jprime cannot parse Newick comments

I tried to run jprime DLRS with a host tree containing comments. 

The program bugged out with the stack trace and error as given below.

The test files are attached. The command was:
   jprime Delirious yeasts_dated1.tree 1.alf 1.gs

# DELIRIOUS
# Arguments: [../yeasts_dated1.tree, 1.alf, 1.gs]
# Current time: 2013-11-20 11:16:10
# Run failed. Reason:
java.lang.IllegalArgumentException: Invalid host tree.
    at se.cbb.jprime.apps.dlrs.ParameterParser.getHostTree(ParameterParser.java:109)
    at se.cbb.jprime.apps.dlrs.Delirious.main(Delirious.java:117)
    at se.cbb.jprime.apps.JPrIMEStarter.main(JPrIMEStarter.java:88)
Caused by: se.cbb.jprime.io.NewickIOException: Error parsing Newick tree. First 
100 remaining unparsed characters:
([The "post-WGD" clade starts 
here](((Vpol:0.2,Tpha:0.2):0.2,Tbla:0.4):0.2,(((Ndai:0.2,Ncas:0.2):0.2
    at se.cbb.jprime.io.NewickTreeReader.readTree(NewickTreeReader.java:104)
    at se.cbb.jprime.io.PrIMENewickTreeReader.readTree(PrIMENewickTreeReader.java:77)
    at se.cbb.jprime.io.PrIMENewickTreeReader.readTree(PrIMENewickTreeReader.java:104)
    at se.cbb.jprime.apps.dlrs.ParameterParser.getHostTree(ParameterParser.java:84)
    ... 2 more
Caused by: se.cbb.jprime.io.NewickIOException: Expected semi-colon when reading 
Newick tree.
    at se.cbb.jprime.io.NewickTreeReader.readTree(NewickTreeReader.java:160)
    at se.cbb.jprime.io.NewickTreeReader.readTree(NewickTreeReader.java:102)
    ... 5 more

Original issue reported on code.google.com by lars.arv...@gmail.com on 20 Nov 2013 at 10:21

Attachments:

arvestad / jprime

jprime cannot parse Newick comments #5