[Biojava-dev] [Bug 2603] New: StringIndexOutOfBoundsException while parsing blastresult

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2603

           Summary: StringIndexOutOfBoundsException while parsing
                    blastresult
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: dtoomey at rcsi.ie


While parsing a blast result I get a StringIndexOutOfBoundsException. I have
narrowed down the cuase of the error to this section

Query= sp|P62368|ISPF_PLAF7 2-C-methyl-D-erythritol
2,4-cyclodiphosphate synthase OS=Plasmodium falciparum (isolate 3D7)
GN=ISPF

What I have found is that if the 3rd line is less than 11 characters long the
error is thrown. If I add text or even extra spaces to this line then the error
does not occur. Also I have noticed that it does not happen to the first entry
in a file containing multiple blast searches.

I have tried this on both Windows and Linux and get the same error. I have been
using blast version 2.2.18 but have also tried 2.2.17


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