[Biojava-dev] [Bug 2187] New: Stack trace printed: org.biojava.bio.program.scf.SCF$V3Parser.parseBases

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2187

           Summary: Stack trace printed:
                    org.biojava.bio.program.scf.SCF$V3Parser.parseBases
           Product: BioJava
           Version: 1.4
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: keiranmraine at gmail.com


Hi,

Just a nicety for anyone using the class in programs for use by
non-programmers.

When catching the IllegalSymbolException the stack trace is printed in
org.biojava.bio.program.scf.SCF$V3Parser.parseBases.

I suggest that the UnsupportedChromatogramFormatException be extended to take
the Throwable and the 'ise.printStackTrace(System.err);' removed.

e.g.

catch (IllegalSymbolException ise) {
  ise.printStackTrace(System.err);
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure");
}

BECOMES

catch (IllegalSymbolException ise) {
  throw new UnsupportedChromatogramFormatException("Base call decoding
failure", ise);
}


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