[med-svn] [figtree] 06/08: Imported Upstream version 1.4.2+dfsg

Andreas Tille tille at debian.org
Tue Dec 1 10:56:01 UTC 2015 

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository figtree.

commit 8f2470a5133a617b408f6f8964aa1509afb63111
Author: Andreas Tille <tille at debian.org>
Date:   Tue Dec 1 11:25:29 2015 +0100

    Imported Upstream version 1.4.2+dfsg
---
 Graphics/CartoonTool.psd                           | Bin
 Graphics/CollapseTool.png                          | Bin
 Graphics/CollapseTool.psd                          | Bin
 Graphics/Darwin's Tree.png                         | Bin
 Graphics/FigTree.icns                              | Bin
 Graphics/FigTreeDocIcon.icns                       | Bin
 Graphics/FigTreeDocIcon.psd                        | Bin
 Graphics/FigTreeDocIcon.tif                        | Bin
 Graphics/FigTreeIcon.png                           | Bin
 Graphics/FigTreeIcon.psd                           | Bin
 Graphics/FigTreeIcon.tif                           | Bin
 Graphics/FigTreeScreen.png                         | Bin
 Graphics/RootingTool.psd                           | Bin
 Graphics/polar_tree.pdf                            |   0
 Graphics/radial_tree.pdf                           | Bin
 Graphics/rect_tree.pdf                             |   0
 build.xml                                          |  32 ++++++++++-----------
 release/Linux/icons/figtree.png                    | Bin
 src/figtree/applet/FigTreeApplet.java              |  10 +++----
 src/figtree/application/ExportTreeDialog.java      |   0
 src/figtree/application/FigTreeApplication.java    |  16 +++++------
 src/figtree/application/FigTreeFrame.java          |   0
 src/figtree/application/FigTreeMenuBarFactory.java |   0
 src/figtree/application/FigTreeNexusExporter.java  |   0
 src/figtree/application/FigTreeNexusImporter.java  |   0
 src/figtree/application/FigTreePDF.java            |   0
 src/figtree/application/FigTreePanel.java          |   0
 src/figtree/application/JSONTreeExporter.java      |   0
 src/figtree/application/images/actionButton.png    | Bin
 .../application/images/actionButtonInactive.png    | Bin
 .../application/images/actionButtonPressed.png     | Bin
 src/figtree/application/images/add.png             | Bin
 src/figtree/application/images/addButton.png       | Bin
 .../application/images/addButtonInactive.png       | Bin
 .../application/images/addButtonPressed.png        | Bin
 src/figtree/application/images/annotation.png      | Bin
 src/figtree/application/images/annotationTool.png  | Bin
 src/figtree/application/images/cartoonNodeTool.png | Bin
 src/figtree/application/images/chartTool.png       | Bin
 .../application/images/collapseNodeTool.png        | Bin
 src/figtree/application/images/coloursTool.png     | Bin
 src/figtree/application/images/crosshairCursor.png | Bin
 src/figtree/application/images/dataEditorTool.png  | Bin
 src/figtree/application/images/document.png        | Bin
 src/figtree/application/images/exportTool.png      | Bin
 src/figtree/application/images/figtree.png         | Bin
 .../application/images/filterBackground.png        | Bin
 src/figtree/application/images/find.png            | Bin
 src/figtree/application/images/findTool.png        | Bin
 src/figtree/application/images/fontBiggerTool.png  | Bin
 src/figtree/application/images/fontSmallerTool.png | Bin
 src/figtree/application/images/import.png          | Bin
 src/figtree/application/images/infoTool.png        | Bin
 src/figtree/application/images/minus.png           | Bin
 src/figtree/application/images/nextButton.png      | Bin
 .../application/images/nextButtonInactive.png      | Bin
 .../application/images/nextButtonPressed.png       | Bin
 src/figtree/application/images/prefsAdvanced.png   | Bin
 src/figtree/application/images/prefsClipboard.png  | Bin
 src/figtree/application/images/prefsGeneral.png    | Bin
 src/figtree/application/images/previousButton.png  | Bin
 .../application/images/previousButtonInactive.png  | Bin
 .../application/images/previousButtonPressed.png   | Bin
 src/figtree/application/images/project.png         | Bin
 src/figtree/application/images/projectTool.png     | Bin
 src/figtree/application/images/publication.png     | Bin
 src/figtree/application/images/removeButton.png    | Bin
 .../application/images/removeButtonInactive.png    | Bin
 .../application/images/removeButtonPressed.png     | Bin
 src/figtree/application/images/rerootTool.png      | Bin
 src/figtree/application/images/rotateCursor.psd    | Bin
 src/figtree/application/images/rotateTool.png      | Bin
 src/figtree/application/images/statisticsTool.png  | Bin
 src/figtree/application/images/tableSelection.png  | Bin
 .../application/images/tableSelectionGray.png      | Bin
 src/figtree/application/menus/TreeMenuFactory.java |   0
 src/figtree/application/menus/TreeMenuHandler.java |   0
 .../preferences/AdvancedPreferencesSection.java    |   0
 .../preferences/AppearancePreferencesSection.java  |   0
 .../preferences/FontsPreferencesSection.java       |   0
 .../preferences/GeneralPreferencesSection.java     |   0
 src/figtree/panel/FigTreePanel.java                |   0
 src/figtree/panel/LabelPainterController.java      |   0
 src/figtree/panel/ScaleBarPainterController.java   |   0
 src/figtree/panel/SimpleLabelPainter.java          |   0
 src/figtree/panel/TreeAppearanceController.java    |   0
 src/figtree/panel/TreeColouringController.java     |   0
 src/figtree/panel/TreeLayoutController.java        |   0
 src/figtree/panel/TreeViewerController.java        |   0
 src/figtree/panel/TreesController.java             |   0
 src/figtree/treeviewer/AnnotationsController.java  |  10 +++----
 src/figtree/treeviewer/AnnotationsListener.java    |   0
 .../treeviewer/AttributeColourController.java      |   0
 .../treeviewer/ContinuousColourScaleDialog.java    |   0
 src/figtree/treeviewer/ContinuousScaleDialog.java  |   0
 src/figtree/treeviewer/DefaultTreeViewer.java      |  10 -------
 .../treeviewer/DiscreteColourScaleDialog.java      |   0
 src/figtree/treeviewer/ExtendedTreeViewer.java     |   0
 src/figtree/treeviewer/FindDialog.java             |   0
 src/figtree/treeviewer/FindPanel.java              |   0
 src/figtree/treeviewer/MultiPaneTreeViewer.java    |   0
 .../treeviewer/MultiPaneTreeViewerController.java  |   0
 .../treeviewer/MultipleTreesController.java        |   0
 .../treeviewer/OldContinuousColourScaleDialog.java |   0
 src/figtree/treeviewer/ScaleAxis.java              |   0
 src/figtree/treeviewer/SizeScaleDialog.java        |   0
 src/figtree/treeviewer/TimeScale.java              |   0
 src/figtree/treeviewer/TimeScaleController.java    |   0
 .../treeviewer/TreeAppearanceController.java       |   0
 src/figtree/treeviewer/TreePane.java               |  10 +------
 src/figtree/treeviewer/TreePaneListener.java       |   0
 src/figtree/treeviewer/TreePaneRollOver.java       |   0
 src/figtree/treeviewer/TreePaneRuler.java          |   0
 src/figtree/treeviewer/TreePaneSelector.java       |   0
 src/figtree/treeviewer/TreeSelectionListener.java  |   0
 src/figtree/treeviewer/TreeViewer.java             |   0
 src/figtree/treeviewer/TreeViewerController.java   |   0
 src/figtree/treeviewer/TreeViewerListener.java     |   0
 src/figtree/treeviewer/TreeViewerPanel.java        |   0
 src/figtree/treeviewer/TreesController.java        |   0
 .../annotations/AnnotationDefinition.java          |   0
 .../annotations/AnnotationDefinitionsDialog.java   |   0
 .../treeviewer/annotations/AnnotationDialog.java   |   0
 .../annotations/DefineAnnotationDialog.java        |   0
 .../decorators/AttributableDecorator.java          |   0
 .../treeviewer/decorators/ColourDecorator.java     |   0
 .../treeviewer/decorators/CompoundDecorator.java   |   0
 .../decorators/ContinuousColourDecorator.java      |   0
 .../treeviewer/decorators/ContinuousScale.java     |   0
 .../decorators/ContinuousStrokeDecorator.java      |   0
 src/figtree/treeviewer/decorators/Decorator.java   |   0
 .../decorators/DiscreteColourDecorator.java        |   0
 .../DiversityContinuousColourDecorator.java        |   0
 .../decorators/HSBContinuousColourDecorator.java   |   0
 .../decorators/InterpolatingColourDecorator.java   |   0
 .../decorators/ParsimonyBranchDecorator.java       |   0
 src/figtree/treeviewer/images/polarTree.png        | Bin
 src/figtree/treeviewer/images/radialTree.png       | Bin
 src/figtree/treeviewer/images/rectangularTree.png  | Bin
 .../treeviewer/painters/AbstractPainter.java       |   0
 .../treeviewer/painters/BasicLabelPainter.java     |   0
 .../treeviewer/painters/CharactersPainter.java     |   0
 src/figtree/treeviewer/painters/LabelPainter.java  |   0
 .../painters/LabelPainterController.java           |   0
 src/figtree/treeviewer/painters/LegendPainter.java |   0
 .../painters/LegendPainterController.java          |   0
 .../treeviewer/painters/NodeBarController.java     |   0
 .../treeviewer/painters/NodeBarPainter.java        |   0
 src/figtree/treeviewer/painters/NodePainter.java   |   0
 .../treeviewer/painters/NodeShapeController.java   |   0
 .../treeviewer/painters/NodeShapePainter.java      |   0
 src/figtree/treeviewer/painters/Painter.java       |   0
 .../treeviewer/painters/PainterListener.java       |   0
 .../treeviewer/painters/ScaleAxisPainter.java      |   0
 .../painters/ScaleAxisPainterController.java       |   0
 .../treeviewer/painters/ScaleBarPainter.java       |   0
 .../painters/ScaleBarPainterController.java        |   0
 .../treeviewer/painters/ScaleGridPainter.java      |   0
 src/figtree/treeviewer/painters/ScalePainter.java  |   0
 src/figtree/treeviewer/painters/StatesPainter.java |   0
 .../treeviewer/treelayouts/AbstractTreeLayout.java |   0
 .../treeviewer/treelayouts/PolarTreeLayout.java    |   0
 .../treelayouts/PolarTreeLayoutController.java     |   0
 .../treeviewer/treelayouts/RadialTreeLayout.java   |   0
 .../treelayouts/RadialTreeLayoutController.java    |   0
 .../treelayouts/RectilinearTreeLayout.java         |   0
 .../RectilinearTreeLayoutController.java           |   0
 src/figtree/treeviewer/treelayouts/TreeLayout.java |   0
 .../treeviewer/treelayouts/TreeLayoutCache.java    |   0
 .../treeviewer/treelayouts/TreeLayoutListener.java |   0
 src/figtree/ui/PercentFormat.java                  |   0
 src/figtree/ui/RomanFormat.java                    |   0
 172 files changed, 34 insertions(+), 54 deletions(-)

diff --git a/Graphics/CartoonTool.psd b/Graphics/CartoonTool.psd
old mode 100644
new mode 100755
diff --git a/Graphics/CollapseTool.png b/Graphics/CollapseTool.png
old mode 100644
new mode 100755
diff --git a/Graphics/CollapseTool.psd b/Graphics/CollapseTool.psd
old mode 100644
new mode 100755
diff --git a/Graphics/Darwin's Tree.png b/Graphics/Darwin's Tree.png
old mode 100644
new mode 100755
diff --git a/Graphics/FigTree.icns b/Graphics/FigTree.icns
old mode 100644
new mode 100755
diff --git a/Graphics/FigTreeDocIcon.icns b/Graphics/FigTreeDocIcon.icns
old mode 100644
new mode 100755
diff --git a/Graphics/FigTreeDocIcon.psd b/Graphics/FigTreeDocIcon.psd
old mode 100644
new mode 100755
diff --git a/Graphics/FigTreeDocIcon.tif b/Graphics/FigTreeDocIcon.tif
old mode 100644
new mode 100755
diff --git a/Graphics/FigTreeIcon.png b/Graphics/FigTreeIcon.png
old mode 100644
new mode 100755
diff --git a/Graphics/FigTreeIcon.psd b/Graphics/FigTreeIcon.psd
old mode 100644
new mode 100755
diff --git a/Graphics/FigTreeIcon.tif b/Graphics/FigTreeIcon.tif
old mode 100644
new mode 100755
diff --git a/Graphics/FigTreeScreen.png b/Graphics/FigTreeScreen.png
old mode 100644
new mode 100755
diff --git a/Graphics/RootingTool.psd b/Graphics/RootingTool.psd
old mode 100644
new mode 100755
diff --git a/Graphics/polar_tree.pdf b/Graphics/polar_tree.pdf
old mode 100644
new mode 100755
diff --git a/Graphics/radial_tree.pdf b/Graphics/radial_tree.pdf
old mode 100644
new mode 100755
diff --git a/Graphics/rect_tree.pdf b/Graphics/rect_tree.pdf
old mode 100644
new mode 100755
diff --git a/build.xml b/build.xml
index e70ee4d..a3ae8db 100755
--- a/build.xml
+++ b/build.xml
@@ -91,7 +91,7 @@
 
     </target>
 
-    <property name="version" value="1.4.3" />
+    <property name="version" value="1.4.2" />
     <property name="release_dir" value="release" />
     <property name="name" value="FigTree" />
 
@@ -101,6 +101,7 @@
     <property name="Linux_dir" value="${release_dir}/Linux" />
     <property name="Windows_dir" value="${release_dir}/Windows" />
 
+    <property name="Mac_package_dir_SL" value="${Mac_dir}/${name} v${version}" />
     <property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
     <property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
     <property name="Windows_package_dir" value="${Windows_dir}/${name} v${version}" />
@@ -169,34 +170,33 @@
         <echo message="Linux/Unix version release is finished." />
     </target>
 
-    <target name="mac_release"
-            description="release Mac version of FigTree">
-        <delete dir="${Mac_package_dir}" />
+    <target name="mac_sl_release"
+            description="release Mac Snow Leopard version of FigTree">
+        <delete dir="${Mac_package_dir_SL}" />
         <!-- Create the release directory -->
-        <mkdir dir="${Mac_package_dir}" />
+        <mkdir dir="${Mac_package_dir_SL}" />
 
-        <copy file="${dist}/figtree.jar" todir="${Mac_package_dir}/lib"/>
-        <copy file="${dist}/figtree-pdf.jar" todir="${Mac_package_dir}/QuickLook Plugin/FigTreeQuickLookPlugin.qlgenerator/Contents/Resources"/>
-        <copy todir="${Mac_package_dir}">
+        <copy file="${dist}/figtree.jar" todir="${Mac_package_dir_SL}/lib"/>
+        <copy file="${dist}/figtree-pdf.jar" todir="${Mac_package_dir_SL}/QuickLook Plugin/FigTreeQuickLookPlugin.qlgenerator/Contents/Resources"/>
+        <copy todir="${Mac_package_dir_SL}">
             <fileset dir="${common_dir}/"/>
         </copy>
-        <copy todir="${Mac_package_dir}/QuickLook Plugin">
+        <copy todir="${Mac_package_dir_SL}/QuickLook Plugin">
             <fileset dir="${Mac_dir}/QuickLook Plugin"/>
         </copy>
 
         <taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
 
         <!-- create a jar bundle for the mac -->
-        <jarbundler dir="${Mac_package_dir}"
+        <jarbundler dir="${Mac_package_dir_SL}"
                     name="${name} v${version}"
                     mainclass="figtree.application.FigTreeApplication"
                     icon="${Mac_dir}/icons/FigTree.icns"
                     jvmversion="1.6+"
                     vmoptions="-Xmx1024M"
-                    stubfile="${Mac_dir}/universalJavaApplicationStub"
                     arguments=""
-                    version="${version}"
-                    infostring="${name} v${version}, Copyright 2006-2015, Andrew Rambaut"
+                    version="${version} SL"
+                    infostring="${name} v${version} SL, Copyright 2006-2014, Andrew Rambaut"
                     bundleid="figtree" >
             <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
             <jarfileset dir="${dist}">
@@ -215,15 +215,13 @@
         </jarbundler>
 
         <!-- remove code signing -->
-        <!--
         <exec executable="/usr/bin/codesign">
             <arg value="-s"/>
             <arg value="-"/>
-            <arg value="- -force"/> remove space from between minus signs
+            <arg value="--force"/>
             <arg value="${Mac_dir}/${name} v${version}/${name} v${version}.app"/>
         </exec>
-		-->
-		
+
         <echo message="Building disk image." />
 
         <!-- create disk image -->
diff --git a/release/Linux/icons/figtree.png b/release/Linux/icons/figtree.png
old mode 100644
new mode 100755
diff --git a/src/figtree/applet/FigTreeApplet.java b/src/figtree/applet/FigTreeApplet.java
old mode 100644
new mode 100755
index 0237ef5..670bda9
--- a/src/figtree/applet/FigTreeApplet.java
+++ b/src/figtree/applet/FigTreeApplet.java
@@ -43,13 +43,13 @@ import java.net.MalformedURLException;
 /**
  * @author Andrew Rambaut
  * @author Alexei Drummond
- * @version $Id: FigTreeApplet.java 235 2014-03-03 09:58:05Z rambaut $
+ * @version $Id$
  *
- * $HeadURL: http://figtree.googlecode.com/svn/trunk/src/figtree/applet/FigTreeApplet.java $
+ * $HeadURL$
  *
- * $LastChangedBy: rambaut $
- * $LastChangedDate: 2014-03-03 10:58:05 +0100 (lun. 03 mars 2014) $
- * $LastChangedRevision: 235 $
+ * $LastChangedBy$
+ * $LastChangedDate$
+ * $LastChangedRevision$
  */
 public class FigTreeApplet extends JApplet {
 	private SimpleTreeViewer treeViewer;
diff --git a/src/figtree/application/ExportTreeDialog.java b/src/figtree/application/ExportTreeDialog.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/FigTreeApplication.java b/src/figtree/application/FigTreeApplication.java
old mode 100644
new mode 100755
index 9f9066e..495267c
--- a/src/figtree/application/FigTreeApplication.java
+++ b/src/figtree/application/FigTreeApplication.java
@@ -25,7 +25,7 @@
  * Description:		An application for analysing MCMC trace files.
  * @author			Andrew Rambaut
  * @author			Alexei Drummond
- * @version			$Id: FigTreeApplication.java 260 2015-03-05 11:24:23Z rambaut $
+ * @version			$Id$
  */
 
 package figtree.application;
@@ -58,18 +58,18 @@ import ch.randelshofer.quaqua.QuaquaManager;
  * Uses JAM Application classes to create a MultiDoc Application.
  *
  * @author Andrew Rambaut
- * @version $Id: FigTreeApplication.java 260 2015-03-05 11:24:23Z rambaut $
+ * @version $Id$
  *
- * $HeadURL: http://figtree.googlecode.com/svn/trunk/src/figtree/application/FigTreeApplication.java $
+ * $HeadURL$
  *
- * $LastChangedBy: rambaut $
- * $LastChangedDate: 2015-03-05 12:24:23 +0100 (jeu. 05 mars 2015) $
- * $LastChangedRevision: 260 $
+ * $LastChangedBy$
+ * $LastChangedDate$
+ * $LastChangedRevision$
  */
 public class FigTreeApplication extends MultiDocApplication {
 
-    public static final String VERSION = "1.4.3";
-    public static final String DATES = "2006-2015";
+    public static final String VERSION = "1.4.2";
+    public static final String DATES = "2006-2014";
 
     public static FigTreeApplication application;
 
diff --git a/src/figtree/application/FigTreeFrame.java b/src/figtree/application/FigTreeFrame.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/FigTreeMenuBarFactory.java b/src/figtree/application/FigTreeMenuBarFactory.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/FigTreeNexusExporter.java b/src/figtree/application/FigTreeNexusExporter.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/FigTreeNexusImporter.java b/src/figtree/application/FigTreeNexusImporter.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/FigTreePDF.java b/src/figtree/application/FigTreePDF.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/FigTreePanel.java b/src/figtree/application/FigTreePanel.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/JSONTreeExporter.java b/src/figtree/application/JSONTreeExporter.java
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/actionButton.png b/src/figtree/application/images/actionButton.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/actionButtonInactive.png b/src/figtree/application/images/actionButtonInactive.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/actionButtonPressed.png b/src/figtree/application/images/actionButtonPressed.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/add.png b/src/figtree/application/images/add.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/addButton.png b/src/figtree/application/images/addButton.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/addButtonInactive.png b/src/figtree/application/images/addButtonInactive.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/addButtonPressed.png b/src/figtree/application/images/addButtonPressed.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/annotation.png b/src/figtree/application/images/annotation.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/annotationTool.png b/src/figtree/application/images/annotationTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/cartoonNodeTool.png b/src/figtree/application/images/cartoonNodeTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/chartTool.png b/src/figtree/application/images/chartTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/collapseNodeTool.png b/src/figtree/application/images/collapseNodeTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/coloursTool.png b/src/figtree/application/images/coloursTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/crosshairCursor.png b/src/figtree/application/images/crosshairCursor.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/dataEditorTool.png b/src/figtree/application/images/dataEditorTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/document.png b/src/figtree/application/images/document.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/exportTool.png b/src/figtree/application/images/exportTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/figtree.png b/src/figtree/application/images/figtree.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/filterBackground.png b/src/figtree/application/images/filterBackground.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/find.png b/src/figtree/application/images/find.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/findTool.png b/src/figtree/application/images/findTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/fontBiggerTool.png b/src/figtree/application/images/fontBiggerTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/fontSmallerTool.png b/src/figtree/application/images/fontSmallerTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/import.png b/src/figtree/application/images/import.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/infoTool.png b/src/figtree/application/images/infoTool.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/minus.png b/src/figtree/application/images/minus.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/nextButton.png b/src/figtree/application/images/nextButton.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/nextButtonInactive.png b/src/figtree/application/images/nextButtonInactive.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/nextButtonPressed.png b/src/figtree/application/images/nextButtonPressed.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/prefsAdvanced.png b/src/figtree/application/images/prefsAdvanced.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/prefsClipboard.png b/src/figtree/application/images/prefsClipboard.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/prefsGeneral.png b/src/figtree/application/images/prefsGeneral.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/previousButton.png b/src/figtree/application/images/previousButton.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/previousButtonInactive.png b/src/figtree/application/images/previousButtonInactive.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/previousButtonPressed.png b/src/figtree/application/images/previousButtonPressed.png
old mode 100644
new mode 100755
diff --git a/src/figtree/application/images/project.png b/src/figtree/application/images/project.png
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diff --git a/src/figtree/application/images/projectTool.png b/src/figtree/application/images/projectTool.png
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diff --git a/src/figtree/application/images/publication.png b/src/figtree/application/images/publication.png
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diff --git a/src/figtree/application/images/removeButton.png b/src/figtree/application/images/removeButton.png
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diff --git a/src/figtree/application/images/removeButtonInactive.png b/src/figtree/application/images/removeButtonInactive.png
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diff --git a/src/figtree/application/images/removeButtonPressed.png b/src/figtree/application/images/removeButtonPressed.png
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diff --git a/src/figtree/application/images/rerootTool.png b/src/figtree/application/images/rerootTool.png
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diff --git a/src/figtree/application/images/rotateCursor.psd b/src/figtree/application/images/rotateCursor.psd
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diff --git a/src/figtree/application/images/rotateTool.png b/src/figtree/application/images/rotateTool.png
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diff --git a/src/figtree/application/images/statisticsTool.png b/src/figtree/application/images/statisticsTool.png
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diff --git a/src/figtree/application/images/tableSelection.png b/src/figtree/application/images/tableSelection.png
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diff --git a/src/figtree/application/images/tableSelectionGray.png b/src/figtree/application/images/tableSelectionGray.png
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diff --git a/src/figtree/application/menus/TreeMenuFactory.java b/src/figtree/application/menus/TreeMenuFactory.java
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diff --git a/src/figtree/application/menus/TreeMenuHandler.java b/src/figtree/application/menus/TreeMenuHandler.java
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diff --git a/src/figtree/application/preferences/AdvancedPreferencesSection.java b/src/figtree/application/preferences/AdvancedPreferencesSection.java
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diff --git a/src/figtree/application/preferences/AppearancePreferencesSection.java b/src/figtree/application/preferences/AppearancePreferencesSection.java
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diff --git a/src/figtree/application/preferences/FontsPreferencesSection.java b/src/figtree/application/preferences/FontsPreferencesSection.java
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diff --git a/src/figtree/application/preferences/GeneralPreferencesSection.java b/src/figtree/application/preferences/GeneralPreferencesSection.java
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diff --git a/src/figtree/panel/FigTreePanel.java b/src/figtree/panel/FigTreePanel.java
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diff --git a/src/figtree/panel/LabelPainterController.java b/src/figtree/panel/LabelPainterController.java
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diff --git a/src/figtree/panel/ScaleBarPainterController.java b/src/figtree/panel/ScaleBarPainterController.java
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diff --git a/src/figtree/panel/SimpleLabelPainter.java b/src/figtree/panel/SimpleLabelPainter.java
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diff --git a/src/figtree/panel/TreeAppearanceController.java b/src/figtree/panel/TreeAppearanceController.java
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diff --git a/src/figtree/panel/TreeColouringController.java b/src/figtree/panel/TreeColouringController.java
old mode 100644
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diff --git a/src/figtree/panel/TreeLayoutController.java b/src/figtree/panel/TreeLayoutController.java
old mode 100644
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diff --git a/src/figtree/panel/TreeViewerController.java b/src/figtree/panel/TreeViewerController.java
old mode 100644
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diff --git a/src/figtree/panel/TreesController.java b/src/figtree/panel/TreesController.java
old mode 100644
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diff --git a/src/figtree/treeviewer/AnnotationsController.java b/src/figtree/treeviewer/AnnotationsController.java
old mode 100644
new mode 100755
index 7a7a124..65bca2f
--- a/src/figtree/treeviewer/AnnotationsController.java
+++ b/src/figtree/treeviewer/AnnotationsController.java
@@ -35,13 +35,13 @@ import java.util.Map;
  *
  *
  * @author Andrew Rambaut
- * @version $Id: AnnotationsController.java 231 2014-03-02 15:45:08Z rambaut $
+ * @version $Id$
  *
- * $HeadURL: http://figtree.googlecode.com/svn/trunk/src/figtree/treeviewer/AnnotationsController.java $
+ * $HeadURL$
  *
- * $LastChangedBy: rambaut $
- * $LastChangedDate: 2014-03-02 16:45:08 +0100 (dim. 02 mars 2014) $
- * $LastChangedRevision: 231 $
+ * $LastChangedBy$
+ * $LastChangedDate$
+ * $LastChangedRevision$
  */
 public class AnnotationsController extends AbstractController {
 
diff --git a/src/figtree/treeviewer/AnnotationsListener.java b/src/figtree/treeviewer/AnnotationsListener.java
old mode 100644
new mode 100755
diff --git a/src/figtree/treeviewer/AttributeColourController.java b/src/figtree/treeviewer/AttributeColourController.java
old mode 100644
new mode 100755
diff --git a/src/figtree/treeviewer/ContinuousColourScaleDialog.java b/src/figtree/treeviewer/ContinuousColourScaleDialog.java
old mode 100644
new mode 100755
diff --git a/src/figtree/treeviewer/ContinuousScaleDialog.java b/src/figtree/treeviewer/ContinuousScaleDialog.java
old mode 100644
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diff --git a/src/figtree/treeviewer/DefaultTreeViewer.java b/src/figtree/treeviewer/DefaultTreeViewer.java
old mode 100644
new mode 100755
index c5f92b1..1163014
--- a/src/figtree/treeviewer/DefaultTreeViewer.java
+++ b/src/figtree/treeviewer/DefaultTreeViewer.java
@@ -288,8 +288,6 @@ public class DefaultTreeViewer extends TreeViewer {
         }
 
         selectTaxa(attributeName, searchType, searchString, caseSensitive);
-
-        scrollToSelectedTips();
     }
 
     public void selectTaxa(String attributeName, TextSearchType searchType, String searchString, boolean caseSensitive) {
@@ -506,14 +504,6 @@ public class DefaultTreeViewer extends TreeViewer {
         return false;
     }
 
-    public void scrollToSelectedTips() {
-        Set<Node> selectedTips = treePane.getSelectedTips();
-        if (selectedTips.size() > 0) {
-            Point point = treePane.getLocationOfTip(selectedTips.iterator().next());
-            treePane.scrollPointToVisible(point);
-        }
-    }
-
     public void cartoonSelectedNodes() {
         treePane.cartoonSelectedNodes();
         fireTreeSettingsChanged();
diff --git a/src/figtree/treeviewer/DiscreteColourScaleDialog.java b/src/figtree/treeviewer/DiscreteColourScaleDialog.java
old mode 100644
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diff --git a/src/figtree/treeviewer/ExtendedTreeViewer.java b/src/figtree/treeviewer/ExtendedTreeViewer.java
old mode 100644
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diff --git a/src/figtree/treeviewer/FindDialog.java b/src/figtree/treeviewer/FindDialog.java
old mode 100644
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diff --git a/src/figtree/treeviewer/FindPanel.java b/src/figtree/treeviewer/FindPanel.java
old mode 100644
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diff --git a/src/figtree/treeviewer/MultiPaneTreeViewer.java b/src/figtree/treeviewer/MultiPaneTreeViewer.java
old mode 100644
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diff --git a/src/figtree/treeviewer/MultiPaneTreeViewerController.java b/src/figtree/treeviewer/MultiPaneTreeViewerController.java
old mode 100644
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diff --git a/src/figtree/treeviewer/MultipleTreesController.java b/src/figtree/treeviewer/MultipleTreesController.java
old mode 100644
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diff --git a/src/figtree/treeviewer/OldContinuousColourScaleDialog.java b/src/figtree/treeviewer/OldContinuousColourScaleDialog.java
old mode 100644
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diff --git a/src/figtree/treeviewer/ScaleAxis.java b/src/figtree/treeviewer/ScaleAxis.java
old mode 100644
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diff --git a/src/figtree/treeviewer/SizeScaleDialog.java b/src/figtree/treeviewer/SizeScaleDialog.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TimeScale.java b/src/figtree/treeviewer/TimeScale.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TimeScaleController.java b/src/figtree/treeviewer/TimeScaleController.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TreeAppearanceController.java b/src/figtree/treeviewer/TreeAppearanceController.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TreePane.java b/src/figtree/treeviewer/TreePane.java
old mode 100644
new mode 100755
index 7fecfda..5724c86
--- a/src/figtree/treeviewer/TreePane.java
+++ b/src/figtree/treeviewer/TreePane.java
@@ -1277,14 +1277,6 @@ public class TreePane extends JComponent implements PainterListener, Printable {
         this.rulerHeight = rulerHeight;
     }
 
-    public Point getLocationOfTip(Node tip) {
-        if (tip == null) {
-            return new Point(0,0);
-        }
-        Shape path = transform.createTransformedShape(treeLayoutCache.getTipLabelPath(tip));
-        return path.getBounds().getLocation();
-    }
-
     public void scrollPointToVisible(Point point) {
         scrollRectToVisible(new Rectangle(point.x, point.y, 0, 0));
     }
@@ -2282,7 +2274,7 @@ public class TreePane extends JComponent implements PainterListener, Printable {
     private Insets insets = new Insets(6, 6, 6, 6);
 
     private Set<Node> selectedNodes = new HashSet<Node>();
-    private Set<Node> selectedTips = new LinkedHashSet<Node>();
+    private Set<Node> selectedTips = new HashSet<Node>();
 
     private double rulerHeight = -1.0;
     private Rectangle2D dragRectangle = null;
diff --git a/src/figtree/treeviewer/TreePaneListener.java b/src/figtree/treeviewer/TreePaneListener.java
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diff --git a/src/figtree/treeviewer/TreePaneRollOver.java b/src/figtree/treeviewer/TreePaneRollOver.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TreePaneRuler.java b/src/figtree/treeviewer/TreePaneRuler.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TreePaneSelector.java b/src/figtree/treeviewer/TreePaneSelector.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TreeSelectionListener.java b/src/figtree/treeviewer/TreeSelectionListener.java
old mode 100644
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diff --git a/src/figtree/treeviewer/TreeViewer.java b/src/figtree/treeviewer/TreeViewer.java
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diff --git a/src/figtree/treeviewer/TreeViewerController.java b/src/figtree/treeviewer/TreeViewerController.java
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diff --git a/src/figtree/treeviewer/TreeViewerListener.java b/src/figtree/treeviewer/TreeViewerListener.java
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diff --git a/src/figtree/treeviewer/TreeViewerPanel.java b/src/figtree/treeviewer/TreeViewerPanel.java
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diff --git a/src/figtree/treeviewer/TreesController.java b/src/figtree/treeviewer/TreesController.java
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diff --git a/src/figtree/treeviewer/annotations/AnnotationDefinition.java b/src/figtree/treeviewer/annotations/AnnotationDefinition.java
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diff --git a/src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java b/src/figtree/treeviewer/annotations/AnnotationDefinitionsDialog.java
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diff --git a/src/figtree/treeviewer/annotations/AnnotationDialog.java b/src/figtree/treeviewer/annotations/AnnotationDialog.java
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diff --git a/src/figtree/treeviewer/annotations/DefineAnnotationDialog.java b/src/figtree/treeviewer/annotations/DefineAnnotationDialog.java
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diff --git a/src/figtree/treeviewer/decorators/AttributableDecorator.java b/src/figtree/treeviewer/decorators/AttributableDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/ColourDecorator.java b/src/figtree/treeviewer/decorators/ColourDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/CompoundDecorator.java b/src/figtree/treeviewer/decorators/CompoundDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/ContinuousColourDecorator.java b/src/figtree/treeviewer/decorators/ContinuousColourDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/ContinuousScale.java b/src/figtree/treeviewer/decorators/ContinuousScale.java
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diff --git a/src/figtree/treeviewer/decorators/ContinuousStrokeDecorator.java b/src/figtree/treeviewer/decorators/ContinuousStrokeDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/Decorator.java b/src/figtree/treeviewer/decorators/Decorator.java
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diff --git a/src/figtree/treeviewer/decorators/DiscreteColourDecorator.java b/src/figtree/treeviewer/decorators/DiscreteColourDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/DiversityContinuousColourDecorator.java b/src/figtree/treeviewer/decorators/DiversityContinuousColourDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/HSBContinuousColourDecorator.java b/src/figtree/treeviewer/decorators/HSBContinuousColourDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/InterpolatingColourDecorator.java b/src/figtree/treeviewer/decorators/InterpolatingColourDecorator.java
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diff --git a/src/figtree/treeviewer/decorators/ParsimonyBranchDecorator.java b/src/figtree/treeviewer/decorators/ParsimonyBranchDecorator.java
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diff --git a/src/figtree/treeviewer/images/polarTree.png b/src/figtree/treeviewer/images/polarTree.png
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diff --git a/src/figtree/treeviewer/images/radialTree.png b/src/figtree/treeviewer/images/radialTree.png
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diff --git a/src/figtree/treeviewer/images/rectangularTree.png b/src/figtree/treeviewer/images/rectangularTree.png
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diff --git a/src/figtree/treeviewer/painters/AbstractPainter.java b/src/figtree/treeviewer/painters/AbstractPainter.java
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diff --git a/src/figtree/treeviewer/painters/BasicLabelPainter.java b/src/figtree/treeviewer/painters/BasicLabelPainter.java
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diff --git a/src/figtree/treeviewer/painters/CharactersPainter.java b/src/figtree/treeviewer/painters/CharactersPainter.java
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diff --git a/src/figtree/treeviewer/painters/LabelPainter.java b/src/figtree/treeviewer/painters/LabelPainter.java
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diff --git a/src/figtree/treeviewer/painters/LabelPainterController.java b/src/figtree/treeviewer/painters/LabelPainterController.java
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diff --git a/src/figtree/treeviewer/painters/LegendPainter.java b/src/figtree/treeviewer/painters/LegendPainter.java
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diff --git a/src/figtree/treeviewer/painters/LegendPainterController.java b/src/figtree/treeviewer/painters/LegendPainterController.java
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diff --git a/src/figtree/treeviewer/painters/NodeBarController.java b/src/figtree/treeviewer/painters/NodeBarController.java
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diff --git a/src/figtree/treeviewer/painters/NodeBarPainter.java b/src/figtree/treeviewer/painters/NodeBarPainter.java
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diff --git a/src/figtree/treeviewer/painters/NodePainter.java b/src/figtree/treeviewer/painters/NodePainter.java
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diff --git a/src/figtree/treeviewer/painters/NodeShapeController.java b/src/figtree/treeviewer/painters/NodeShapeController.java
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diff --git a/src/figtree/treeviewer/painters/NodeShapePainter.java b/src/figtree/treeviewer/painters/NodeShapePainter.java
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diff --git a/src/figtree/treeviewer/painters/Painter.java b/src/figtree/treeviewer/painters/Painter.java
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diff --git a/src/figtree/treeviewer/painters/PainterListener.java b/src/figtree/treeviewer/painters/PainterListener.java
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diff --git a/src/figtree/treeviewer/painters/ScaleAxisPainter.java b/src/figtree/treeviewer/painters/ScaleAxisPainter.java
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diff --git a/src/figtree/treeviewer/painters/ScaleAxisPainterController.java b/src/figtree/treeviewer/painters/ScaleAxisPainterController.java
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diff --git a/src/figtree/treeviewer/painters/ScaleBarPainter.java b/src/figtree/treeviewer/painters/ScaleBarPainter.java
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diff --git a/src/figtree/treeviewer/painters/ScaleBarPainterController.java b/src/figtree/treeviewer/painters/ScaleBarPainterController.java
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diff --git a/src/figtree/treeviewer/painters/ScaleGridPainter.java b/src/figtree/treeviewer/painters/ScaleGridPainter.java
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diff --git a/src/figtree/treeviewer/painters/ScalePainter.java b/src/figtree/treeviewer/painters/ScalePainter.java
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diff --git a/src/figtree/treeviewer/painters/StatesPainter.java b/src/figtree/treeviewer/painters/StatesPainter.java
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diff --git a/src/figtree/treeviewer/treelayouts/AbstractTreeLayout.java b/src/figtree/treeviewer/treelayouts/AbstractTreeLayout.java
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diff --git a/src/figtree/treeviewer/treelayouts/PolarTreeLayout.java b/src/figtree/treeviewer/treelayouts/PolarTreeLayout.java
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diff --git a/src/figtree/treeviewer/treelayouts/PolarTreeLayoutController.java b/src/figtree/treeviewer/treelayouts/PolarTreeLayoutController.java
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diff --git a/src/figtree/treeviewer/treelayouts/RadialTreeLayout.java b/src/figtree/treeviewer/treelayouts/RadialTreeLayout.java
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diff --git a/src/figtree/treeviewer/treelayouts/RadialTreeLayoutController.java b/src/figtree/treeviewer/treelayouts/RadialTreeLayoutController.java
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diff --git a/src/figtree/treeviewer/treelayouts/RectilinearTreeLayout.java b/src/figtree/treeviewer/treelayouts/RectilinearTreeLayout.java
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diff --git a/src/figtree/treeviewer/treelayouts/RectilinearTreeLayoutController.java b/src/figtree/treeviewer/treelayouts/RectilinearTreeLayoutController.java
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diff --git a/src/figtree/treeviewer/treelayouts/TreeLayout.java b/src/figtree/treeviewer/treelayouts/TreeLayout.java
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diff --git a/src/figtree/treeviewer/treelayouts/TreeLayoutCache.java b/src/figtree/treeviewer/treelayouts/TreeLayoutCache.java
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diff --git a/src/figtree/treeviewer/treelayouts/TreeLayoutListener.java b/src/figtree/treeviewer/treelayouts/TreeLayoutListener.java
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diff --git a/src/figtree/ui/PercentFormat.java b/src/figtree/ui/PercentFormat.java
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diff --git a/src/figtree/ui/RomanFormat.java b/src/figtree/ui/RomanFormat.java
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