<div dir="ltr"><p dir="ltr">Hi,</p>
<p dir="ltr">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.<br></p><p dir="ltr"><br></p><p>Regards,</p><p>Jacek<br></p><br><div style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi Paolo,<br>
<br>
I don't remember the full history of this, but after having reviewed the<br>
code I think the story is like this:<br>
<br>
The "proxy" means that an entry can be fetched from an external DB based<br>
on a reference ID.<br>
<br>
Then there is another requirement to read a single record from a file<br>
containing many entries. (hence the differences between InputStream and<br>
Bufferedreader), which might explain the different approaches.s<br>
<br>
Having said that, I do think the API is inconsistent and could benefit from<br>
some cleanup and also we need better documentation for this. Any pull<br>
requests are welcome!<br>
<br>
Andreas<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
On Sat, Nov 22, 2014 at 12:10 PM, Paolo Pavan <<a href="mailto:paolo.pavan@gmail.com" target="_blank">paolo.pavan@gmail.com</a>> wrote:<br>
<br>
> Dear all,<br>
> Me and Jacek Grzebyta have added support for reading features, qualifiers<br>
> and nested locations with "split" indications in genbank files and we hope<br>
> this feature will be included in the next 4.0 release.<br>
><br>
> Anyway we face the existing of two ways to parse a genbank file: via<br>
> GenbankProxySequenceReader and via GenbankReader. Both use the same<br>
> underlying GenbankSequenceParser now updated, but in different ways.<br>
><br>
> Is there a reason that escapes to me of why such a dichotomy design or is<br>
> just the result of the efforts of two independent working groups? This<br>
> ?proxy? naming suggests me it wants to add something more to the standard<br>
> GenbankReader, isn?t it? There is an advised one? One difference is that<br>
> one is using an InputStream, the second a BufferedReader.<br>
><br>
> Can someone of the original authors add any note on that?<br>
><br>
> Thank you very much,<br>
> Paolo<br>
><br>
> _______________________________________________<br>
> biojava-dev mailing list<br>
> <a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
> <a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
><br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <<a href="http://mailman.open-bio.org/pipermail/biojava-dev/attachments/20141124/7b9d0f9a/attachment-0001.html" target="_blank">http://mailman.open-bio.org/pipermail/biojava-dev/attachments/20141124/7b9d0f9a/attachment-0001.html</a>><br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
biojava-dev mailing list<br>
<a href="mailto:biojava-dev@mailman.open-bio.org" target="_blank">biojava-dev@mailman.open-bio.org</a><br>
<a href="http://mailman.open-bio.org/mailman/listinfo/biojava-dev" target="_blank">http://mailman.open-bio.org/mailman/listinfo/biojava-dev</a><br>
<br>
End of biojava-dev Digest, Vol 140, Issue 4<br>
*******************************************<br>
</div>
</div>