[Biojava-l] how to get properties of a Feature from a GenBank file

[Richard Holland]

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Hello,

Your code for getting the Note named "gene" is correct. I agree, a
shorthand way of doing this would be lovely, but doesn't currently
exist. (Such a method would have to do the same thing internally
anyway). If you'd like to write one and add it in then you'd be most
welcome! :)

At the time that the BioJavaX extensions were written compatibility with
Java 1.4 was still required and so we could not make use of any new Java
features that were introduced in Java 1.5. Set<Feature>, being an
example of Generics, is one of these.

Future versions of BioJava will require the user to install Java 1.6 or
later and so we will be able to use these newer features in both new and
existing code, depending on feasibility (for instance it is not always
possible to convert older code to use Generics in a sensible manner, and
it is not always possible to write Generics code that can interface
sensibly with older non-Generics modules).

cheers,
Richard



Martin Jones wrote:
> Hi,
> 
> I'm just getting started with BioJava so this may be a simple
> question.  I'm reading a RichSequence from a GenBank file and want to
> get the gene name of each CDS feature.  The following code gets hold
> of the features I'm interested in
> 
> for (Object o : mySeq.getFeatureSet()){
>       RichFeature f = (RichFeature) o;
>       if (f.getType().equals("CDS")){
>             //get gene name here
>       }
> }
> 
> but I'm not sure how best to get the gene name.  The following seems to work:
> 
> for (Object o2 : f.getNoteSet()){
>      Note n = (Note) o2;
>      if (n.getTerm().getName().equals("gene")){
>                  System.out.println("gene name is " + n.getValue());
>      }
> }
> 
> but seems overly verbose - ideally I'd like to be able to pass the
> Feature to another part of my program,  but writing the above whenever
> I want to get the name seems like overkill.  Is there a shorter way -
> something along the lines of
> 
> String name = f.getNoteByName("gene").getValue();
> 
> Thanks in advance for any help.
> 
> PS one more question - is there a reason why e.g.  getNoteSet returns
> a Set rather than a Set<Feature>, which makes it necessary to do all
> the type casts?
> 
> Thanks,
> 
> Martin
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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