Re: (no subject)

Hi Aditya

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.

Regarding your question, in the biojava wiki we have a guide to set it 
up in Netbeans (simplest is option 3):

http://biojava.org/wiki/How_to_integrate_BioJava_in_NetBeans_IDE

I don't have so much experience with Netbeans, only with eclipse. For 
how to set up with eclipse, see:

http://biojava.org/wiki/BioJava3_eclipse

(especially option 3, which is the simplest and should work well with 
eclipse 4.4 or later)

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:

https://spring.io/guides/gs/maven/

Hope this helps

Jose


On 15.08.2015 06:21, ADITYA MANTHA wrote:
> 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 .
>
> On Sat, Aug 15, 2015 at 2:06 AM, Jose Manuel Duarte 
> <[email protected] <mailto:[email protected]>> wrote:
>
>     How to get and parse data from the PDB:
>
>     https://github.com/biojava/biojava-tutorial/blob/master/structure/firststeps.md
>
>     How to get the data once parsed the file into a Structure object:
>
>     https://github.com/biojava/biojava-tutorial/blob/master/structure/structure-data-model.md
>
>     Jose
>
>
>
>     On 14.08.2015 22:30, ADITYA MANTHA wrote:
>>     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 .
>>
>>     On Sat, Aug 15, 2015 at 1:48 AM, Jose Manuel Duarte
>>     <[email protected] <mailto:[email protected]>> wrote:
>>
>>         Did you check the biojava tutorial? It explains how to do the
>>         file parsing and how to retrieve the data:
>>
>>         https://github.com/biojava/biojava-tutorial
>>
>>         Jose
>>
>>
>>
>>
>>         On 14.08.2015 20:13, ADITYA MANTHA wrote:
>>>         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 .
>>>
>>>         -- 
>>>         Best Regards
>>>
>>>         ADITYA MANTHA
>>>         Sophomore
>>>         Instrumentation Engineering
>>>         Department of Electrical Engineering
>>>         IIT KHARAGPUR
>>>         9800192364
>>>
>>>
>>>         _______________________________________________
>>>         Biojava-l mailing list  [email protected]  <mailto:[email protected]>
>>>         http://mailman.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>>         _______________________________________________
>>         Biojava-l mailing list  - [email protected]
>>         <mailto:[email protected]>
>>         http://mailman.open-bio.org/mailman/listinfo/biojava-l
>>
>>
>>
>>
>>     -- 
>>     Best Regards
>>
>>     ADITYA MANTHA
>>     Sophomore
>>     Instrumentation Engineering
>>     Department of Electrical Engineering
>>     IIT KHARAGPUR
>>     9800192364
>
>
>
>
> -- 
> Best Regards
>
> ADITYA MANTHA
> Sophomore
> Instrumentation Engineering
> Department of Electrical Engineering
> IIT KHARAGPUR
> 9800192364

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