[Biojava-l] Issue with FASTA reader

[Jose Duarte]

Dear Dak

The best way of fixing it yourself is that you modify the code in your own
github fork (ideally in a branch, not in master) and then submit a pull
request so that your patch can be peer reviewed.

All the best

Jose


On Thu, Jun 1, 2017 at 8:25 AM, Rojnuckarin, Dak <atipatr at amgen.com> wrote:

> Hello,
>
>
>
> Andreas mentioned he created a branch in github to contain my test code:
>
>
>
> https://github.com/biojava/biojava/commit/9de8e3633a8d66fc4050f14b2e2168
> 4605cf2f7b
>
>
>
> but I have not heard back in a while.
>
>
>
> What’s the process/etiquette of getting involved and attempt the fix
> myself?
>
>
>
> Thanks,
>
> dak
>
>
>
> *From:* andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] *On
> Behalf Of *Andreas Prlic
> *Sent:* Wednesday, April 19, 2017 4:34 PM
> *To:* Rojnuckarin, Dak <atipatr at amgen.com>
> *Cc:* biojava-l at mailman.open-bio.org
> *Subject:* Re: [Biojava-l] Issue with FASTA reader
>
>
>
> Thanks, Dak. I'll create a branch in git which will contain your test,
> then we can take it from there.
>
>
>
> Andreas
>
>
>
>
>
>
>
> On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, Dak <atipatr at amgen.com>
> wrote:
>
> Hi,
>
>
>
> I have a FASTA file that contain one sequence. I initialized FASTA reader
> as described in the tutorial, called process() and get one record as
> expected. However, if I re-initialized another FASTA reader opening the
> same one-record file, called process(1) and null is returned. If I tried to
> read two-record FASTA file, the first process(1) works, but not the second
> call to process(1) return null. Based on a superficial glance, it looks
> like the if statement at line 194 of FastaReader.java may be the culprit.
>
>
>
> Test code attached.
>
>
>
> Thanks,
>
> Dak Rojnuckarin
>
> Research Informatics
>
> Amgen
>
>
>
>
>
>
> _______________________________________________
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>
>
>
>
>
> --
>
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> RCSB PDB Protein Data Bank
>
> Technical & Scientific Team Lead
>
> University of California, San Diego
>
>
>
> Editor Software Section
>
> PLOS Computational Biology
>
>
>
> BioJava Project Lead
> -----------------------------------------------------------------------
>
> _______________________________________________
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> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>
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