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github.com/rambaut/figtree
/ types & classes
Types & classes
285 in github.com/rambaut/figtree
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2,432
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Types & classes
285
↓ 1 callers
Class
_stat
packaging_tools/windows/launch4j/head_src/head.c:417
Class
AboutActionListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:355
Class
AbstractAcceptListener
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/AbstractAcceptListener.java:49
Class
AbstractPainter
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/painters/AbstractPainter.java:36
Class
AbstractTreeLayout
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/treelayouts/AbstractTreeLayout.java:36
Class
AcceptClasspathListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/ClassPathFormImpl.java:113
Class
AdvancedPreferencesSection
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/application/preferences/AdvancedPreferencesSection.java:40
Class
AnnotationDefinition
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/annotations/AnnotationDefinition.java:38
Class
AnnotationDefinitionsDialog
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java:46
Class
AnnotationDialog
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/annotations/AnnotationDialog.java:45
Class
AnnotationTableModel
src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java:155
Class
AnnotationsController
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/AnnotationsController.java:46
Interface
AnnotationsListener
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/AnnotationsListener.java:33
Class
AntClassPath
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/ant/AntClassPath.java:47
Class
AntConfig
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/ant/AntConfig.java:54
Class
AntJre
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/ant/AntJre.java:47
Class
AntLog
packaging_tools/windows/launch4j/src/net/sf/launch4j/Log.java:75
Class
AppearancePreferencesSection
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/application/preferences/AppearancePreferencesSection.java:44
Class
ArgumentException
src/figtree/application/Arguments.java:45
Class
Arguments
Parses a set of command line arguments according to the given definitions. Can parse simple switches, numerical arguments, string arguments from a lis
src/figtree/application/Arguments.java:41
Class
AttributableDecorator
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/decorators/AttributableDecorator.java:38
Class
AttributeColourController
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/AttributeColourController.java:46
Class
AttributeComboHelper
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/painters/AttributeComboHelper.java:46
Interface
AttributeComboHelperListener
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/painters/AttributeComboHelperListener.java:33
Enum
Axis
src/figtree/treeviewer/decorators/HSBDiscreteColourDecorator.java:39
Enum
AxisType
src/figtree/treeviewer/treelayouts/TreeLayout.java:40
Class
BasicForm
packaging_tools/windows/launch4j/src/net/sf/launch4j/form/BasicForm.java:19
Class
BasicFormImpl
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/BasicFormImpl.java:52
Class
BasicLabelPainter
A simple implementation of LabelPainter that can be used to display tip, node or branch labels. It can display, taxon names, branch lengths, node heig
src/figtree/treeviewer/painters/BasicLabelPainter.java:51
Interface
Binding
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Binding.java:44
Class
BindingException
Signals a runtime error, a missing property in a Java Bean for example. @author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/BindingException.java:44
Class
Bindings
Creates and handles bindings. @author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/binding/Bindings.java:61
Class
BrowseActionListener
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/BrowseActionListener.java:51
Class
BuildActionListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/MainFrame.java:300
Class
Builder
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:54
Class
BuilderException
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/BuilderException.java:42
Class
ChangeHandler
Listener to handle model change events. This calculates the thumb locations and repaints the slider if the value change is not caused by dragging a t
src/figtree/ui/components/RangeSliderUI.java:420
Class
CharactersPainter
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/painters/CharactersPainter.java:43
Class
ClassPath
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ClassPath.java:47
Class
ClassPathForm
packaging_tools/windows/launch4j/src/net/sf/launch4j/form/ClassPathForm.java:18
Class
ClassPathFormImpl
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/ClassPathFormImpl.java:64
Class
ClasspathCheckListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/ClassPathFormImpl.java:92
Class
ClasspathSelectionListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/ClassPathFormImpl.java:134
Class
Cmd
packaging_tools/windows/launch4j/src/net/sf/launch4j/Builder.java:156
Class
ColorRenderer
src/figtree/treeviewer/DiscreteColourScaleDialog.java:261
Class
ColorWell
src/figtree/ui/components/ColorWellButton.java:98
Class
ColorWellButton
@version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/ui/components/ColorWellButton.java:39
Class
ColourDecorator
This decorator takes an attribute name and a set of attibutable Objects. Colours are given to each individual value. If the data take more values tha
src/figtree/treeviewer/decorators/ColourDecorator.java:47
Interface
ColourSchemePanel
src/figtree/treeviewer/DiscreteColourScaleDialog.java:371
Interface
ColourSchemePanel
src/figtree/treeviewer/ContinuousColourScaleDialog.java:227
Class
ColourSettings
src/figtree/treeviewer/OldContinuousColourScaleDialog.java:48
Class
ColourTableModel
src/figtree/treeviewer/DiscreteColourScaleDialog.java:193
Class
CompoundDecorator
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/decorators/CompoundDecorator.java:40
Class
Config
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/Config.java:49
Class
ConfigForm
packaging_tools/windows/launch4j/src/net/sf/launch4j/form/ConfigForm.java:16
Class
ConfigFormImpl
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/ConfigFormImpl.java:51
Class
ConfigPersister
@author Copyright (C) 2014 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersister.java:64
Class
ConfigPersisterException
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/config/ConfigPersisterException.java:42
Class
ConsoleApp
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/demo/ConsoleApp/src/net/sf/launch4j/example/ConsoleApp.java:43
Class
ConsoleLog
packaging_tools/windows/launch4j/src/net/sf/launch4j/Log.java:65
Class
ContinuousColourDecorator
This decorator takes an attribute name and a set of attibutable Objects. It autodetects the type of attributes and then provides a colouring scheme fo
src/figtree/treeviewer/decorators/ContinuousColourDecorator.java:43
Class
ContinuousColourScaleDialog
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/ContinuousColourScaleDialog.java:53
Class
ContinuousScale
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/decorators/ContinuousScale.java:38
Class
ContinuousScaleDialog
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/ContinuousScaleDialog.java:46
Class
ContinuousStrokeDecorator
This decorator takes an attribute name and a set of attibutable Objects. It autodetects the type of attributes and then provides a colouring scheme fo
src/figtree/treeviewer/decorators/ContinuousStrokeDecorator.java:42
Class
ControllerOptionsPanel
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/ControllerOptionsPanel.java:39
Class
CustomDiscreteColourDecorator
A special class for customized colour schemes for various projects. Not generally for public use. @author Andrew Rambaut @version $Id$ $HeadURL$ $La
src/figtree/treeviewer/decorators/CustomDiscreteColourDecorator.java:41
Interface
Decorator
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/decorators/Decorator.java:39
Class
DefaultTreeViewer
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/DefaultTreeViewer.java:49
Class
DefineAnnotationDialog
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/annotations/DefineAnnotationDialog.java:38
Class
DiscreteColourDecorator
This decorator takes an attribute name and a set of attibutable Objects. Colours are given to each individual value. If the data take more values tha
src/figtree/treeviewer/decorators/DiscreteColourDecorator.java:45
Class
DiscreteColourScaleDialog
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/DiscreteColourScaleDialog.java:53
Class
DiversityContinuousColourDecorator
This draws a continuous colour spectrum to show diversity across the tree. @author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChan
src/figtree/treeviewer/decorators/DiversityContinuousColourDecorator.java:42
Class
DontWrapJarChangeListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/BasicFormImpl.java:85
Enum
DragMode
src/figtree/treeviewer/TreePaneSelector.java:49
Class
EnvActionListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/JreFormImpl.java:130
Class
EnvOptionActionListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/JreFormImpl.java:166
Class
EnvPropertyActionListener
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/JreFormImpl.java:151
Class
EnvironmentVarsForm
packaging_tools/windows/launch4j/src/net/sf/launch4j/form/EnvironmentVarsForm.java:15
Class
EnvironmentVarsFormImpl
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/EnvironmentVarsFormImpl.java:45
Class
ExecException
@author Copyright (C) 2005 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/ExecException.java:42
Class
ExportTreeDialog
Dialog presenting options for exporting one or more trees from FigTree @author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedD
src/figtree/application/ExportTreeDialog.java:42
Class
ExtendedTreeViewer
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/ExtendedTreeViewer.java:49
Class
FigTreeApplet
@author Andrew Rambaut @author Alexei Drummond @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/applet/FigTreeApplet.java:54
Class
FigTreeApplication
Application class for FigTree including main() method for invoking it. Uses JAM Application classes to create a MultiDoc Application. @author Andrew
src/figtree/application/FigTreeApplication.java:67
Class
FigTreeDefaultFileMenuFactory
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/application/menus/FigTreeDefaultFileMenuFactory.java:38
Interface
FigTreeFileMenuHandler
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/application/menus/FigTreeFileMenuHandler.java:35
Class
FigTreeFrame
Primary window for FigTree. The window contains a toolbar, a control panel and a panel displaying the tree. It responds to menu commands and hot keys
src/figtree/application/FigTreeFrame.java:83
Class
FigTreeMacFileMenuFactory
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/application/menus/FigTreeMacFileMenuFactory.java:39
Class
FigTreeMenuBarFactory
Register all the menus used by the FigTree app. @author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevisi
src/figtree/application/FigTreeMenuBarFactory.java:39
Class
FigTreeNexusExporter
An extension of the NexusExporter from JEBL to write FigTree settings in a FigTree block. @author Andrew Rambaut @version $Id: FigTreeApplication.jav
src/figtree/application/FigTreeNexusExporter.java:43
Class
FigTreeNexusImporter
An extension of the NexusImporter from JEBL to parse FigTree settings from a FigTree block. @author Andrew Rambaut @version $Id$ $HeadURL$ $LastCha
src/figtree/application/FigTreeNexusImporter.java:44
Class
FigTreePanel
This is a panel that has a TreeViewer and a BasicControlPalette with the default Controllers and Painters. @author Andrew Rambaut @version $Id$ $Hea
src/figtree/panel/FigTreePanel.java:50
Class
FigTreePanel
This is a panel that has a TreeViewer and a BasicControlPalette with the default Controllers and Painters. @author Andrew Rambaut @version $Id$ $Hea
src/figtree/application/FigTreePanel.java:47
Class
FigTreeWebApplication
src/figtree/webui/FigTreeWebApplication.java:42
Class
FileChooser
@author Copyright (C) 2006 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/formimpl/FileChooser.java:47
Class
FileChooserFilter
@author Copyright (C) 2004 Grzegorz Kowal
packaging_tools/windows/launch4j/src/net/sf/launch4j/FileChooserFilter.java:46
Class
FileUploadWidget
src/figtree/webui/FileUploadWidget.java:12
Class
FindDialog
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/FindDialog.java:49
Class
FindPanel
@author Andrew Rambaut @version $Id$ $HeadURL$ $LastChangedBy$ $LastChangedDate$ $LastChangedRevision$
src/figtree/treeviewer/FindPanel.java:43
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