Re: Parsing embl format with biojava4

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On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <[email protected]>
wrote:

> Hello,
>
> First, thanks for the great Biojava project!
>
> Is it possible to parse embl files using (Bio)Java?
>
> By Googling "biojava  embl format" I get some hits for the legacy Biojava
> 1.9 but I'm wondering weather I could (should?) use the more recent Biojava
> 4?
>

If biojava-legacy works fine for you, feel confident using it.  It is
actively maintained; there just won't be any new features.



> A more general question... Which is the primary source of documentation
> for Biojava 4? Is it the tutorial at https://github.com/biojava/
> biojava-tutorial together with the Javadocs (http://biojava.org/docs/api4.
> 2.1/)?
>
> I find the home page Biojava.org a little confusing... The tutorial page
> http://biojava.org/wiki/BioJava:CookBook4.0/ gives me a 404 error. The
> wiki pages http://biojava.org/wiki.html seem a mixture of various topics.
>

The biojava.org website didn't survive a wiki migration to github without
running into some problems.  If you find any, please file them as issues at

https://github.com/biojava/biojava.github.io

   michael

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<div dir=3D"ltr">On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <span dir=
=3D"ltr">&lt;<a href=3D"mailto:[email protected]" target=3D"_blank">d=
[email protected]</a>&gt;</span> wrote:<br><div class=3D"gmail_extra">=
<div class=3D"gmail_quote"><blockquote class=3D"gmail_quote" style=3D"margi=
n:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex=
"><div dir=3D"ltr">Hello,<div><br></div><div>First, thanks for the great Bi=
ojava project!</div><div><br></div><div>Is it possible to parse embl files =
using (Bio)Java?=C2=A0</div><div><br></div><div>By Googling &quot;biojava =
=C2=A0embl format&quot; I get some hits for the legacy Biojava 1.9 but I&#3=
9;m wondering weather I could (should?) use the more recent Biojava 4?</div=
></div></blockquote><div><br></div><div>If biojava-legacy works fine for yo=
u, feel confident using it.=C2=A0 It is actively maintained; there just won=
&#39;t be any new features.<br><br></div><div>=C2=A0</div><blockquote class=
=3D"gmail_quote" style=3D"margin:0px 0px 0px 0.8ex;border-left:1px solid rg=
b(204,204,204);padding-left:1ex"><div dir=3D"ltr"><div>A more general quest=
ion... Which is the primary source of documentation for Biojava 4? Is it th=
e tutorial at <a href=3D"https://github.com/biojava/biojava-tutorial" targe=
t=3D"_blank">https://github.com/biojava/<wbr>biojava-tutorial</a> together =
with the Javadocs (<a href=3D"http://biojava.org/docs/api4.2.1/" target=3D"=
_blank">http://biojava.org/docs/api4.<wbr>2.1/</a>)?=C2=A0</div><div><br></=
div><div>I find the home page Biojava.org a little confusing... The tutoria=
l page=C2=A0<a href=3D"http://biojava.org/wiki/BioJava:CookBook4.0/" target=
=3D"_blank">http://biojava.org/wiki/<wbr>BioJava:CookBook4.0/</a> gives me =
a 404 error. The wiki pages=C2=A0<a href=3D"http://biojava.org/wiki.html" t=
arget=3D"_blank">http://biojava.org/wiki.<wbr>html</a> seem a mixture of va=
rious topics.</div></div></blockquote><div><br></div><div>The <a href=3D"ht=
tp://biojava.org">biojava.org</a> website didn&#39;t survive a wiki migrati=
on to github without running into some problems.=C2=A0 If you find any, ple=
ase file them as issues at<br><br><a href=3D"https://github.com/biojava/bio=
java.github.io">https://github.com/biojava/biojava.github.io<br></a><br></d=
iv>=C2=A0=C2=A0 michael<br></div></div></div>

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