[Biojava-dev] [Bug 2941] New: NEXUS parser fails with tree nodes called p[0-9]+

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2941

           Summary: NEXUS parser fails with tree nodes called p[0-9]+
           Product: BioJava
           Version: unspecified
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Others
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: tiagoantao at gmail.com


The Nexus parser fails to return a weighted graph if a tree node is called
p[0-9+].

This happens because the internal representation creates nodes with this name
pattern.

Example Tree :
tree tree2 = ((1:0.1,2:0.2):0.15,p1:0.3);

Note the p1 node at the end.

Typical error:

Exception in thread "main" java.lang.IllegalArgumentException: loops not
allowed
        at org.jgrapht.graph.AbstractBaseGraph.addEdge(Unknown Source)
        at
org.biojavax.bio.phylo.io.nexus.TreesBlock.getTreeAsWeightedJGraphT(TreesBlock.java:547)

This happens on 1.7 (there is no version 1.7 on bugzilla, by the way)


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