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< DoubleReal > &q_value_thresholds, MSSpectrum<> &points)
bool	loadCurve (const String &file_name, MSSpectrum<> &points)
	calls 'getPoints()' after loading the idXML file and returns the result
bool	addSearchFile (const String &file_name)
void	openFileDialog ()
	shows the dialog for opening files
void	saveImageAs ()
	saves the plot - querying for a filename first
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
void	showStatusMessage (std::string msg, OpenMS::UInt time)
	Shows a status message in the status bar.
bool	loadFiles (const StringList &list)
	shows x,y coordinates in the status bar
void	showURL ()
Public Member Functions
	IDEvaluationBase (QWidget *parent=0)
	Constructor.
virtual	~IDEvaluationBase ()
	Destructor.
QSize	sizeHint () const
void	setVisibleArea (double low, double high)
const MSExperiment &	getPoints () const
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`
void	showLogMessage_ (LogState state, const String &heading, const String &body)
	Shows a log message in the log_ window.
reimplemented Qt events

void	closeEvent (QCloseEvent *event)
void	keyPressEvent (QKeyEvent *e)
Protected Attributes
QTextEdit *	log_
	enable/disable menu entries depending on the current state
QTextEdit *	desc_
	Workflow Description window.
QWorkspace *	ws_
	Main workspace.
Spectrum1DWidget *	spec_1d_
QLabel *	message_label_
	Label for messages in the status bar.
String	current_path_
std::vector< DoubleReal >	q_value_thresholds_
MSExperiment	data_
Toolbar

QToolBar *	tool_bar_
QButtonGroup *	intensity_button_group_

Detailed Description

Main window of the IDEvaluation tool.

Member Enumeration Documentation

enum LogState [protected]

Log message states.

Enumerator:

LS_NOTICE	Notice.
LS_WARNING	Warning.
LS_ERROR	Fatal error.

Constructor & Destructor Documentation

IDEvaluationBase ( QWidget * parent = 0 )

~IDEvaluationBase ( ) [virtual]

Destructor.

Member Function Documentation

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(), 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().

void closeEvent ( QCloseEvent * event ) [protected]

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().

const MSExperiment & getPoints ( ) const

References IDEvaluationBase::data_.

Referenced by IDEvaluationBase::loadCurve().

bool getPoints	(	std::vector< PeptideIdentification > &	peptides,
		const std::vector< DoubleReal > &	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< PeakT >::clear(), Param::copy(), LOG_FATAL_ERROR, DefaultParamHandler::param_, and DefaultParamHandler::setParameters().

StringList getSupportedImageFormats ( ) [static]

References StringList::create().

void keyPressEvent ( QKeyEvent * e ) [protected]

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, LOG_ERROR, IDEvaluationBase::q_value_thresholds_, and MetaInfoInterface::setMetaValue().

Referenced by IDEvaluationBase::addSearchFile().

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().

void openFileDialog ( ) [slot]

shows the dialog for opening files

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

Referenced by IDEvaluationBase::IDEvaluationBase().

void resetZoom ( ) [slot]

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

Referenced by IDEvaluationBase::IDEvaluationBase().

void saveImageAs ( ) [slot]

saves the plot - querying for a filename first

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

Referenced by IDEvaluationBase::IDEvaluationBase().

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().

void setVisibleArea	(	double	low,
		double	high
	)

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

void showAboutDialog ( ) [slot]

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

Shows the 'About' dialog

References VersionInfo::getVersion().

Referenced by IDEvaluationBase::IDEvaluationBase().

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().

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_.

void showURL ( ) [slot]

Referenced by IDEvaluationBase::IDEvaluationBase().

QSize sizeHint ( ) const

TOPPASWidget* window_ ( int id ) const [protected]

returns the window with id id

Member Data Documentation

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().

MSExperiment data_ [protected]

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

QTextEdit* desc_ [protected]

Workflow Description window.

QButtonGroup* intensity_button_group_ [protected]

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

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_().

QLabel* message_label_ [protected]

Label for messages in the status bar.

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

std::vector<DoubleReal> q_value_thresholds_ [protected]

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

Spectrum1DWidget* spec_1d_ [protected]

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