[Biojava-dev] Biojava.util package?

[Hannes Brandstätter-Müller]

Yes, something like a simplifying and unifying wrapper would be what I
am thinking of.

Hannes

On Thu, Mar 29, 2012 at 05:55, Andreas Prlic <andreas at sdsc.edu> wrote:
> 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
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------