[Biojava-dev] BioJava 3 Proposal

[Andy Yates]

It seems like this would be a good way of pushing out fixes/format 
changes to parsers in between official releases of the API. I just don't 
want to go down the route of "everything can be solved with this api" 
which I know I've been guilty of with other toolkits. Overall though the 
concept is sound :)

george waldon wrote:
> I will.
> 
> Another thought. You could also have an SPI for lookup itself. LookupProviders could be declared in the manifest and provide dynamically all sorts of services at runtime. You could also have a way to register in the main lookup classes you don't want to show during the process, making possible to prevent conflicts (when several implementations are available and only one is desirable).
> 
> - George
> 
> 
>> -----Original Message-----
>> From: Richard Holland [mailto:holland at ebi.ac.uk]
>> Sent: Friday, October 05, 2007 10:57 AM
>> To: george waldon
>> Cc: markjschreiber at gmail.com; biojava-dev at biojava.org
>> Subject: Re: [Biojava-dev] BioJava 3 Proposal
>>
>> That sounds cool. Could you add your suggestion to the wiki?
>>
>> cheers,
>> Richard
>>
>> On Fri, October 5, 2007 6:24 pm, george waldon wrote:
>>> Would-it be helpful to implement SPI for manipulating sequence formats?
>>>
>>> For example, we could have:
>>>
>>> RichSequenceFormat fasta =
>> Lookup.getDefault().lookup(FastaFormat.class);
>>> This would allow anyone to implement their own version of sequence
>> format.
>>> The lookup would return the internal implementation by default or an
>>> external one is any is found.
>>>
>>> - George
>>>
>>>
>>>> -----Original Message-----
>>>> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
>>>> bounces at lists.open-bio.org] On Behalf Of Mark Schreiber
>>>> Sent: Tuesday, October 02, 2007 4:59 AM
>>>> To: Richard Holland
>>>> Cc: biojava-dev at biojava.org
>>>> Subject: Re: [Biojava-dev] BioJava 3 Proposal
>>>>
>>>> Hi -
>>>>
>>>> There was some talk of making biojava3 aware of plugins and service
>>>> provider interfaces (SPI). It is therefore timely that Sun have
>>>> released an article on how this can easily be achieved now that the
>>>> ServiceLoader API has been exposed in JSE6
>>>>
>>>> http://java.sun.com/developer/technicalArticles/javase/extensible/
>>>>
>>>> - Mark
>>>>
>>>> On 10/1/07, Richard Holland <holland at ebi.ac.uk> wrote:
>>>>> -----BEGIN PGP SIGNED MESSAGE-----
>>>>> Hash: SHA1
>>>>>
>>>>> I see it's all gone a bit quiet this last week or two!
>>>>>
>>>>> Here is the current proposal as it stands:
>>>>>
>>>>> http://biojava.org/wiki/BioJava3_Proposal
>>>>>
>>>>> (There's also quite a bit of discussion on the topic on the
>> associated
>>>>> 'discussion' page).
>>>>>
>>>>> Please make comments directly to the wiki page. The more comments we
>>>>> get, the more likely it is we will proceed with a development plan
>>>> which
>>>>> suits the majority of our users.
>>>>>
>>>>> I plan to make a summary of this page public to biojava-l sometime in
>>>>> November. This summary page would then be put through the same
>>>> feedback
>>>>> and discussion process, and would be open for anyone to comment
>>>>> (including, most importantly, our users). The final plan would be
>>>> based
>>>>> on the outcome of these public discussions.
>>>>>
>>>>> cheers,
>>>>> Richard
>>>>> -----BEGIN PGP SIGNATURE-----
>>>>> Version: GnuPG v1.4.2.2 (GNU/Linux)
>>>>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org
>>>>>
>>>>> iD8DBQFHAOC34C5LeMEKA/QRAqQzAJoDxrSbqBcxZQZayKIzx0k5NJguNwCeO+c4
>>>>> 58Id2MR4Ql1+Cd474YaneqE=
>>>>> =XO63
>>>>> -----END PGP SIGNATURE-----
>>>>> _______________________________________________
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>>>>>
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>>
>> --
>> Richard Holland
>> BioMart (http://www.biomart.org/)
>> EMBL-EBI
>> Hinxton, Cambridgeshire CB10 1SD, UK
> 
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