[Biojava-dev] help (F1 F1) regarding biojava

[Richard Holland]

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Hello.

First thing you need to do is provide the full stack trace, not just the
last message. This will help us to pinpoint the problem.

Secondly, I notice you are using NCBISequenceDB and GenbankSequenceDB.
These are deprecated and have been replaced with GenbankRichSequenceDB:

http://www.biojava.org/docs/api15/org/biojavax/bio/db/ncbi/GenbankRichSequenceDB.html

Thirdly, I notice you are trying to set proxy settings. BioJava does not
currently support proxies for either GenbankRichSequenceDB or the
deprecated NCBISequenceDB/GenbankSequenceDB (internally it is making
direct connections to the server using Socket and not using
HttpURLConnection which knows about proxies). If you need this to be
changed, please do raise a bug report requesting it at
http://bugzilla.open-bio.org/ and we will do our best to come up with a
patch to fix it.

cheers,
Richard

pranav waila wrote:
> package org.biojava.bio.seq.db;
> 
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.io.*;
> import org.biojava.bio.*;
> import org.biojava.bio.seq.db.*;
> import org.biojava.bio.seq.io.*;
> import java.net.*;
> class test{
>     public static SequenceFormat sf;
> 
>     public static void main(String args[]){
> 
>         System.getProperties().put("proxySet","true");
> 
>         System.getProperties().put("proxyPort","3128");
>         System.getProperties().put("proxyHost","172.16.0.6");
> 
>         Sequence s;
>         sf=new FastaFormat();
>         //sf=new GenbankXmlFormat();
>                 NCBISequenceDB ncbi = new NCBISequenceDB(
> NCBISequenceDB.DB_PROTEIN,sf);//new FastaFormat());
> //        GenbankSequenceDB gdb=new GenbankSequenceDB();
>         //ncbi.setSequenceFormat(FASTA);
>     try{
> 
> 
> 
> //        Sequence sequenceFromGenbank = ncbi.getSequence("P10659");
> //        System.out.println(sequenceFromGenbank.getName());
> 
> // older code
>         s=ncbi.getSequence("P10659");
> 
>         //s=gdb.getAddress();//getSequence("P10659");//3789789");
>         System.out.print("check");
>         System.out.println(ncbi.getSequence("190786"));
> 
> //
>     }
>     catch(Exception e){
>         e.printStackTrace();
>         //System.out.println("protien name is : zinteminia");
>     }
> 
>     }
> }
> 
> 
> This is my code for fetching the sequence from NCBI but it is giving somany
> exceptions. can u provide me some code to do so..
> 
> the errors are as follows :
> 
> Bio java exception could not read sequence
> 
> CAN U PLEASE HELP ME.
> 
> waiting for reply
> 
> PRANAV WAILA
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
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