[Biojava-dev] Renewed Genbank files parsing support

[Andreas Prlic]

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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