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

[Andy Yates]

As with most things the answer is a yes & no. It shouldn't break 
interfaces as in the contract setup between the interface & a consumer 
since generics are erased after compilation.

However if we're looking at class incompatibility errors then it's quite 
likely that the new interface will have a different signature to the 
original one & may cause runtime errors in classes which haven't been 
recompiled against the new interface. A solution in some other projects 
is to have to sets of interfaces; one with generics & one without but 
that can be quite a nightmare to maintain.

Andy

Mark Schreiber wrote:
> These are good points.  Can we generify interfaces without breaking them?
> Certainly the addition of generics to the biojavax packages would remove a
> lot of nasty casting.  Adding convenience methods would certainly also help
> biojavax code does get a bit verbose.  Again this would break interfaces
> unless we put them in some kind of tools class.
> 
> These are certainly good points to remember for future designs (eg biojava2)
> usability should be a test criteria as well. BioJavaX gives excellent ORM
> with BioSQL and great capture of detail in it's parsers but the coding style
> is a bit unwieldy. 2 out of 3 is not bad though : )
> 
> - Mark
> 
> On Thu, Mar 27, 2008 at 10:11 PM, Richard Holland <holland at ebi.ac.uk> wrote:
> 
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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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