[Biojava-dev] AbstractSequence private access

[Scooter Willis]

Richard

I agree that set/get can also work but want to minimize methods that should only be used by an advance user which should be immutable data element. Lazy loading is accomplished by the ProxySequence class itself which is currently an option in the constructor. Using protected with a set/get method would allow the advance developer to extend the class and handle the specific use case. 

Thanks

Scooter



On Oct 13, 2010, at 7:26 AM, Richard Holland wrote:

> I'd be happier with a set/get method pair rather than exposing the field itself, but generally I don't see a problem with allowing it to be mutable.
> 
> The reason for the set/get approach is there may (in some implementations) be other fields or caches internally to the object that need to know if the sequenceStorage has changed and therefore need to reset themselves. By using a set/get we can allow people to detect that change by overriding the set method, and the get method allows transparent wraps/unwraps/caching/lazyloading etc. as necessary. Generally its good programming practice to use a set/get pair anyway.
> 
> 
> On 13 Oct 2010, at 11:42, PATERSON Trevor wrote:
> 
>> Hi
>> 
>> you may recall that many months ago I was attempting to use BioJava3 objects in our Java EnsemblAPI project http://jensembl.sourceforge.net/
>> 
>> I have just been looking at how your recent code updates affect our demo
>> 
>> our original basic problem was that
>> 
>> 1. we need to subclass DNASequence (which subclasses Abstract Sequence)
>> 2. we need to be able to set the ProxySequenceReader ***after*** we have made a subclassed DNASequence Object
>> 
>> there are various very clunky workarounds we could do for this - either by using reflection to set the ProxySequenceReader
>> or replacing existing DNASequence Objects with  a new DNASequence Object constructed with a ProxySequenceReader  as we need to
>> 
>> however the clean fix I hacked into a previous version of your code was to change the modifier in AbsractSequence from
>> 
>> private SequenceReader<C> sequenceStorage;
>> 
>> to
>> 
>> protected SequenceReader<C> sequenceStorage;
>> 
>> so that I could then use Subclasses as a bean rather than immutable object
>> 
>> I don't think that our use case is particularly unreasonable - because I can easily imagine scenarios where you might want to
>> change the Datasource for a DNASequence object on the fly - which could be done by resetting its reader.
>> 
>> Is there any reason why the sequenceStorage field must be private rather than protected?
>> 
>> (And without any in depth knowledge of BioJava, is this design pattern widespread, because it has implications for any occasion
>> where Objects are populated by lazy load from datasources)
>> 
>> 
>> cheers
>> 
>> trevor
>> 
>> ps good to see that biojava3 is coming to fruition after all your hard work
>> 
>> 
>> 
>> 
>> Trevor Paterson PhD
>> new email trevor.paterson at roslin.ed.ac.uk<mailto:trevor.paterson at roslin.ed.ac.uk>
>> 
>> Bioinformatics
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> 
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
> 
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