FigTree v1.3

[Kurt Wollenberg]

Hello:

FigTree v1.3.0 doesn't appear to run on Mac OS 10.5.8. Attempting to
run in the Terminal gives:

[LaunchRunner Error]
figtree.application.FigTreeApplication.main(String[]) threw an
exception:
java.lang.UnsupportedClassVersionError: Bad version number in .class
file

Was it perchance compiled under Java 1.6?

Cheers,
Kurt Wollenberg

[Patrice Showers Corneli]

For what it's worth, v1.3 works great on my Mac with 10.6.2. Is it written perhaps for Snow Leopard?

Patrice Showers Corneli

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[Kurt Wollenberg]

Hi:

I've downloaded the latest build of FigTree 1.3.0 and I'm still having
problems with it. Now it will give me a FigTree window after double-
clicking on the icon. However, if I try to open a tree file I never
see a tree figure and the window does not update its appearance if I
change anything (such as opening a menu in the sidebar). I hear my
hard drive spinning like mad and when I check the Activity Monitor I
see that syslogd is using ~170% of the CPU (i.e., it's using multiple
cores). After I quit FigTree then syslogd eventually goes back down to
low-level (~0) CPU usage. I am running system 10.5.8 on a quad core
G5.

On Dec 16, 3:52 pm, Patrice Showers Corneli <pcorn...@earthlink.net>
wrote:

Cheers,
Kurt Wollenberg

[Chris]

I have it running under OSX 10.5.8 with Java version 1.5.0_20

Cheers, Chris

[pete cowman]

HI.
Just trying out the new version of figtree.
first of all, after i downloaded the package for mac, i went to
install the quicklook feature, but the file
"FigTreeQuickLookPlugin.qlgenerator" that is to be dragged to the
Library/quicklook folder shows zero kb. would this be a problem with
the download itself?
Also i loaded up a tree i just got from an analysis in garli and while
the tree comes up, if i try to collapse or cartoon from any node the
tree graphic disappears. this also happens with the carnivore.tree
example file that comes with the package.
Whenever i go to change the size of the font for the taxa names, the
dialog box that opens up is very long and goes off the screen, to such
an extent that i have to pull it over to change the font size.
I am running Figtree on an dual quad core mac pro with 10.6.2.
(also when ever i open up a file in figtree, a second blank window of
the program opens up behind the tree i have opened)

Peter

[Andrew Rambaut]

On 17 Dec 2009, at 00:05, pete cowman wrote:

> Just trying out the new version of figtree.
> first of all, after i downloaded the package for mac, i went to
> install the quicklook feature, but the file
> "FigTreeQuickLookPlugin.qlgenerator" that is to be dragged to the
> Library/quicklook folder shows zero kb. would this be a problem with
> the download itself?

There was an issue with the download (or rather the upload that I made to my server). Please try downloading the mac package again.

> Also i loaded up a tree i just got from an analysis in garli and while
> the tree comes up, if i try to collapse or cartoon from any node the
> tree graphic disappears. this also happens with the carnivore.tree
> example file that comes with the package.

This is not a universal problem - I have tried it on 3 different macs. Are you using any special features (circular trees etc)?

> Whenever i go to change the size of the font for the taxa names, the
> dialog box that opens up is very long and goes off the screen, to such
> an extent that i have to pull it over to change the font size.
> I am running Figtree on an dual quad core mac pro with 10.6.2.
> (also when ever i open up a file in figtree, a second blank window of
> the program opens up behind the tree i have opened)

It sounds like one of your fonts might have a very long name. Is the font name menu very wide?

Andrew

___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624

--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[pete cowman]

Ok will download it again and give it a try.
as for the problem with the collapse and cartoon, im not making any
other changes, i just opened the carnivore.tree and selected a node
and press either of the cartoon and collapse button and the graphic
disappears, when i click it again, it reappears.
Yes there is a very old font, so that seems to be the problem with the
window. is there a way i can exclude the font?
Thanks

Peter

>   EMAIL - a.ramb...@ed.ac.uk                TEL - +44 131 6508624      

[pete cowman]

Thanks for the Help Andrew.
The quick look works now.
How ever im still having the issue with the collapse/cartoon
function..
i opened the app from the terminal and then tried to collapse one of
the nodes of the carnivore.tree. i gont the following output from the
terminal, maybey it can shed some light on the problem:

petermacpro:lib petercowman$ java -jar figtree.jarpetermacpro:lib
petercowman$ java -jar figtree.jar carnivore.tree
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at
figtree.treeviewer.treelayouts.RectilinearTreeLayout.constructNodeAreas
(Unknown Source)
at
figtree.treeviewer.treelayouts.RectilinearTreeLayout.constructNodeAreas
(Unknown Source)
at
figtree.treeviewer.treelayouts.RectilinearTreeLayout.constructNodeAreas
(Unknown Source)
at figtree.treeviewer.treelayouts.RectilinearTreeLayout.layout
(Unknown Source)
at figtree.treeviewer.TreePane.calibrate(Unknown Source)
at figtree.treeviewer.TreePane.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(JComponent.java:852)
at javax.swing.JComponent.paint(JComponent.java:1026)
at javax.swing.JViewport.paint(JViewport.java:747)
at javax.swing.JComponent._paintImmediately(JComponent.java:5086)
at javax.swing.JComponent.paintImmediately(JComponent.java:4870)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:
829)
at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:
714)
at javax.swing.RepaintManager.seqPaintDirtyRegions
(RepaintManager.java:694)
at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run
(SystemEventQueueUtilities.java:125)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:633)
at java.awt.EventDispatchThread.pumpOneEventForFilters
(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter
(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy
(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:
188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
(this repeats many times)...........
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
(repeated)........

[Andrew Rambaut]

As FigTree is used by many people who are not on the BEAST mailing list, I have created a FigTree specific discussion group:

http://groups.google.com/group/figtree-discuss

I suggest all FigTree specific posting goes there. Obviously anything related to BEAST _and_ FigTree can go to this group.

Andrew

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___________________________________________________________________

Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT

EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624

[Paolo Zanotto]

Dear Andy,

Thanks for the the updated FigTree v1.3. Great work.

I was wondering if it would not be useful to other users to be able
to have the following features added on to future release versions:

1) to be able to select a "clade" and then copy it out of the entire
tree in nexus/Newick format.

2) to be able to select specific terminal taxa (either by a "select
by" button or "Comand-click") and then extract the tree including
only this set of taxa as above.

3) to be able to export patristic distance matrices for the complete
trees or for sub-trees selected as in 1) and 2).

4) I guess that some people would also like to see most of TreeEdit
features added to future versions of FigTree.

Best wishes,
Paolo

C.c./ Beast-O-Philes