<div dir="ltr">Dear Dak<div><br></div><div>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.</div><div><br></div><div>All the best</div><div><br></div><div>Jose</div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 1, 2017 at 8:25 AM, Rojnuckarin, Dak <span dir="ltr"><<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hello,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Andreas mentioned he created a branch in github to contain my test code:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><a href="https://github.com/biojava/biojava/commit/9de8e3633a8d66fc4050f14b2e21684605cf2f7b" target="_blank">https://github.com/biojava/<wbr>biojava/commit/<wbr>9de8e3633a8d66fc4050f14b2e2168<wbr>4605cf2f7b</a><u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">but I have not heard back in a while.
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">What’s the process/etiquette of getting involved and attempt the fix myself?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Thanks,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">dak<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <a href="mailto:andreas.prlic@gmail.com" target="_blank">andreas.prlic@gmail.com</a> [mailto:<a href="mailto:andreas.prlic@gmail.com" target="_blank">andreas.prlic@gmail.<wbr>com</a>]
<b>On Behalf Of </b>Andreas Prlic<br>
<b>Sent:</b> Wednesday, April 19, 2017 4:34 PM<br>
<b>To:</b> Rojnuckarin, Dak <<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>><br>
<b>Cc:</b> <a href="mailto:biojava-l@mailman.open-bio.org" target="_blank">biojava-l@mailman.open-bio.org</a><br>
<b>Subject:</b> Re: [Biojava-l] Issue with FASTA reader<u></u><u></u></span></p><div><div class="h5">
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<p class="MsoNormal">Thanks, Dak. I'll create a branch in git which will contain your test, then we can take it from there.<u></u><u></u></p>
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<p class="MsoNormal">Andreas<u></u><u></u></p>
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<p class="MsoNormal">On Mon, Apr 17, 2017 at 9:43 AM, Rojnuckarin, Dak <<a href="mailto:atipatr@amgen.com" target="_blank">atipatr@amgen.com</a>> wrote:<u></u><u></u></p>
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<p class="MsoNormal">Hi,<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">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. <u></u><u></u></p>
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<p class="MsoNormal">Test code attached.<u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<p class="MsoNormal">Thanks,<u></u><u></u></p>
<p class="MsoNormal">Dak Rojnuckarin<u></u><u></u></p>
<p class="MsoNormal">Research Informatics<u></u><u></u></p>
<p class="MsoNormal">Amgen<u></u><u></u></p>
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<p class="MsoNormal">-- <u></u><u></u></p>
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<p class="MsoNormal">------------------------------<wbr>------------------------------<wbr>-----------<br>
Dr. Andreas Prlic<br>
RCSB PDB Protein Data Bank<u></u><u></u></p>
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<p class="MsoNormal">Technical & Scientific Team Lead<u></u><u></u></p>
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