[Biojava-l] SwissProt FeatureTable

[mark.schreiber at group.novartis.com]

Hello Joerg,

Biojava usually places feature information in the FeatureHolder of the 
Sequence that is generated when parsing the file. As you state the 
annotation entries end up in the Annotation object. You can get an 
Iterator over the FeatureHolder using sequence.features(). Each feature 
will contain some basic information such as the type and location plus it 
will also contain an Annotation bundle itself with any annotations 
specific to that feature.

To view where everything will end up after parsing take a look at:

http://www.biojava.org/docs/bj_in_anger/filter.htm

- Mark






Joerg Krebs <krebsj at cip.ifi.lmu.de>
Sent by: biojava-l-bounces at portal.open-bio.org
03/11/2005 09:03 AM

 
        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] SwissProt FeatureTable


Hi,
does anyone know how to parse the FeatureTable Entries of a SwissProt
File via the biojava package.
With getAnnotation I can only get the annotation entries without the
FeatureTable-Entries :(

In the Source-Code of biojava 1.4pre1 exists a
SwissprotFeatureTableParser.java in src/org/biojava/bio/seq/io/
but it seems to be not yet ready to use.

Maybe someone can help me with my Problem.

Thanks
        Joerg

-- 
Joerg Krebs <krebsj at cip.ifi.lmu.de>

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