Main window of the IDEvaluation tool. More...
#include <OpenMS/VISUAL/APPLICATIONS/IDEvaluationBase.h>
 
  
 | 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  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 MSExperiment & | 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 ¶m) | 
| Sets the parameters.  More... | |
| const Param & | getParameters () const | 
| Non-mutable access to the parameters.  More... | |
| const Param & | getDefaults () const | 
| Non-mutable access to the default parameters.  More... | |
| const String & | getName () const | 
| Non-mutable access to the name.  More... | |
| void | setName (const String &name) | 
| Mutable access to the name.  More... | |
| const std::vector< String > & | getSubsections () const | 
| Non-mutable access to the registered subsections.  More... | |
| Static Public Member Functions | |
| 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 idMore... | |
| 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< DoubleReal > | q_value_thresholds_ | 
| MSExperiment | 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... | |
Main window of the IDEvaluation tool.
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 | protected | 
| IDEvaluationBase | ( | QWidget * | parent = 0 | ) | 
Constructor.
References Spectrum1DWidget::canvas(), DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), DefaultParamHandler::getParameters(), SpectrumCanvas::IM_LOG, SpectrumCanvas::IM_NONE, SpectrumCanvas::IM_PERCENTAGE, SpectrumCanvas::IM_SNAP, Param::insert(), IDEvaluationBase::intensity_button_group_, IDEvaluationBase::log_, IDEvaluationBase::message_label_, IDEvaluationBase::openFileDialog(), IDEvaluationBase::q_value_thresholds_, IDEvaluationBase::resetZoom(), IDEvaluationBase::saveImageAs(), IDEvaluationBase::setIntensityMode(), AxisWidget::setLegend(), DefaultParamHandler::setParameters(), Param::setValue(), IDEvaluationBase::showAboutDialog(), IDEvaluationBase::showURL(), IDEvaluationBase::spec_1d_, IDEvaluationBase::tool_bar_, IDEvaluationBase::ws_, and SpectrumWidget::xAxis().
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 | virtual | 
Destructor.
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 | slot | 
opens the file in a new window
References SpectrumCanvas::addLayer(), MSExperiment< PeakT, ChromatogramPeakT >::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().
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 | protected | 
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 | 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().
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 | 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_, Peak1D::setMZ(), and DefaultParamHandler::setParameters().
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 | static | 
References StringList::create().
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 | protected | 
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 | 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().
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 | 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().
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 | slot | 
shows the dialog for opening files
References IDEvaluationBase::addSearchFile(), IDEvaluationBase::current_path_, and String::toQString().
Referenced by IDEvaluationBase::IDEvaluationBase().
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 | slot | 
References Spectrum1DWidget::canvas(), SpectrumCanvas::resetZoom(), and IDEvaluationBase::spec_1d_.
Referenced by IDEvaluationBase::IDEvaluationBase().
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 | slot | 
saves the plot - querying for a filename first
References IDEvaluationBase::current_path_, IDEvaluationBase::exportAsImage(), and String::toQString().
Referenced by IDEvaluationBase::IDEvaluationBase().
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 | 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().
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 | slot | 
changes the current path according to the currently active window/layer
Shows the 'About' dialog
References VersionInfo::getVersion().
Referenced by IDEvaluationBase::IDEvaluationBase().
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 | 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().
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 | 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_.
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 | slot | 
Referenced by IDEvaluationBase::IDEvaluationBase().
| QSize sizeHint | ( | ) | const | 
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 | protected | 
returns the window with id id 
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 | 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().
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 | protected | 
Referenced by IDEvaluationBase::addSearchFile(), and IDEvaluationBase::getPoints().
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 | protected | 
Workflow Description window.
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 | protected | 
Referenced by IDEvaluationBase::IDEvaluationBase(), and IDEvaluationBase::setIntensityMode().
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 | 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_().
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 | protected | 
Label for messages in the status bar.
Referenced by IDEvaluationBase::IDEvaluationBase(), and IDEvaluationBase::showStatusMessage().
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 | protected | 
Referenced by IDEvaluationBase::IDEvaluationBase(), and IDEvaluationBase::loadCurve().
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 | protected | 
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 | protected | 
Referenced by IDEvaluationBase::IDEvaluationBase().
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 | protected | 
Main workspace.
Referenced by IDEvaluationBase::IDEvaluationBase().
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5 |