[Biojava-dev] Biojava.util package?

[Andreas Prlic]

Hi Hannes,

I guess this is pretty similar to:

http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite

we have also been using "proxy" objects to fetch sequence data on the fly

http://biojava.org/wiki/BioJava:CookBook:Core:Sequences

As such I think we should discuss this a bit more. If we can find a
common api that is simple and works with both local files as well as
remote proxy objects, that would be nice. There should be no need to
change much of the existing code, but perhaps there could be a
simplified wrapper for what is already there.

 Andreas

On Wed, Mar 28, 2012 at 12:04 PM, Hannes Brandstätter-Müller
<biojava at hannes.oib.com> wrote:
> Hi,
>
> I browsed around in the sister projects Biopython and Bioperl a bit,
> and noticed that many of the user interaction with the code goes
> through classes like SeqIO, SearchIO, AlignIO...
>
> So that got me thinking: how about we create similar "Interface"
> classes in Biojava?
>
> PROS:
>
>  - easy change for programmers who switch languages
>  - easy base interface that can be used in cookbook examples
>  - makes code more readable if designed properly
>  - easy access to features that are spread over the whole codebase but
> are connected anyway, like all file parsers
>
> CONS:
>
>  - another thing to maintain
>  - creates possible cross-dependencies (but if you don't want that,
> just use the existing classes directly)
>
>
> What are your thoughts?
>
> python from http://biopython.org/wiki/SeqIO:
>
> from Bio import SeqIO
> handle = open("example.fasta", "rU")
> for record in SeqIO.parse(handle, "fasta") :
>    print record.id
> handle.close()
>
> possible equivalent in biojava (support for streaming API, Iterators, etc?):
>
> import org.biojava3.util.SeqIO;
>
> File file = new File("example.fasta");
> SeqIO seqIO = new SeqIO(file, SeqIO.FASTA);
> while (seqIO.hasNext()) {
>    System.out.println(seqIO.next());
> }
> file.close();
>
> Hannes
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
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-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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