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
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