jalview.gui
	AlignExportSettings
		AlignExportSettings(boolean, boolean, String) (4 matches)
	AlignFrame
		delete_actionPerformed(ActionEvent) (4 matches)
		drop(DropTargetDropEvent) (6 matches)
		gatherSequencesForAlignment() (3 matches)
		loadJalviewDataFile(String, String, String, SequenceI) (2 matches)
		loadTreeMenuItem_actionPerformed(ActionEvent) (4 matches)
		newTreePanel(String, String, String) (6 matches)
		pairwiseAlignmentMenuItem_actionPerformed(ActionEvent) (2 matches)
		PCAMenuItem_actionPerformed(ActionEvent) (2 matches)
		runGroovy_actionPerformed() (2 matches)
		saveAlignment(String, String) (2 matches)
		saveAs_actionPerformed(ActionEvent) (2 matches)
		showTranslation_actionPerformed(ActionEvent) (4 matches)
		tabbedPane_mousePressed(MouseEvent) (2 matches)
		updateUserColourMenu()
		new MouseAdapter() {...}
		offerRemoval(JRadioButtonMenuItem) (3 matches)
		warningMessage(String, String) (2 matches)
	AlignViewport
		openLinkedAlignment(AlignmentI, String) (3 matches)
	AnnotationPanel
		actionPerformed(ActionEvent) (2 matches)
	AppJmol
		fetchPdbFiles() (2 matches)
		AssociatePdbFileWithSeq
		associatePdbWithSeq(String, String, SequenceI, boolean, StructureSelectionManagerProvider) (2 matches)
	ChimeraViewFrame
		closeViewer(boolean) (5 matches)
		initChimera() (2 matches)
		run() (2 matches)
	CrossRefAction
		run() (2 matches)
	CutAndPasteTransfer
		ok_actionPerformed(ActionEvent) (6 matches)
	DasSourceBrowser
		amendLocal(boolean) (3 matches)
		editRemoveLocalSource(MouseEvent) (5 matches)
	Desktop
		checkURLLinks()
		new Runnable() {...}
		run() (2 matches)
		groovyShell_actionPerformed() (2 matches)
		inputURLMenuItem_actionPerformed(AlignViewport) (5 matches)
		JalviewServicesChanged(PropertyChangeEvent)
		new Runnable() {...}
		run() (3 matches)
		loadState_actionPerformed(ActionEvent)
		new Runnable() {...}
		run() (2 matches)
		saveState_actionPerformed(ActionEvent)
		new Runnable() {...}
		run() (2 matches)
		showUrl(String, IProgressIndicator)
		new Runnable() {...}
		run() (2 matches)
		vamsasImport_actionPerformed(ActionEvent) (2 matches)
		vamsasSave_actionPerformed(ActionEvent) (2 matches)
	EditNameDialog
		EditNameDialog(String, String, String, String, String, JComponent) (3 matches)
	EPSOptions
		EPSOptions() (4 matches)
	FeatureRenderer
		amendFeatures(SequenceI[], SequenceFeature[], boolean, AlignmentPanel) (7 matches)
	FeatureSettings
		noDasSourceActive() (3 matches)
	Finder
		doSearch(boolean) (4 matches)
		isInvalidSearchString(String) (2 matches)
	FontChooser
		changeFont() (2 matches)
	HTMLOptions
		HTMLOptions() (4 matches)
	IdPanel
		mouseClicked(MouseEvent) (2 matches)
	Jalview2XML
		reportErrors(boolean)
		new Runnable() {...}
		run() (2 matches)
	Jalview2XML_V1
		LoadJalviewAlign(jarInputStreamProvider)
		new Runnable() {...}
		run() (2 matches)
		new Runnable() {...}
		run() (2 matches)
	OOMWarning
		run() (2 matches)
	PCAPanel
		PCAPanel(AlignmentPanel) (2 matches)
	PopupMenu
		sequenceName_actionPerformed() (2 matches)
		showLink(String) (2 matches)
	Preferences
		deleteLink_actionPerformed(ActionEvent) (2 matches)
		editLink_actionPerformed(ActionEvent) (5 matches)
		newLink_actionPerformed(ActionEvent) (3 matches)
		structureViewer_actionPerformed(String) (4 matches)
		userIdWidth_actionPerformed() (2 matches)
		validateChimeraPath() (2 matches)
	PromptUserConfig
		raiseDialog() (6 matches)
	RestInputParamEditDialog
		frame
		new JalviewDialog() {...}
		cancelPressed()
		okPressed()
		initFor(RestServiceEditorPane, RestServiceDescription, InputType) (2 matches)
	SeqPanel
		doMousePressedDefineMode(MouseEvent) (2 matches)
	SequenceFetcher
		SequenceFetcher(IProgressIndicator, String, String)
		new Runnable() {...}
		run()
		new Runnable() {...}
		run() (2 matches)
		showErrorMessage(String)
		new Runnable() {...}
		run() (2 matches)
	StructureChooser
		fetchStructuresMetaData() (2 matches)
		filterResultSet(String)
		new Runnable() {...}
		run() (2 matches)
	StructureViewerBase
		addAlreadyLoadedFile(SequenceI[], String[], AlignmentPanel, String) (4 matches)
		addToExistingViewer(PDBEntry, SequenceI[], String[], AlignmentPanel, String) (2 matches)
		chooseAlignStructureToViewer(String, StructureViewerBase) (2 matches)
	SVGOptions
		SVGOptions() (4 matches)
	TextColourChooser
		chooseColour(AlignmentPanel, SequenceGroup) (4 matches)
	UserDefinedColours
		applyButton_actionPerformed(ActionEvent) (2 matches)
		okButton_actionPerformed(ActionEvent) (2 matches)
		savebutton_actionPerformed(ActionEvent) (5 matches)
	UserQuestionnaireCheck
		run() (4 matches)
	VamsasApplication
		addStoreDocumentHandler()
		new PropertyChangeListener() {...}
		propertyChange(PropertyChangeEvent) (4 matches)
		initClientSession(String, File, String) (2 matches)
	WebserviceInfo
		warnUser(String, String)
		new Runnable() {...}
		run() (2 matches)
	WsJobParameters
		actionPerformed(ActionEvent)
		new Runnable() {...}
		run() (2 matches)
		doPreferenceComboStateChange(String) (3 matches)
	WsParamSetManager
		deleteParameterSet(WsParamSetI) (3 matches)
	WsPreferences
		editUrl(String, String) (14 matches)
jalview.io
	FileLoader
		run() (2 matches)
		new Runnable() {...}
		run() (2 matches)
		new Runnable() {...}
		run() (2 matches)
		new Runnable() {...}
		run() (2 matches)
	JalviewFileChooser
		showSaveDialog(Component) (3 matches)
	WSWUBlastClient
		updateIds() (3 matches)
jalview.jbgui
	GAlignFrame
		GAlignFrame()
		new MouseAdapter() {...}
		offerRemoval(JRadioButtonMenuItem) (3 matches)
	GSequenceLink
		checkValid() (2 matches)
jalview.ws
	DasSequenceFeatureFetcher
		DasSequenceFeatureFetcher(SequenceI[], FeatureSettings, List<jalviewSourceI>, boolean, boolean, boolean) (5 matches)
jalview.ws.jws1
	Discoverer
		getServices(URL) (2 matches)
	JPredClient
		locateWebService() (2 matches)
	MsaWSClient
		MsaWSClient(ServiceHandle, String, AlignmentView, boolean, boolean, AlignmentI, AlignFrame) (4 matches)
	SeqSearchWSClient
		SeqSearchWSClient(ServiceHandle, String, AlignmentView, String, AlignmentI, AlignFrame) (4 matches)
jalview.ws.jws2
	MsaWSClient
		MsaWSClient(Jws2Instance, WsParamSetI, List<Argument>, boolean, String, AlignmentView, boolean, boolean, AlignmentI, AlignFrame) (4 matches)
		startMsaWSClient(String, AlignmentView, boolean, boolean, AlignmentI) (2 matches)
jalview.ws.rest
	RestClient
		constructJob() (2 matches)
MCview
	PDBViewer
		jbInit()
		new MouseAdapter() {...}
		offerRemoval(JRadioButtonMenuItem) (3 matches)