[Biojava-l] A bug in Class "org.biojavax.bio.seq.io.GenbankFormat"

Huijie Qiao huijieqiao at gmail.com
Fri Apr 2 03:02:37 UTC 2010

version 1.7.1

line 361
else if (sectionKey.equals(SOURCE_TAG)) {
      // ignore - can get all this from the first feature

actually the content in the SOURCE_TAG and the first feature are different
in some gb file.

For example, the example file in

The Source TAG is
SOURCE      Bos taurus (cattle)
  ORGANISM  Bos taurus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
            Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia;
            Pecora; Bovidae; Bovinae; Bos.

and the first feature tag is
FEATURES             Location/Qualifiers
     source          1..1136
                     /organism="Bos taurus"

I can't get the hierarchy info through the follow codes.
NCBITaxon taxon = seq.getTaxon();
System.out.println(taxon.getNameHierarchy()); output is "."

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