Opening PhyloBayes trees from command line

[Joran Martijn]

For some reason that I have not been able to figure out is that I am not able to open trees generated by PhyloBayes from command line interface.

What I would like to do is, on the command line, do

figtree <phylobayes.newick> &

And then the tree would be opened in FigTree. This is what happens right now if I do that: it asks for the node/branch label names, then it displays the following message in the terminal

Exception

and it crashes.

I currently work around it by first opening FigTree manually, and then do File->Open, but it is just extremely annoying if you have several tens of trees to inspect.
Strangely enough opening trees via command line only crashes with PhyloBayes trees. I have currently no issues with RAxML or FastTree generated trees.

[Andrew Rambaut]

Hi Joran,

Send me an example file and I will look in to it. I suspect it may be the fact that it asks for the label names. Presumably it would be useful to be able to specify these on the command line

too.

A.

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[Joran Martijn]

Sorry, in my openingspost I did not specify the full error message that occurs when trying to open a PhyloBayes tree from command line.
See below:

Exception in thread "main" java.lang.ClassCastException: java.lang.Integer cannot be cast to java.lang.Double
        at java.lang.Double.compareTo(Double.java:49)
        at java.util.TreeMap.put(TreeMap.java:560)
        at java.util.TreeSet.add(TreeSet.java:255)
        at figtree.treeviewer.decorators.ContinuousScale.setAttributes(Unknown Source)
        at figtree.treeviewer.AttributeColourController.getDecoratorForAttribute(Unknown Source)
        at figtree.treeviewer.AttributeColourController.getColourDecorator(Unknown Source)
        at figtree.treeviewer.painters.LegendPainterController$1.attributeComboChanged(Unknown Source)
        at figtree.treeviewer.painters.AttributeComboHelper.fireAttributeSelectionChanged(Unknown Source)
        at figtree.treeviewer.painters.AttributeComboHelper.access$200(Unknown Source)
        at figtree.treeviewer.painters.AttributeComboHelper$2.actionPerformed(Unknown Source)
        at javax.swing.JComboBox.fireActionEvent(JComboBox.java:1260)
        at javax.swing.JComboBox.setSelectedItem(JComboBox.java:588)
        at figtree.treeviewer.painters.AttributeComboHelper$1.treeChanged(Unknown Source)
        at figtree.treeviewer.DefaultTreeViewer.fireTreeChanged(Unknown Source)
        at figtree.treeviewer.DefaultTreeViewer.showTree(Unknown Source)
        at figtree.treeviewer.ExtendedTreeViewer.showTree(Unknown Source)
        at figtree.treeviewer.DefaultTreeViewer.setTrees(Unknown Source)
        at figtree.application.FigTreeFrame.readData(Unknown Source)
        at figtree.application.FigTreeFrame.readFromFile(Unknown Source)
        at jam.framework.DocumentFrame.openFile(Unknown Source)
        at jam.framework.MultiDocApplication.doOpenFile(Unknown Source)
        at figtree.application.FigTreeApplication.doOpenFile(Unknown Source)
        at jam.framework.Application.doOpen(Unknown Source)
        at figtree.application.FigTreeApplication.main(Unknown Source)

[Joran Martijn]

Hej Andrew,

Thanks for your quick reply! Please see attached an example tree.

Some other specifications that might be useful:
I'm using FigTree 1.4.2 on an OpenSUSE 12.2
I'm using an alias to run figtree:
alias figtree='java -jar /usr/local/bin/figtree-1.4.2/figtree.jar'

[Ugo Cenci]

Hi,

What did you do to fix it finally?

Thanks,