[Biojava-l] Fwd: read fasta entry by entry

[P. Troshin]

Hi Andreas,

Sorry I am a bit short of time at the moment. I think that simply moving
this code into core as is is not going to help anyone, it could just cause
confusion. At a very list someone need to write a bit of documentation for
the users. We need to unify different BioJava FASTA parsers. I wanted to do
with someone else help, within GSOC, but the project did not go ahead. So
may be next year?

Regards,
Peter

On 12 May 2012 00:10, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Peter and Scooter,
>
> It would be great to improve the documentation for this on the wiki
> and to consolidate the two Fasta parsers. Peter: utility methods are
> better in -core, rather than in the specialized modules. They are hard
> to find that way and create unexpected module dependencies. Any chance
> to move this to the core module?
>
> Thanks,
>
> Andreas
>
> On Wed, May 9, 2012 at 4:41 PM, P. Troshin <to.petr at gmail.com> wrote:
> > Hi,
> >
> > Try SequenceUtil.readFasta(InputStream in). It would read sequences
> > regardless of the type.
> > This is a small tool in the disorder predictor package.
> >
> > Hope that helps,
> > Regards,
> > Peter
> >
> >
> >
> > On 9 May 2012 04:45, Mic <mictadlo at gmail.com> wrote:
> >
> >> Hello,
> >> I have found this
> >> http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite example,
> but
> >> it looks like that the whole fasta file is stored in memory.
> >>
> >> Is it possible to read any fasta entry by entry i.e. without
> >> to specify whether it is DNA/Protein?
> >>
> >> Thank you in advance.
> >>
> >> Mic
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