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Hi Aditya<br>
<br>
First of all some mail list etiquette: please always send your
replies to the list so that everyone can benefit from the answers,
second try to always have a subject so that people can easily find
out if they are interested in the thread.<br>
<br>
Regarding your question, in the biojava wiki we have a guide to set
it up in Netbeans (simplest is option 3):<br>
<br>
<a class="moz-txt-link-freetext" href="http://biojava.org/wiki/How_to_integrate_BioJava_in_NetBeans_IDE">http://biojava.org/wiki/How_to_integrate_BioJava_in_NetBeans_IDE</a><br>
<br>
I don't have so much experience with Netbeans, only with eclipse.
For how to set up with eclipse, see:<br>
<br>
<a class="moz-txt-link-freetext" href="http://biojava.org/wiki/BioJava3_eclipse">http://biojava.org/wiki/BioJava3_eclipse</a><br>
<br>
(especially option 3, which is the simplest and should work well
with eclipse 4.4 or later)<br>
<br>
Biojava uses maven as a build system and to take care of the
external dependencies (like slf4j). Although not required for your
project, it is recommendable to use maven in your project since it
will make things easier. This is a quick guide to setting up a new
maven project:<br>
<br>
<a class="moz-txt-link-freetext" href="https://spring.io/guides/gs/maven/">https://spring.io/guides/gs/maven/</a><br>
<br>
Hope this helps<br>
<br>
Jose<br>
<br>
<br>
<div class="moz-cite-prefix">On 15.08.2015 06:21, ADITYA MANTHA
wrote:<br>
</div>
<blockquote
cite="mid:CAM_xwEa1Vcr7YAUj64+qpSwXSMKUJMCxiegpRa1qqunCBXQ8-w@mail.gmail.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<div dir="ltr">Thank you very much . But I am getting a
"org/slf4j/LoggerFactory" error . Even if i add the .jar file
of slf4j , i am still having a problem . So can you tell me what
all .jar files i have to install to use biojava in netbeans
environment .</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sat, Aug 15, 2015 at 2:06 AM, Jose
Manuel Duarte <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jose.duarte@psi.ch" target="_blank">jose.duarte@psi.ch</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> How to get and parse
data from the PDB:<br>
<br>
<a moz-do-not-send="true"
href="https://github.com/biojava/biojava-tutorial/blob/master/structure/firststeps.md"
target="_blank">https://github.com/biojava/biojava-tutorial/blob/master/structure/firststeps.md</a><br>
<br>
How to get the data once parsed the file into a Structure
object:<br>
<br>
<a moz-do-not-send="true"
href="https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md"
target="_blank">https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md</a><span
class="HOEnZb"><font color="#888888"><br>
<br>
Jose</font></span>
<div>
<div class="h5"><br>
<br>
<br>
<div>On 14.08.2015 22:30, ADITYA MANTHA wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">well , i tried to. But i could not
find a proper solution . Can you tell the specific
example with some sample codes . As i am new to
BioInformatics .</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sat, Aug 15, 2015 at
1:48 AM, Jose Manuel Duarte <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:jose.duarte@psi.ch"
target="_blank">jose.duarte@psi.ch</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Did you
check the biojava tutorial? It explains how
to do the file parsing and how to retrieve
the data:<br>
<br>
<a moz-do-not-send="true"
href="https://github.com/biojava/biojava-tutorial"
target="_blank">https://github.com/biojava/biojava-tutorial</a><br>
<br>
Jose
<div>
<div><br>
<br>
<br>
<br>
<div>On 14.08.2015 20:13, ADITYA MANTHA
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">Currently, I am trying
to implement Chou Fasman Algorithm
in Java . For this i need to
retrieve information regarding Name
, Primary Sequence and Secondary
Structure information . Can someone
help me out how to parse this data
from a PDB file .<br clear="all">
<div><br>
</div>
-- <br>
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>Best Regards</div>
<div><br>
</div>
ADITYA MANTHA
<div>Sophomore</div>
<div>Instrumentation
Engineering</div>
<div>Department of
Electrical Engineering</div>
<div>IIT KHARAGPUR</div>
<div>9800192364</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
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</blockquote>
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<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>Best Regards</div>
<div><br>
</div>
ADITYA MANTHA
<div>Sophomore</div>
<div>Instrumentation Engineering</div>
<div>Department of Electrical Engineering</div>
<div>IIT KHARAGPUR</div>
<div>9800192364</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>Best Regards</div>
<div><br>
</div>
ADITYA MANTHA
<div>Sophomore</div>
<div>Instrumentation Engineering</div>
<div>Department of Electrical Engineering</div>
<div>IIT KHARAGPUR</div>
<div>9800192364</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
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