

QAction* linkZoom_action_ [protected]

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

QTextEdit* log_ [protected]

Log output window.

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

QLabel* message_label_ [protected]

Label for messages in the status bar.

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

QLabel* mz_label_ [protected]

m/z label for messages in the status bar

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

String out

Referenced by TOPPViewBase::getSpectrumParameters().

Param param

Referenced by TOPPViewBase::showSpectrumAlignmentDialog().

QProcess* process

QAction* projections_2d_ [protected]

Referenced by TOPPViewBase::TOPPViewBase().

std::vector<QAction*> recent_actions_ [protected]

list of the recently opened files actions (menu entries)

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

QStringList recent_files_ [protected]

list of the recently opened files

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

QLabel* rt_label_ [protected]

RT label for messages in the status bar.

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

SpectraIdentificationViewWidget* spectra_identification_view_widget_ [protected]

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

SpectraViewWidget* spectra_view_widget_ [protected]

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

TOPPViewSpectraViewBehavior* spectraview_behavior_ [protected]

TOPPView behavior for the spectra view.

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

Size spectrum_id

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().

QTime timer

String tool

QToolBar* tool_bar_ [protected]

Referenced by TOPPViewBase::TOPPViewBase().

QToolBar* tool_bar_1d_ [protected]

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

QToolBar* tool_bar_2d_cons_ [protected]

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

QToolBar* tool_bar_2d_feat_ [protected]

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

QToolBar* tool_bar_2d_ident_ [protected]

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

QToolBar* tool_bar_2d_peak_ [protected]

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

struct { ... } topp_ [protected]

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().

TOPPViewBehaviorInterface* view_behavior_ [protected]

The current TOPPView view behavior.

Referenced by TOPPViewBase::activate1DSpectrum(), TOPPViewBase::deactivate1DSpectrum(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::viewChanged().

QDockWidget* views_dockwidget_ [protected]

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

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(), and TOPPViewBase::viewChanged().

bool visible

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

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().

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_().

UInt window_id

Referenced by TOPPViewBase::updateTabBar().

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::metadataDatabaseDialog(), TOPPViewBase::showCurrentPeaksAs2D(), TOPPViewBase::showCurrentPeaksAs3D(), TOPPViewBase::showSpectrumWidgetInWindow(), TOPPViewBase::tileHorizontal(), TOPPViewBase::tileVertical(), TOPPViewBase::TOPPViewBase(), and TOPPViewBase::window_().