[Biojava-dev] biojava-dev Digest, Vol 140, Issue 4

[Jacek Grzebyta]

Hi,

If it than looks like that I suggest to change the proxy Interface. It
could have a getter for data source instance from
org.biojava3.core.sequence.DataSource. Than create an abstract Proxy
instance which will map a datasource into relevant URI. But we need to take
into consideration that each (or more of them) would require unique API
anyway to proxy a data. Long time ago I tried to do it but gave up after I
discovered RDF and semantic web. anyway I will do changes and submit to my
branch repository.


Regards,

Jacek


Hi Paolo,

I don't remember the full history of this, but after having reviewed the
code I think the story is like this:

 The "proxy" means that an entry can be fetched from an external DB based
on a reference ID.

Then there is another requirement to read a single record from a file
containing many entries. (hence the differences between InputStream and
Bufferedreader), which might explain the different approaches.s

Having said that, I do think the API is inconsistent and could benefit from
some cleanup and also we need better documentation for this. Any pull
requests are welcome!

Andreas








On Sat, Nov 22, 2014 at 12:10 PM, Paolo Pavan <paolo.pavan at gmail.com> wrote:

> Dear all,
> Me and Jacek Grzebyta have added support for reading features, qualifiers
> and nested locations with "split" indications in genbank files and we hope
> this feature will be included in the next 4.0 release.
>
> Anyway we face the existing of two ways to parse a genbank file: via
> GenbankProxySequenceReader and via GenbankReader. Both use the same
> underlying GenbankSequenceParser now updated, but in different ways.
>
> Is there a reason that escapes to me of why such a dichotomy design or is
> just the result of the efforts of two independent working groups? This
> ?proxy? naming suggests me it wants to add something more to the standard
> GenbankReader, isn?t it? There is an advised one? One difference is that
> one is using an InputStream, the second a BufferedReader.
>
> Can someone of the original authors add any note on that?
>
> Thank you very much,
> Paolo
>
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