Re: Issue with FASTA reader

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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 <[email protected]> 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
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  [email protected]
> http://mailman.open-bio.org/mailman/listinfo/biojava-l
>



-- 
-----------------------------------------------------------------------
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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<div dir=3D"ltr">Thanks, Dak. I&#39;ll create a branch in git which will co=
ntain your test, then we can take it from there.<div><br></div><div>Andreas=
<br><div><br></div><div><br></div></div></div><div class=3D"gmail_extra"><b=
r><div class=3D"gmail_quote">On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, =
Dak <span dir=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=3D"_b=
lank">[email protected]</a>&gt;</span> wrote:<br><blockquote class=3D"gmail=
_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:=
1ex">





<div lang=3D"EN-US" link=3D"#0563C1" vlink=3D"#954F72">
<div class=3D"m_3540772077852758111WordSection1">
<p class=3D"MsoNormal">Hi,<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">I have a FASTA file that contain one sequence. I ini=
tialized FASTA reader as described in the tutorial, called process() and ge=
t 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 FAST=
A file, the first process(1) works, but not the second call to process(1) r=
eturn null. Based on a superficial glance, it looks like the if statement a=
t line 194 of FastaReader.java may
 be the culprit. <u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Test code attached.<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">Thanks,<u></u><u></u></p>
<p class=3D"MsoNormal">Dak Rojnuckarin<u></u><u></u></p>
<p class=3D"MsoNormal">Research Informatics<u></u><u></u></p>
<p class=3D"MsoNormal">Amgen<u></u><u></u></p>
<p class=3D"MsoNormal"><u></u>=C2=A0<u></u></p>
<p class=3D"MsoNormal">=C2=A0=C2=A0<u></u><u></u></p>
</div>
</div>

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nfo/biojava-l</a><br></blockquote></div><br><br clear=3D"all"><div><br></di=
v>-- <br><div class=3D"gmail_signature" data-smartmail=3D"gmail_signature">=
<div dir=3D"ltr"><div><div dir=3D"ltr">------------------------------------=
-----------------------------------<br>Dr. Andreas Prlic<br>RCSB PDB Protei=
n Data Bank</div><div>Technical &amp; Scientific Team Lead</div><div dir=3D=
"ltr">University of California, San Diego<div><br></div><div>Editor Softwar=
e Section=C2=A0<br><div>PLOS Computational Biology<div><div><div><br></div>=
<div>BioJava Project Lead<br>----------------------------------------------=
-------------------------<br></div></div></div></div></div></div></div></di=
v></div>
</div>

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