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Viewing all changes in revision 1.

Committer: Bazaar Package Importer
Author(s): Andreas Tille
Date: 2011-02-21 08:17:38 UTC
Revision ID: james.westby@ubuntu.com-20110221081738-80pe2ulo8rg7up10

Tags: upstream-1.3.1

Import upstream version 1.3.1

files added:

.classpath

.project

Graphics

Graphics/CartoonTool.psd

Graphics/CollapseTool.png

Graphics/CollapseTool.psd

Graphics/Darwin's Tree.png

Graphics/FigTree.icns

Graphics/FigTreeDocIcon.icns

Graphics/FigTreeDocIcon.psd

Graphics/FigTreeDocIcon.tif

Graphics/FigTreeIcon.png

Graphics/FigTreeIcon.psd

Graphics/FigTreeIcon.tif

Graphics/FigTreeScreen.png

Graphics/HilightTool.png

Graphics/HilightTool.psd

Graphics/RootingTool.psd

Graphics/polar_tree.pdf

Graphics/radial_tree.pdf

Graphics/rect_tree.pdf

WebRoot

WebRoot/META-INF

WebRoot/META-INF/MANIFEST.MF

WebRoot/META-INF/context.xml

WebRoot/WEB-INF

WebRoot/WEB-INF/context.xml

WebRoot/WEB-INF/jetty-web.xml

WebRoot/WEB-INF/web.xml

WebRoot/figtree.css

build.xml

build_applet.xml

examples

examples/HA_continuous_MCC.tre

examples/HA_discrete_MCC.tre

lib

release

release/Linux

release/Linux/icons

release/Linux/icons/figtree.png

release/Linux/lib

release/Linux/scripts

release/Linux/scripts/figtree

release/common

release/common/README.txt

release/common/carnivore.tree

release/common/influenza.tree

release/common/lib

src

src/figtree

src/figtree/applet

src/figtree/applet/FigTreeApplet.java

src/figtree/application

src/figtree/application/Arguments.java

src/figtree/application/ExportTreeDialog.java

src/figtree/application/FigTreeApplication.java

src/figtree/application/FigTreeFrame.java

src/figtree/application/FigTreeMenuBarFactory.java

src/figtree/application/FigTreeNexusExporter.java

src/figtree/application/FigTreeNexusImporter.java

src/figtree/application/FigTreePDF.java

src/figtree/application/FigTreePanel.java

src/figtree/application/Utils.java

src/figtree/application/images

src/figtree/application/images/actionButton.png

src/figtree/application/images/actionButtonInactive.png

src/figtree/application/images/actionButtonPressed.png

src/figtree/application/images/add.png

src/figtree/application/images/addButton.png

src/figtree/application/images/addButtonInactive.png

src/figtree/application/images/addButtonPressed.png

src/figtree/application/images/annotation.png

src/figtree/application/images/annotationTool.png

src/figtree/application/images/cartoonNodeTool.png

src/figtree/application/images/chartTool.png

src/figtree/application/images/collapseNodeTool.png

src/figtree/application/images/coloursTool.png

src/figtree/application/images/crosshairCursor.png

src/figtree/application/images/dataEditorTool.png

src/figtree/application/images/document.png

src/figtree/application/images/exportTool.png

src/figtree/application/images/figtree.png

src/figtree/application/images/figtreeLogo.png

src/figtree/application/images/filterBackground.png

src/figtree/application/images/find.png

src/figtree/application/images/findTool.png

src/figtree/application/images/fontBiggerTool.png

src/figtree/application/images/fontSmallerTool.png

src/figtree/application/images/hilightTool.png

src/figtree/application/images/import.png

src/figtree/application/images/infoTool.png

src/figtree/application/images/minus.png

src/figtree/application/images/next.png

src/figtree/application/images/nextButton.png

src/figtree/application/images/nextButtonInactive.png

src/figtree/application/images/nextButtonPressed.png

src/figtree/application/images/prefsAdvanced.png

src/figtree/application/images/prefsClipboard.png

src/figtree/application/images/prefsFonts.png

src/figtree/application/images/prefsGeneral.png

src/figtree/application/images/prev.png

src/figtree/application/images/previousButton.png

src/figtree/application/images/previousButtonInactive.png

src/figtree/application/images/previousButtonPressed.png

src/figtree/application/images/project.png

src/figtree/application/images/projectTool.png

src/figtree/application/images/publication.png

src/figtree/application/images/removeButton.png

src/figtree/application/images/removeButtonInactive.png

src/figtree/application/images/removeButtonPressed.png

src/figtree/application/images/rerootTool.png

src/figtree/application/images/rotateCursor.psd

src/figtree/application/images/rotateTool.png

src/figtree/application/images/statisticsTool.png

src/figtree/application/images/tableSelection.png

src/figtree/application/images/tableSelectionGray.png

src/figtree/application/menus

src/figtree/application/menus/FigTreeDefaultFileMenuFactory.java

src/figtree/application/menus/FigTreeFileMenuHandler.java

src/figtree/application/menus/FigTreeMacFileMenuFactory.java

src/figtree/application/menus/PyromaniaDefaultFileMenuFactory.java

src/figtree/application/menus/PyromaniaFileMenuHandler.java

src/figtree/application/menus/PyromaniaMacFileMenuFactory.java

src/figtree/application/menus/PyromaniaMenuBarFactory.java

src/figtree/application/menus/TreeMenuFactory.java

src/figtree/application/menus/TreeMenuHandler.java

src/figtree/application/preferences

src/figtree/application/preferences/AdvancedPreferencesSection.java

src/figtree/application/preferences/AppearancePreferencesSection.java

src/figtree/application/preferences/FontsPreferencesSection.java

src/figtree/application/preferences/GeneralPreferencesSection.java

src/figtree/flutree

src/figtree/flutree/FluTreeApplet.java

src/figtree/panel

src/figtree/panel/FigTreePanel.java

src/figtree/panel/LabelPainterController.java

src/figtree/panel/ScaleBarPainterController.java

src/figtree/panel/SimpleControlPalette.java

src/figtree/panel/SimpleLabelPainter.java

src/figtree/panel/SimpleTreeViewer.java

src/figtree/panel/TreeAppearanceController.java

src/figtree/panel/TreeColouringController.java

src/figtree/panel/TreeLayoutController.java

src/figtree/panel/TreeViewerController.java

src/figtree/panel/TreesController.java

src/figtree/treeviewer

src/figtree/treeviewer/AnnotationsController.java

src/figtree/treeviewer/AnnotationsListener.java

src/figtree/treeviewer/ColourScaleDialog.java

src/figtree/treeviewer/ControllerOptionsPanel.java

src/figtree/treeviewer/DefaultTreeViewer.java

src/figtree/treeviewer/ExtendedTreeViewer.java

src/figtree/treeviewer/FindDialog.java

src/figtree/treeviewer/FindPanel.java

src/figtree/treeviewer/FontDialog.java

src/figtree/treeviewer/MultiPaneTreeViewer.java

src/figtree/treeviewer/MultiPaneTreeViewerController.java

src/figtree/treeviewer/MultipleTreesController.java

src/figtree/treeviewer/Parsimony.java

src/figtree/treeviewer/ReRootedTree.java

src/figtree/treeviewer/ScaleAxis.java

src/figtree/treeviewer/TimeScale.java

src/figtree/treeviewer/TimeScaleController.java

src/figtree/treeviewer/TreeAppearanceController.java

src/figtree/treeviewer/TreePane.java

src/figtree/treeviewer/TreePaneListener.java

src/figtree/treeviewer/TreePaneRollOver.java

src/figtree/treeviewer/TreePaneRuler.java

src/figtree/treeviewer/TreePaneSelector.java

src/figtree/treeviewer/TreeSelectionListener.java

src/figtree/treeviewer/TreeViewer.java

src/figtree/treeviewer/TreeViewerController.java

src/figtree/treeviewer/TreeViewerListener.java

src/figtree/treeviewer/TreeViewerPanel.java

src/figtree/treeviewer/TreesController.java

src/figtree/treeviewer/WidthScaleDialog.java

src/figtree/treeviewer/annotations

src/figtree/treeviewer/annotations/AnnotationDefinition.java

src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java

src/figtree/treeviewer/annotations/AnnotationDialog.java

src/figtree/treeviewer/annotations/DefineAnnotationDialog.java

src/figtree/treeviewer/annotations/SelectAnnotationDialog.java

src/figtree/treeviewer/decorators

src/figtree/treeviewer/decorators/AttributableDecorator.java

src/figtree/treeviewer/decorators/CompoundDecorator.java

src/figtree/treeviewer/decorators/ContinousScale.java

src/figtree/treeviewer/decorators/ContinuousColorDecorator.java

src/figtree/treeviewer/decorators/ContinuousStrokeDecorator.java

src/figtree/treeviewer/decorators/Decorator.java

src/figtree/treeviewer/decorators/DiscreteColorDecorator.java

src/figtree/treeviewer/decorators/ParsimonyBranchDecorator.java

src/figtree/treeviewer/images

src/figtree/treeviewer/images/polarTree.png

src/figtree/treeviewer/images/radialTree.png

src/figtree/treeviewer/images/rectangularTree.png

src/figtree/treeviewer/painters

src/figtree/treeviewer/painters/AbstractPainter.java

src/figtree/treeviewer/painters/BasicLabelPainter.java

src/figtree/treeviewer/painters/CharactersPainter.java

src/figtree/treeviewer/painters/LabelPainter.java

src/figtree/treeviewer/painters/LabelPainterController.java

src/figtree/treeviewer/painters/NodeBarController.java

src/figtree/treeviewer/painters/NodeBarPainter.java

src/figtree/treeviewer/painters/NodePainter.java

src/figtree/treeviewer/painters/NodeShapeController.java

src/figtree/treeviewer/painters/NodeShapePainter.java

src/figtree/treeviewer/painters/Painter.java

src/figtree/treeviewer/painters/PainterListener.java

src/figtree/treeviewer/painters/PercentFormat.java

src/figtree/treeviewer/painters/Roman.java

src/figtree/treeviewer/painters/ScaleAxisPainter.java

src/figtree/treeviewer/painters/ScaleAxisPainterController.java

src/figtree/treeviewer/painters/ScaleBarPainter.java

src/figtree/treeviewer/painters/ScaleBarPainterController.java

src/figtree/treeviewer/painters/ScaleGridPainter.java

src/figtree/treeviewer/painters/ScalePainter.java

src/figtree/treeviewer/painters/StatesPainter.java

src/figtree/treeviewer/treelayouts

src/figtree/treeviewer/treelayouts/AbstractTreeLayout.java

src/figtree/treeviewer/treelayouts/PolarTreeLayout.java

src/figtree/treeviewer/treelayouts/PolarTreeLayoutController.java

src/figtree/treeviewer/treelayouts/RadialTreeLayout.java

src/figtree/treeviewer/treelayouts/RadialTreeLayoutController.java

src/figtree/treeviewer/treelayouts/RectilinearTreeLayout.java

src/figtree/treeviewer/treelayouts/RectilinearTreeLayoutController.java

src/figtree/treeviewer/treelayouts/TreeLayout.java

src/figtree/treeviewer/treelayouts/TreeLayoutCache.java

src/figtree/treeviewer/treelayouts/TreeLayoutListener.java

src/figtree/ui

src/figtree/ui/FontChooserPanel.java

src/figtree/ui/components

src/figtree/ui/components/ColorWellButton.java

src/figtree/ui/components/JVerticalLabel.java

src/figtree/ui/components/RealNumberField.java

src/figtree/ui/components/WholeNumberField.java

src/figtree/webui

src/figtree/webui/FigTreeWebApplication.java

src/figtree/webui/FileUploadWidget.java

src/figtree/webui/Main.java

src/figtree/webui/TreeWidget.java

Show diffs side-by-side

added added

removed removed

Graphics/CartoonTool.psd

Graphics/CollapseTool.png

Graphics/CollapseTool.psd

Graphics/Darwin's Tree.png

Graphics/FigTree.icns

Graphics/FigTreeDocIcon.icns

Graphics/FigTreeDocIcon.psd

Graphics/FigTreeDocIcon.tif

Graphics/FigTreeIcon.png

Graphics/FigTreeIcon.psd

Graphics/FigTreeIcon.tif

Graphics/FigTreeScreen.png

Graphics/HilightTool.png

Graphics/HilightTool.psd

Graphics/RootingTool.psd

Graphics/polar_tree.pdf

Graphics/radial_tree.pdf

Graphics/rect_tree.pdf

WebRoot/META-INF/

WebRoot/META-INF/MANIFEST.MF

WebRoot/META-INF/context.xml

WebRoot/WEB-INF/

WebRoot/WEB-INF/context.xml

WebRoot/WEB-INF/jetty-web.xml

WebRoot/WEB-INF/web.xml

WebRoot/figtree.css

build_applet.xml

examples/HA_continuous_MCC.tre

examples/HA_discrete_MCC.tre

release/Linux/icons/

release/Linux/icons/figtree.png

release/Linux/lib/

release/Linux/scripts/

release/Linux/scripts/figtree

release/common/

release/common/README.txt

release/common/carnivore.tree

release/common/influenza.tree

release/common/lib/

src/figtree/applet/

src/figtree/applet/FigTreeApplet.java

src/figtree/application/

src/figtree/application/Arguments.java

src/figtree/application/ExportTreeDialog.java

src/figtree/application/FigTreeApplication.java

src/figtree/application/FigTreeFrame.java

src/figtree/application/FigTreeMenuBarFactory.java

src/figtree/application/FigTreeNexusExporter.java

src/figtree/application/FigTreeNexusImporter.java

src/figtree/application/FigTreePDF.java

src/figtree/application/FigTreePanel.java

src/figtree/application/Utils.java

src/figtree/application/images/

src/figtree/application/images/actionButton.png

src/figtree/application/images/actionButtonInactive.png

src/figtree/application/images/actionButtonPressed.png

src/figtree/application/images/add.png

src/figtree/application/images/addButton.png

src/figtree/application/images/addButtonInactive.png

src/figtree/application/images/addButtonPressed.png

src/figtree/application/images/annotation.png

src/figtree/application/images/annotationTool.png

src/figtree/application/images/cartoonNodeTool.png

src/figtree/application/images/chartTool.png

src/figtree/application/images/collapseNodeTool.png

src/figtree/application/images/coloursTool.png

src/figtree/application/images/crosshairCursor.png

src/figtree/application/images/dataEditorTool.png

src/figtree/application/images/document.png

src/figtree/application/images/exportTool.png

src/figtree/application/images/figtree.png

src/figtree/application/images/figtreeLogo.png

src/figtree/application/images/filterBackground.png

src/figtree/application/images/find.png

src/figtree/application/images/findTool.png

src/figtree/application/images/fontBiggerTool.png

src/figtree/application/images/fontSmallerTool.png

src/figtree/application/images/hilightTool.png

src/figtree/application/images/import.png

src/figtree/application/images/infoTool.png

src/figtree/application/images/minus.png

src/figtree/application/images/next.png

src/figtree/application/images/nextButton.png

src/figtree/application/images/nextButtonInactive.png

src/figtree/application/images/nextButtonPressed.png

src/figtree/application/images/prefsAdvanced.png

src/figtree/application/images/prefsClipboard.png

src/figtree/application/images/prefsFonts.png

src/figtree/application/images/prefsGeneral.png

src/figtree/application/images/prev.png

src/figtree/application/images/previousButton.png

src/figtree/application/images/previousButtonInactive.png

src/figtree/application/images/previousButtonPressed.png

src/figtree/application/images/project.png

src/figtree/application/images/projectTool.png

src/figtree/application/images/publication.png

src/figtree/application/images/removeButton.png

src/figtree/application/images/removeButtonInactive.png

src/figtree/application/images/removeButtonPressed.png

src/figtree/application/images/rerootTool.png

src/figtree/application/images/rotateCursor.psd

src/figtree/application/images/rotateTool.png

src/figtree/application/images/statisticsTool.png

src/figtree/application/images/tableSelection.png

src/figtree/application/images/tableSelectionGray.png

src/figtree/application/menus/

src/figtree/application/menus/FigTreeDefaultFileMenuFactory.java

src/figtree/application/menus/FigTreeFileMenuHandler.java

src/figtree/application/menus/FigTreeMacFileMenuFactory.java

src/figtree/application/menus/PyromaniaDefaultFileMenuFactory.java

src/figtree/application/menus/PyromaniaFileMenuHandler.java

src/figtree/application/menus/PyromaniaMacFileMenuFactory.java

src/figtree/application/menus/PyromaniaMenuBarFactory.java

src/figtree/application/menus/TreeMenuFactory.java

src/figtree/application/menus/TreeMenuHandler.java

src/figtree/application/preferences/

src/figtree/application/preferences/AdvancedPreferencesSection.java

src/figtree/application/preferences/AppearancePreferencesSection.java

src/figtree/application/preferences/FontsPreferencesSection.java

src/figtree/application/preferences/GeneralPreferencesSection.java

src/figtree/flutree/

src/figtree/flutree/FluTreeApplet.java

src/figtree/panel/

src/figtree/panel/FigTreePanel.java

src/figtree/panel/LabelPainterController.java

src/figtree/panel/ScaleBarPainterController.java

src/figtree/panel/SimpleControlPalette.java

src/figtree/panel/SimpleLabelPainter.java

src/figtree/panel/SimpleTreeViewer.java

src/figtree/panel/TreeAppearanceController.java

src/figtree/panel/TreeColouringController.java

src/figtree/panel/TreeLayoutController.java

src/figtree/panel/TreeViewerController.java

src/figtree/panel/TreesController.java

src/figtree/treeviewer/

src/figtree/treeviewer/AnnotationsController.java

src/figtree/treeviewer/AnnotationsListener.java

src/figtree/treeviewer/ColourScaleDialog.java

src/figtree/treeviewer/ControllerOptionsPanel.java

src/figtree/treeviewer/DefaultTreeViewer.java

src/figtree/treeviewer/ExtendedTreeViewer.java

src/figtree/treeviewer/FindDialog.java

src/figtree/treeviewer/FindPanel.java

src/figtree/treeviewer/FontDialog.java

src/figtree/treeviewer/MultiPaneTreeViewer.java

src/figtree/treeviewer/MultiPaneTreeViewerController.java

src/figtree/treeviewer/MultipleTreesController.java

src/figtree/treeviewer/Parsimony.java

src/figtree/treeviewer/ReRootedTree.java

src/figtree/treeviewer/ScaleAxis.java

src/figtree/treeviewer/TimeScale.java

src/figtree/treeviewer/TimeScaleController.java

src/figtree/treeviewer/TreeAppearanceController.java

src/figtree/treeviewer/TreePane.java

src/figtree/treeviewer/TreePaneListener.java

src/figtree/treeviewer/TreePaneRollOver.java

src/figtree/treeviewer/TreePaneRuler.java

src/figtree/treeviewer/TreePaneSelector.java

src/figtree/treeviewer/TreeSelectionListener.java

src/figtree/treeviewer/TreeViewer.java

src/figtree/treeviewer/TreeViewerController.java

src/figtree/treeviewer/TreeViewerListener.java

src/figtree/treeviewer/TreeViewerPanel.java

src/figtree/treeviewer/TreesController.java

src/figtree/treeviewer/WidthScaleDialog.java

src/figtree/treeviewer/annotations/

src/figtree/treeviewer/annotations/AnnotationDefinition.java

src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java

src/figtree/treeviewer/annotations/AnnotationDialog.java

src/figtree/treeviewer/annotations/DefineAnnotationDialog.java

src/figtree/treeviewer/annotations/SelectAnnotationDialog.java

src/figtree/treeviewer/decorators/

src/figtree/treeviewer/decorators/AttributableDecorator.java

src/figtree/treeviewer/decorators/CompoundDecorator.java

src/figtree/treeviewer/decorators/ContinousScale.java

src/figtree/treeviewer/decorators/ContinuousColorDecorator.java

src/figtree/treeviewer/decorators/ContinuousStrokeDecorator.java

src/figtree/treeviewer/decorators/Decorator.java

src/figtree/treeviewer/decorators/DiscreteColorDecorator.java

src/figtree/treeviewer/decorators/ParsimonyBranchDecorator.java

src/figtree/treeviewer/images/

src/figtree/treeviewer/images/polarTree.png

src/figtree/treeviewer/images/radialTree.png

src/figtree/treeviewer/images/rectangularTree.png

src/figtree/treeviewer/painters/

src/figtree/treeviewer/painters/AbstractPainter.java

src/figtree/treeviewer/painters/BasicLabelPainter.java

src/figtree/treeviewer/painters/CharactersPainter.java

src/figtree/treeviewer/painters/LabelPainter.java

src/figtree/treeviewer/painters/LabelPainterController.java

src/figtree/treeviewer/painters/NodeBarController.java

src/figtree/treeviewer/painters/NodeBarPainter.java

src/figtree/treeviewer/painters/NodePainter.java

src/figtree/treeviewer/painters/NodeShapeController.java

src/figtree/treeviewer/painters/NodeShapePainter.java

src/figtree/treeviewer/painters/Painter.java

src/figtree/treeviewer/painters/PainterListener.java

src/figtree/treeviewer/painters/PercentFormat.java

src/figtree/treeviewer/painters/Roman.java

src/figtree/treeviewer/painters/ScaleAxisPainter.java

src/figtree/treeviewer/painters/ScaleAxisPainterController.java

src/figtree/treeviewer/painters/ScaleBarPainter.java

src/figtree/treeviewer/painters/ScaleBarPainterController.java

src/figtree/treeviewer/painters/ScaleGridPainter.java

src/figtree/treeviewer/painters/ScalePainter.java

src/figtree/treeviewer/painters/StatesPainter.java

src/figtree/treeviewer/treelayouts/

src/figtree/treeviewer/treelayouts/AbstractTreeLayout.java

src/figtree/treeviewer/treelayouts/PolarTreeLayout.java

src/figtree/treeviewer/treelayouts/PolarTreeLayoutController.java

src/figtree/treeviewer/treelayouts/RadialTreeLayout.java

src/figtree/treeviewer/treelayouts/RadialTreeLayoutController.java

src/figtree/treeviewer/treelayouts/RectilinearTreeLayout.java

src/figtree/treeviewer/treelayouts/RectilinearTreeLayoutController.java

src/figtree/treeviewer/treelayouts/TreeLayout.java

src/figtree/treeviewer/treelayouts/TreeLayoutCache.java

src/figtree/treeviewer/treelayouts/TreeLayoutListener.java

src/figtree/ui/

src/figtree/ui/FontChooserPanel.java

src/figtree/ui/components/

src/figtree/ui/components/ColorWellButton.java

src/figtree/ui/components/JVerticalLabel.java

src/figtree/ui/components/RealNumberField.java

src/figtree/ui/components/WholeNumberField.java

src/figtree/webui/

src/figtree/webui/FigTreeWebApplication.java

src/figtree/webui/FileUploadWidget.java

src/figtree/webui/Main.java

src/figtree/webui/TreeWidget.java

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