rambaut / figtree Goto Github PK

Select "Define Annotations", add a new annotation, select "Done". Annotation 
definition will not be 
stored.

In Mac OS X, the Preferences option is available from the Application menu. For 
other platforms, it 
needs to put into a standard menu. Need to decide what the standard place is 
for different 
platforms.

What steps will reproduce the problem?
1. Reroot any tree in a file containing multiple trees
2. Scroll to the next / previous tree in the file

What is the expected output? What do you see instead?

Instead of scrolling to the next / previous tree, FigTree continues to display 
the current, rerooted 
topology.

What version of the product are you using? On what operating system?

v1.2.2 on a Mac running 10.5.6

From Heiko Schmidt:

I just encountered one possible error which is obvious to
me but might not be to other users. If you use the node label
as the place to store bootstrap or other support values as done
by some programs (like MrBayes, clustalw, TREE-PUZZLE...),
you can use this as branch label in FigTree.
However, if you now reroot the tree the label is then moved
to the branch now root-wards of the respective node, which is
not the branch anymore corresponding to the support value.

Hence, my question could you maybe add a branch-label-class
(like "label, support") that can deal with this problem?
Off course there might be lables where this behaviour might
be the wanted one.

I am not sure if you are still actively developing FigTree.  I have been using 
this nice program and just noticed a bit of a possible issue.  So I thought to 
write you about it.  Attached is a ultrametric tree, so it is a rooted tree.  
Although this tree itself doesn't require re-rooting, I'm using it as a sample 
tree to write a little code to calculate a tree height.  Since calculating a 
tree height is the same as finding the midpoint rooting, I thought to check it 
with FigTree.  If you do this, you get a strange result.  It looks like one of 
the branch is missing, specifically the branch with the length of 0.3442.  I'm 
guessing that since the original tree is rooted, that are two branch lengths at 
the root, which may be confusing FigTree.  I didn't think FigTree has a problem 
with rooted trees.  But do you know if this could be the case?

What steps will reproduce the problem?
1. Click "Preferences"

What is the expected output? What do you see instead?

What I see is this:
Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException:
java.lang.Float cannot be cast to java.lang.Double
    at java.lang.Double.compareTo(Double.java:32)
    at javax.swing.SpinnerNumberModel.incrValue(SpinnerNumberModel.java:332)
    at
javax.swing.SpinnerNumberModel.getPreviousValue(SpinnerNumberModel.java:371)
    at
javax.swing.plaf.basic.BasicSpinnerUI.updateEnabledState(BasicSpinnerUI.java:489
)
    at
javax.swing.plaf.basic.BasicSpinnerUI.updateEnabledState(BasicSpinnerUI.java:470
)
    at javax.swing.plaf.basic.BasicSpinnerUI.access$200(BasicSpinnerUI.java:33)
    at
javax.swing.plaf.basic.BasicSpinnerUI$Handler.stateChanged(BasicSpinnerUI.java:1
047)
    at javax.swing.JSpinner.fireStateChanged(JSpinner.java:434)
    at javax.swing.JSpinner$ModelListener.stateChanged(JSpinner.java:361)
    at
javax.swing.AbstractSpinnerModel.fireStateChanged(AbstractSpinnerModel.java:102)
    at javax.swing.SpinnerNumberModel.setValue(SpinnerNumberModel.java:430)
    at javax.swing.JSpinner.setValue(JSpinner.java:329)
    at
figtree.application.preferences.AppearancePreferencesSection.retrievePreferences
(Unknown
Source)
    at jam.preferences.PreferencesDialog.showDialog(Unknown Source)
    at jam.framework.Application.doPreferences(Unknown Source)
    at jam.framework.Application$7.actionPerformed(Unknown Source)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
    at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
    at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at javax.swing.AbstractButton.doClick(AbstractButton.java:357)
    at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1225)
    at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.jav
a:1266)
    at java.awt.Component.processMouseEvent(Component.java:6263)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
    at java.awt.Component.processEvent(Component.java:6028)
    at java.awt.Container.processEvent(Container.java:2041)
    at java.awt.Component.dispatchEventImpl(Component.java:4630)
    at java.awt.Container.dispatchEventImpl(Container.java:2099)
    at java.awt.Component.dispatchEvent(Component.java:4460)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
    at java.awt.Container.dispatchEventImpl(Container.java:2085)
    at java.awt.Window.dispatchEventImpl(Window.java:2475)
    at java.awt.Component.dispatchEvent(Component.java:4460)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
    at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269
)
    at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174
)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)


What version of the product are you using? On what operating system?
- Sun java compiler, 64-bit Linux

Please provide any additional information below.

When ticking off 'Automatic grid' and trying to enter a value in 'Tick spacing'

Both for development and 1.2.3

What steps will reproduce the problem?
1. Run "java -jar figtree.jar" on Ubuntu Hardy
2. Choose a tree file (I used a Newick file)
3. It crashes.

Also, if you give the tree file on the command line, then it crashes
immediately, instead of giving a dialog box.

Q1. What is the output?

Exception in thread "main" java.lang.NullPointerException
    at sun.font.FontDesignMetrics$MetricsKey.init(FontDesignMetrics.java:199)
    at sun.font.FontDesignMetrics.getMetrics(FontDesignMetrics.java:267)
    at sun.swing.SwingUtilities2.getFontMetrics(SwingUtilities2.java:915)
    at javax.swing.JComponent.getFontMetrics(JComponent.java:1597)
    at
javax.swing.plaf.synth.SynthGraphicsUtils.getMaximumCharHeight(SynthGraphicsUtil
s.java:228)
    at javax.swing.plaf.synth.SynthSliderUI.layout(SynthSliderUI.java:269)
    at
javax.swing.plaf.synth.SynthSliderUI.calculateGeometry(SynthSliderUI.java:246)
    at
javax.swing.plaf.basic.BasicSliderUI$Handler.propertyChange(BasicSliderUI.java:1
448)
    at
java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:3
39)
    at
java.beans.PropertyChangeSupport.firePropertyChange(PropertyChangeSupport.java:2
76)
    at java.awt.Component.firePropertyChange(Component.java:7865)
    at java.awt.Component.setFont(Component.java:1648)
    at java.awt.Container.setFont(Container.java:1571)
    at javax.swing.JComponent.setFont(JComponent.java:2721)
    at javax.swing.JSlider.setFont(JSlider.java:746)
    at figtree.treeviewer.ControllerPanel.adjustComponent(Unknown Source)
    at org.virion.jam.panels.OptionsPanel.addComponents(OptionsPanel.java:114)
    at
org.virion.jam.panels.OptionsPanel.addComponentWithLabel(OptionsPanel.java:102)
    at
figtree.treeviewer.treelayouts.RectilinearTreeLayoutController.<init>(Unknown
Source)
    at figtree.treeviewer.TreeViewerController.<init>(Unknown Source)
    at figtree.application.FigTreePanel.<init>(Unknown Source)
    at figtree.application.FigTreeFrame.<init>(Unknown Source)
    at figtree.application.FigTreeApplication$1.createDocumentFrame(Unknown
Source)
    at
org.virion.jam.framework.MultiDocApplication.createDocumentFrame(MultiDocApplica
tion.java:66)
    at
org.virion.jam.framework.MultiDocApplication.doOpenFile(MultiDocApplication.java
:84)
    at org.virion.jam.framework.Application.doOpen(Application.java:207)
    at figtree.application.FigTreeApplication.main(Unknown Source)


Q2. What version of the product are you using? On what operating system?

Figtree 1.1 on an AMD64 box running Linux 2.6.24-rc3

Q3. Please provide any additional information below.
$ java -version
java version "1.6.0_03"
Java(TM) SE Runtime Environment (build 1.6.0_03-b05)
Java HotSpot(TM) 64-Bit Server VM (build 1.6.0_03-b05, mixed mode)

Add option to colour node bars by an attribute.

Polar tree could be partly out of the page bounds when align taxa is selected. 

I'm playing around with FigTree version 1.1.2 here (I intend to use it for an 
exercise this 
afternoon...), and noticed what I think is a bug:

If I reroot a tree using the button in FigTree and then save the file, the 
resulting treefile contains 
the original newicktree, not the rerooted form.

For instance, the following tree:

 ((D,E),(C,(A,B)));

is saved as:

 begin trees;   
    tree [&r] tree_1 = ((D:1.0,E:1.0):1.0,(C:1.0,(A:1.0,B:1.0):1.0):1.0);
 end;

regardless of whether I reroot it on (A,B) or not.

Best regards!
Anders

[deleted issue]

If you type text into the filter box it filters by the name label, not what is 
currently displayed.

Add function to collapse branches to polytomies and resolve them

Here is a version that does work.  It stops trying to copy JEBL from a
location where it does not exist to a location where it already is.

User specified taxa colors are not saved in the nexus "figtree" section.

For font sizes, lines widths or what not

# What steps will reproduce the problem?
1. Try to instantiate an object of type
jebl.evolution.trees.GreedyRootedConsensusTreeBuilder when using figtree.

# What is the expected output? What do you see instead?
It is not possible to instantiate an object of this type, because this type
is not declared as public in the jebl-version that is included in figtree.

# What version of the product are you using? On what operating system?
Linux-version of figtree on Fedora, OpenJDK 1.6.

# Please provide any additional information below.
The problem is that I need figtree as well as the current version of JEBL
(in particular, the class mentioned above) in the same project and this is
not possible because of classpath-ambiguities...

Selecting branches whilst in the 'Taxa' selection mode should result in taxon 
labels being selected. 
At present it doesn't. It would seem the branches are being selected as they 
become highlighted 
when the selection mode is switched to Node or Clade.

At present (with multi-tree files), selecting a root in one tree does not root 
the other trees. The rooting is only done when the tree is displayed. Need to 
specify a taxon or set of taxon that defines the root position so it can be 
used to root any tree displayed.

If you select nodes/taxa using the Find function and the press the colour 
button, the colouring is 
not applied

I downloaded the latest version of FigTree (1.3) and am having trouble
with the 'Reroot' option.  Sometimes after you open a treefile, and
then reroot the tree it works just fine the first time, but then if
you select a different taxon in the same tree and try reroot, nothing
happens.  Any idea why this might be occurring?

What steps will reproduce the problem?
1. Load a tree
2. Export Graphic (EPS or PDF)

What is the expected output? What do you see instead?
 I would expect to see a tree with the tip labels next to the tips they
correspond to.  Instead, the tip labels correspond (roughly) to the leaf
immediately above.

What version of the product are you using? On what operating system?
 1.2.2 on Ubuntu Linux with the "java-6-openjdk" package.

Please provide any additional information below.
 I also tried compiling from trunk/ but this did not fix it.

I seem to be having trouble with the find and filter functions. I am assuming 
that the results of 
using find should be that the relevant taxa etc. should be selected? However, I 
have so far not been 
able to get anything selected, even when searching for taxon labels I know (and 
can see) are in my 
tree. Did I misunderstand something, or is there perhaps a bug? I have similar 
problems with the 
filter field. If I for instance enter "a" then some, but not all, taxa 
containing an "a" get selected. If I 
enter "avi" then none of my taxa get selected (despite there being about 50 
such taxa in my tree). 

One final observation: By testing on some other trees, it now appears that it 
has to do with 
uppercase vs lowercase: I can search on uppercase parts of labels, I can not 
search on lowercase 
parts of those names (and position in label has nothing to do with it...)

In windows and java version, when I press the find button, the new drop-down 
search bar starts 
changing size continously, until it reaches a proper size after a minute or 
so... This only happens 
when I have a tree loaded, and I have only tried with a relatively big tree 
(1600 taxa).

I also have problems with the persistence of "contains" vs. "starting with" in 
the filter method field: 
If I start by selecting "starting with" and then enter text in the field, the 
method reverts to "contains" 
(as judged by seeing what gets selected, and by checking where the method 
selection is by clicking 
on the disclosure triangle in the filter field). 

Semi-colon missing at end of Newick export tree

$figtree -help

                 FigTree v1.2.4, 2006-2009
                  Tree Figure Drawing Tool
                       Andrew Rambaut

             Institute of Evolutionary Biology
                  University of Edinburgh
                     [email protected]

                 http://tree.bio.ed.ac.uk/
     Uses the Java Evolutionary Biology Library (JEBL)
                http://jebl.sourceforge.net/
 Thanks to Alexei Drummond, Joseph Heled, Philippe Lemey,
       Tulio de Oliveira, Beth Shapiro & Marc Suchard

  Usage: figtree [-graphic <PDF|SVG|SWF|PS|EMF|GIF>] [-width <i>] [-height
<i>] [-help] [<tree-file-name>] [<graphic-file-name>]
    -graphic produce a graphic with the given format
    -width the width of the graphic in pixels
    -height the height of the graphic in pixels
    -help option to print this message

  Example: figtree test.tree
  Example: figtree -graphic PDF test.tree test.pdf
  Example: figtree -graphic GIF -width 320 -height 320 test.tree test.gif

$ figtree -graphic PNG -width 320 -height 320  Rho_full_14taxa-s1.trees.nex
Rho_full_14taxa-s1.trees.nex.png

Argument, -graphic has a bad string value: PNG


                 FigTree v1.2.4, 2006-2009
                  Tree Figure Drawing Tool
                       Andrew Rambaut

             Institute of Evolutionary Biology
                  University of Edinburgh
                     [email protected]

                 http://tree.bio.ed.ac.uk/
     Uses the Java Evolutionary Biology Library (JEBL)
                http://jebl.sourceforge.net/
 Thanks to Alexei Drummond, Joseph Heled, Philippe Lemey,
       Tulio de Oliveira, Beth Shapiro & Marc Suchard

  Usage: figtree [-graphic <PDF|SVG|SWF|PS|EMF|GIF>] [-width <i>] [-height
<i>] [-help] [<tree-file-name>] [<graphic-file-name>]
    -graphic produce a graphic with the given format
    -width the width of the graphic in pixels
    -height the height of the graphic in pixels
    -help option to print this message

  Example: figtree test.tree
  Example: figtree -graphic PDF test.tree test.pdf
  Example: figtree -graphic GIF -width 320 -height 320 test.tree test.gif

[deleted issue]

Unfortunately, figtree was unable to display my tree because I have a couple of 
redundant taxon 
names.  Error message says:

Error reading tree file: 
jebl.evolution.io.ImportException$DuplicateTaxaException

Basically, highlighting does not respect the collapse function. The highlight 
box remains absolutely 
in place rather than tracking with the clade to which it belongs. So, if you 
collapse a clade, the 
highlight box could be misplaced. (It's also difficult to remove the 
highlighting in that case as well.)

After download and copying to the application folder, upon launch the icon 
bounces a few times 
and then goes away.

Quicktime is back at version 7.2. 
Java reports:
java version "1.4.2_07"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.4.2_07-215)

(I had v. 1.0 previously installed, but didn't find any prefs files.)

Thanks,
Steve

Extract subtree to clipboard that subtends the selected taxa and or nodes.

What steps will reproduce the problem?
1.
2.
3.

What is the expected output? What do you see instead?


Please use labels and text to provide additional information.

Is it possible to get a real copy and paste function in FigTree where one can 
copy the image (not 
just the nexus tree description) to another program? Sort of like MacClade 
allows you to do. As 
good as FigTree is, it can't do everything and sometimes I need to use 
something like Illustrator to 
help out a bit (e.g., positioning node labels so they're all readable). 
Copy-paste is the easiest and 
most effective way here.

If you select a attribute of the node (e.g., height) it isn't displayed.

Also, for whatever reason posterior probabilities have been expressed as 
percentages over the years 
(for comparison to bootstrap values I guess). Is it possible to add a 
percentages option for branch 
labels? Again no big problem as they are, afterall, probabilities and one could 
argue they should be 
expressed as such. 

What steps will reproduce the problem?
1. activate "node labels" 
2. change "display" to "label" under "node labels" 
3.reroot -> crash 

Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: 
jebl.evolution.trees.RootedFromUnrooted$1 cannot be cast to 
jebl.evolution.trees.SimpleRootedTree$SimpleRootedNode
    at jebl.evolution.trees.SimpleRootedTree.getTaxon(SimpleRootedTree.java:335)
    at jebl.evolution.trees.RootedFromUnrooted.getTaxon(RootedFromUnrooted.java:187)
    at figtree.treeviewer.painters.BasicLabelPainter.getLabel(Unknown Source)
    at figtree.treeviewer.painters.BasicLabelPainter.calibrate(Unknown Source)
    at figtree.treeviewer.painters.BasicLabelPainter.calibrate(Unknown Source)
    at figtree.treeviewer.TreePane.calibrate(Unknown Source)
    at figtree.treeviewer.TreePane.paint(Unknown Source)
    at javax.swing.JComponent.paintChildren(JComponent.java:864)
    at javax.swing.JComponent.paint(JComponent.java:1036)
    at javax.swing.JViewport.paint(JViewport.java:747)
    at javax.swing.JComponent.paintToOffscreen(JComponent.java:5122)
    at 
javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:
1382)
    at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1313)
    at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:301)
    at javax.swing.RepaintManager.paint(RepaintManager.java:1128)
    at javax.swing.JComponent._paintImmediately(JComponent.java:5070)
    at javax.swing.JComponent.paintImmediately(JComponent.java:4880)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:723)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:679)
    at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:659)
    at 
javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueU
tilities.j
ava:128)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)

When I untick the "Automatic" tickbox all disappear except the bar 

If a clade at the top of the tree is collapsed then it can be partially clipped.

TreeBase and Mesquite use a 'TITLE' and 'LINK' command in Trees block but 
FigTree doesn't recognise these. Should skip them at a minimum.

1. When we try to re root the tree, it re roots for only the first tree,
and displays the same rerooted figure for the rest of the trees.
2. After we select 're root' on a branch, and try to re root on another
branch from tree->root on branch, it doesn't seem to do anything.

The colour-by (and line-weight) options should autorange if required. For 
posterior support, a 
fixed range 0,1 is appropriate. For other properties the colour range should 
match the observed 
range (e.g., rates etc).

I find some strange behaviour with FigTree 1.3.1 running on Linux with Sun's 
java 1.6.0_15.

First of all, "save" doesn't seem to save changes like cartooned clades and 
changed colours. I'm using "save as" instead.

Opening a saved, rerooted tree with several clades as cartoons seems to open it 
rooted in a different way which wreaks havoc with 
cartoons. Furthermore, it can't be rerooted back to work again. There's an 
exception thrown when trying to reroot, see below. I also 
attach two tree files, one before rerooting and introducing cartoons, one after.

Exception:

Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: 
jebl.evolution.trees.SimpleRootedTree cannot be cast to 
figtree.treeviewer.ReRootedTree
       at figtree.treeviewer.TreePane.setRootLocation(Unknown Source)
       at figtree.treeviewer.TreePane.rerootOnSelectedBranch(Unknown Source)
       at figtree.treeviewer.DefaultTreeViewer.rerootOnSelectedBranch(Unknown Source)
       at figtree.application.FigTreeFrame.rerootTree(Unknown Source)
       at figtree.application.FigTreeFrame.access$2100(Unknown Source)
       at figtree.application.FigTreeFrame$29.actionPerformed(Unknown Source)
       at figtree.application.FigTreeFrame$4.actionPerformed(Unknown Source)
       at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
       at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
       at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
       at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
       at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
       at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
       at java.awt.Component.processMouseEvent(Component.java:6263)
       at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
       at java.awt.Component.processEvent(Component.java:6028)
       at java.awt.Container.processEvent(Container.java:2041)
       at java.awt.Component.dispatchEventImpl(Component.java:4630)
       at java.awt.Container.dispatchEventImpl(Container.java:2099)
       at java.awt.Component.dispatchEvent(Component.java:4460)
       at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)
       at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
       at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
       at java.awt.Container.dispatchEventImpl(Container.java:2085)
       at java.awt.Window.dispatchEventImpl(Window.java:2475)
       at java.awt.Component.dispatchEvent(Component.java:4460)
       at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
       at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
       at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
       at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
       at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
       at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
       at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

it would be great if the tip labels in the polar and radial layouts could be 
all oriented in the 
horizontal plane, and not just follow the orientation of their branch. 

For colouring with a range within [0,1], autoscaling of the colour range was 
failing (defaulting to 
[0,1]).

Implement user interface to set the spacing between the taxon labels and the 
terminal nodes.

Open a tree file

change Time Scale| Scale fator to a value other than 1

Midpoint root. Then:
- I saved it: it works when re-opened under Figtree ;
- I exported it, either under nexus or newick, ticking the "as currently 
displayed" box, but the file 
written is the same than the original one, but without the semi-column:

A bug perhaps, but when I select and then color the branches of a clade, the 
branch-labels options 
returns to the default (branch times) from my choice of label. Not big deal as 
I can change it back 
once I've colored the branches but a bit puzzling why that should happen.