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rambaut
Problem rendering trees with node labels (with non-alphanumerics?)
What steps will reproduce the problem?
1. Load the attached tree file.
2.
3.
What is the expected output? What do you see instead?
The tree should appear in the FigTree viewer. Instead, the program asks what
the user node labels should be called (as it should) and then nothing further
happens.
What version of the product are you using? On what operating system?
Version 1.4.0 on Mac OS 10.8.2.
Please provide any additional information below.
Removing all the < signs and the label n/a in the tree description will cause
the file to load properly; removing only one class or the other will not. At
first, I though it was a general problem with having non-alphanumerics in the
node labels; however, other similar (but smaller) test trees made by hand work
fine. Only larger trees like this seem to fail.
Original issue reported on code.google.com by [email protected] on 12 Feb 2013 at 7:57
Attachments:
At the moment FigTree assumes node labels in Newick/Nexus trees are numerical.
Original comment by [email protected] on 7 Jun 2013 at 3:57
- Changed state: Accepted
- Added labels: v1.4, Milestone-Release1.4.1
This occurs because there is a "<1" value for one or more of the nodes. The
temporary fix is to disallow these or remove them.
Original comment by [email protected] on 14 Jun 2014 at 11:50
Original comment by [email protected] on 14 Jun 2014 at 2:59
- Added labels: Milestone-Release1.4.2
- Removed labels: Milestone-Release1.4.1
Original comment by [email protected] on 4 Jul 2014 at 8:07
- Added labels: Priority-Low, Milestone-Release1.4.3
- Removed labels: Priority-Medium, Milestone-Release1.4.2
The issue is the bootstrap values are not strictly numerical (includes 'n/a' and '<1' etc. May need to allow alphanumerical labels.
It is throwing an exception -
Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: java.lang.Double cannot be cast to java.lang.String
at java.lang.String.compareTo(String.java:111)
at java.util.TreeMap.put(TreeMap.java:568)
at java.util.TreeSet.add(TreeSet.java:255)
at figtree.treeviewer.decorators.DiscreteColourDecorator.setAttributes(DiscreteColourDecorator.java:107)
at figtree.treeviewer.decorators.ColourDecorator.
