[Biojava-dev] [Bug 3083] New: PHYLIP parser goes into infinite loop on files with empty lines

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3083

           Summary: PHYLIP parser goes into infinite loop on files with
                    empty lines
           Product: BioJava
           Version: unspecified
          Platform: All
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Others
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: rb-openbio at rbyers.net


The PHYLIP file format allows blank lines (and in fact many examples use blank
lines to separate blocks).  The PHYLIPFileFormat class appears to have had this
in mind, but the implementation is broken - blank lines cause an infinite loop
in the parser.

I will attacha repro input file as well as a simple patch to fix the problem.


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