Main window of the IDEvaluation tool. More...

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

Inheritance diagram for IDEvaluationBase:

Public Slots
void	resetZoom ()

void	setIntensityMode (int index)

bool	getPoints (std::vector< PeptideIdentification > &peptides, const std::vector< double > &q_value_thresholds, MSSpectrum &points)

bool	loadCurve (const String &file_name, MSSpectrum &points)
	calls 'getPoints()' after loading the idXML file and returns the result More...

bool	addSearchFile (const String &file_name)

void	openFileDialog ()
	shows the dialog for opening files More...

void	saveImageAs ()
	saves the plot - querying for a filename first More...

bool	exportAsImage (const QString &file_name, String &error_message, const QString &format="")

void	showAboutDialog ()
	changes the current path according to the currently active window/layer More...

void	showStatusMessage (std::string msg, OpenMS::UInt time)
	Shows a status message in the status bar. More...

bool	loadFiles (const StringList &list)
	shows x,y coordinates in the status bar More...

void	showURL ()

Public Member Functions
	IDEvaluationBase (QWidget *parent=0)
	Constructor. More...

virtual	~IDEvaluationBase ()
	Destructor. More...

QSize	sizeHint () const

void	setVisibleArea (double low, double high)

const PeakMap &	getPoints () const

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 StringList	getSupportedImageFormats ()

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

Protected Member Functions
TOPPASWidget *	window_ (int id) const
	returns the window with id `id` More...

void	showLogMessage_ (LogState state, const String &heading, const String &body)
	Shows a log message in the log_ window. More...

reimplemented Qt events
void	closeEvent (QCloseEvent *event)

void	keyPressEvent (QKeyEvent *e)

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
QTextEdit *	log_
	enable/disable menu entries depending on the current state More...

QTextEdit *	desc_
	Workflow Description window. More...

QWorkspace *	ws_
	Main workspace. More...

Spectrum1DWidget *	spec_1d_

QLabel *	message_label_
	Label for messages in the status bar. More...

String	current_path_

std::vector< double >	q_value_thresholds_

PeakMap	data_

Toolbar
QToolBar *	tool_bar_

QButtonGroup *	intensity_button_group_

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...

Detailed Description

Main window of the IDEvaluation tool.

Member Enumeration Documentation

◆ LogState

enum LogState

protected

Log message states.

Enumerator
LS_NOTICE	Notice.
LS_WARNING	Warning.
LS_ERROR	Fatal error.

Constructor & Destructor Documentation

◆ IDEvaluationBase()

IDEvaluationBase ( QWidget * parent = 0 )

◆ ~IDEvaluationBase()

~IDEvaluationBase ( )

virtual

Destructor.

Member Function Documentation

◆ addSearchFile

bool addSearchFile ( const String & file_name )

slot

opens the file in a new window

Returns: false on error (no idXML file or missing information preventing FDR computation)

References SpectrumCanvas::addLayer(), MSExperiment::addSpectrum(), Spectrum1DWidget::canvas(), IDEvaluationBase::data_, SpectrumCanvas::getLayerCount(), MetaInfoInterface::getMetaValue(), SpectrumCanvas::IM_SNAP, IDEvaluationBase::loadCurve(), IDEvaluationBase::setIntensityMode(), SpectrumCanvas::setLayerName(), and IDEvaluationBase::spec_1d_.

Referenced by IDEvaluationBase::loadFiles(), and IDEvaluationBase::openFileDialog().

◆ closeEvent()

void closeEvent ( QCloseEvent * event )

protected

◆ exportAsImage

bool exportAsImage	(	const QString &	file_name,
		String &	error_message,
		const QString &	format = `""`
	)

slot

exports the current pipeline as image returns true on success, otherwise false + error_message

References Param::getValue(), OpenMS::Constants::h, DefaultParamHandler::param_, Spectrum1DWidget::renderForImage(), and IDEvaluationBase::spec_1d_.

Referenced by IDEvaluationBase::saveImageAs().

◆ getPoints() [1/2]

const PeakMap & getPoints ( ) const

References IDEvaluationBase::data_.

Referenced by IDEvaluationBase::loadCurve().

◆ getPoints [2/2]

bool getPoints	(	std::vector< PeptideIdentification > &	peptides,
		const std::vector< double > &	q_value_thresholds,
		MSSpectrum &	points
	)

slot

compute q-values from ids and store as vector of points for plotting returns false on error, the return vector 'points' will also be empty in this case

References FalseDiscoveryRate::apply(), MSSpectrum::clear(), Param::copy(), LOG_FATAL_ERROR, DefaultParamHandler::param_, Peak1D::setMZ(), and DefaultParamHandler::setParameters().

◆ getSupportedImageFormats()

StringList getSupportedImageFormats ( )

static

◆ keyPressEvent()

void keyPressEvent ( QKeyEvent * e )

protected

◆ loadCurve

bool loadCurve	(	const String &	file_name,
		MSSpectrum &	points
	)

slot

calls 'getPoints()' after loading the idXML file and returns the result

References IDEvaluationBase::getPoints(), FileHandler::getType(), FileTypes::IDXML, IdXMLFile::load(), LOG_ERROR, IDEvaluationBase::q_value_thresholds_, and MetaInfoInterface::setMetaValue().

Referenced by IDEvaluationBase::addSearchFile().

◆ loadFiles

bool loadFiles ( const StringList & list )

slot

shows x,y coordinates in the status bar

closes the active window updates the toolbar load Target/Decoy annotated files, return FALSE if any of these files did not contain target/decoy information or any other error which prevents FDR calculation

References IDEvaluationBase::addSearchFile().

◆ openFileDialog

void openFileDialog ( )

slot

shows the dialog for opening files

References IDEvaluationBase::addSearchFile(), IDEvaluationBase::current_path_, and String::toQString().

Referenced by IDEvaluationBase::IDEvaluationBase().

◆ resetZoom

void resetZoom ( )

slot

References Spectrum1DWidget::canvas(), SpectrumCanvas::resetZoom(), and IDEvaluationBase::spec_1d_.

Referenced by IDEvaluationBase::IDEvaluationBase().

◆ saveImageAs

void saveImageAs ( )

slot

saves the plot - querying for a filename first

References IDEvaluationBase::current_path_, IDEvaluationBase::exportAsImage(), and String::toQString().

Referenced by IDEvaluationBase::IDEvaluationBase().

◆ setIntensityMode

void setIntensityMode ( int index )

slot

References SpectrumCanvas::IM_LOG, SpectrumCanvas::IM_NONE, SpectrumCanvas::IM_PERCENTAGE, SpectrumCanvas::IM_SNAP, IDEvaluationBase::intensity_button_group_, SpectrumWidget::setIntensityMode(), AxisWidget::setLegend(), IDEvaluationBase::spec_1d_, and SpectrumWidget::yAxis().

Referenced by IDEvaluationBase::addSearchFile(), and IDEvaluationBase::IDEvaluationBase().

◆ setVisibleArea()

void setVisibleArea	(	double	low,
		double	high
	)

References Spectrum1DWidget::canvas(), Spectrum1DCanvas::setVisibleArea(), and IDEvaluationBase::spec_1d_.

◆ showAboutDialog

void showAboutDialog ( )

slot

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

Shows the 'About' dialog

References VersionInfo::getRevision(), and VersionInfo::getVersion().

Referenced by IDEvaluationBase::IDEvaluationBase().

◆ showLogMessage_()

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

protected

Shows a log message in the log_ window.

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

◆ 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 IDEvaluationBase::message_label_.

◆ showURL

void showURL ( )

slot

Referenced by IDEvaluationBase::IDEvaluationBase().

◆ sizeHint()

QSize sizeHint ( ) const

◆ window_()

TOPPASWidget* window_ ( int id ) const

protected

returns the window with id id

Member Data Documentation

◆ 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 IDEvaluationBase::openFileDialog(), and IDEvaluationBase::saveImageAs().

◆ data_

PeakMap data_

protected

Referenced by IDEvaluationBase::addSearchFile(), and IDEvaluationBase::getPoints().

◆ desc_

QTextEdit* desc_

protected

Workflow Description window.

◆ intensity_button_group_

QButtonGroup* intensity_button_group_

protected

Referenced by IDEvaluationBase::IDEvaluationBase(), and IDEvaluationBase::setIntensityMode().

◆ log_

QTextEdit* log_

protected

enable/disable menu entries depending on the current state

Shows the widget as window in the workspace (the special_id is only used for the first untitled widget (to be able to auto-close it later) Log output window

Referenced by IDEvaluationBase::IDEvaluationBase(), and IDEvaluationBase::showLogMessage_().

◆ message_label_

QLabel* message_label_

protected

Label for messages in the status bar.

Referenced by IDEvaluationBase::IDEvaluationBase(), and IDEvaluationBase::showStatusMessage().

◆ q_value_thresholds_

std::vector<double> q_value_thresholds_

protected

Referenced by IDEvaluationBase::IDEvaluationBase(), and IDEvaluationBase::loadCurve().

◆ spec_1d_

Spectrum1DWidget* spec_1d_

protected

Referenced by IDEvaluationBase::addSearchFile(), IDEvaluationBase::exportAsImage(), IDEvaluationBase::IDEvaluationBase(), IDEvaluationBase::resetZoom(), IDEvaluationBase::setIntensityMode(), and IDEvaluationBase::setVisibleArea().

◆ tool_bar_

QToolBar* tool_bar_

protected

Referenced by IDEvaluationBase::IDEvaluationBase().

◆ ws_

QWorkspace* ws_

protected

Main workspace.

Referenced by IDEvaluationBase::IDEvaluationBase().

Public Slots

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ LogState

Constructor & Destructor Documentation

◆ IDEvaluationBase()

◆ ~IDEvaluationBase()

Member Function Documentation

◆ addSearchFile

◆ closeEvent()

◆ exportAsImage

◆ getPoints() [1/2]

◆ getPoints [2/2]

◆ getSupportedImageFormats()

◆ keyPressEvent()

◆ loadCurve

◆ loadFiles

◆ openFileDialog

◆ resetZoom

◆ saveImageAs

◆ setIntensityMode

◆ setVisibleArea()

◆ showAboutDialog

◆ showLogMessage_()

◆ showStatusMessage

◆ showURL

◆ sizeHint()

◆ window_()

Member Data Documentation

◆ current_path_

◆ data_

◆ desc_

◆ intensity_button_group_

◆ log_

◆ message_label_

◆ q_value_thresholds_

◆ spec_1d_

◆ tool_bar_

◆ ws_