[Biojava-l] Problem with downloading Genbank-sequence

[Thomas Down]

Hi Felix,

This doesn't look like a problem specific to GenbankSequenceDB  
itself, but a problem with initialising some core BioJava machinary  
(from the exception you report, it looks like the static initializer  
for the FeatureFilter.OnlyChildren class is failing -- I assume the  
real problem is occuring somewhere in WalkerFactory, but the exact  
problem isn't being reporter in your exception.

What version of Java are you using?

Do you have an up-to-date bytecode.jar somewhere where it will be  
picked up (I notice you're using JavaServer Faces, I'm afraid I don't  
have any experience with this -- is there anyone on the list that does?)

What happens if you put a line like:

        WalkerFactory.getInstance().addTypeWithParent 
(FeatureFilter.OnlyChildren.class);

somewhere in your code?  I'd expect this to fail, too, but hopefully  
it with give a more informative exception.

              Thomas.

On 30 Nov 2005, at 15:06, Felix Dreher wrote:

> Hello,
>
> I used to download DNA-sequences from Genbank with the  
> 'getSequence'-method from the class 'GenbankSequenceDB' (Biojava  
> 1.4). After I installed the latest cvs-version, it seems to be not  
> working anymore.
>
> This is where I call the method:
>
>
> public class GenbankDownload {
>    static private GenbankSequenceDB gbDb= new GenbankSequenceDB();
>    static public Sequence loadGenBankSequence(String id){
>        try{
>            return gbDb.getSequence(id);         }catch(Exception e){
>            return null;
>        }
>    }
>
>
> This is the exception report:
>
>
> java.lang.ExceptionInInitializerError
>
>    org.biojava.bio.seq.FeatureFilter.(FeatureFilter.java:1813)
>    org.biojava.bio.seq.impl.SimpleSequence.getFeatureHolder 
> (SimpleSequence.java:144)
>    org.biojava.bio.seq.impl.SimpleSequence.createFeature 
> (SimpleSequence.java:224)
>    org.biojava.bio.seq.io.SequenceBuilderBase.makeSequence 
> (SequenceBuilderBase.java:175)
>    org.biojava.bio.seq.io.SmartSequenceBuilder.makeSequence 
> (SmartSequenceBuilder.java:103)
>    org.biojava.bio.seq.io.SequenceBuilderFilter.makeSequence 
> (SequenceBuilderFilter.java:99)
>    org.biojava.bio.seq.io.StreamReader.nextSequence 
> (StreamReader.java:102)
>    org.biojava.bio.seq.db.GenbankSequenceDB.getSequence 
> (GenbankSequenceDB.java:130)
>    rnai.GenbankDownload.loadGenBankSequence(GenbankDownload.java:23)
>    rnai.seq_input2.prerender(seq_input2.java:312)
>    com.sun.web.ui.appbase.faces.ViewHandlerImpl.prerender 
> (ViewHandlerImpl.java:788)
>    com.sun.web.ui.appbase.faces.ViewHandlerImpl.renderView 
> (ViewHandlerImpl.java:282)
>    com.sun.faces.lifecycle.RenderResponsePhase.execute 
> (RenderResponsePhase.java:87)
>    com.sun.faces.lifecycle.LifecycleImpl.phase(LifecycleImpl.java:221)
>    com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java: 
> 117)
>    javax.faces.webapp.FacesServlet.service(FacesServlet.java:198)
>    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>    sun.reflect.NativeMethodAccessorImpl.invoke 
> (NativeMethodAccessorImpl.java:39)
>    sun.reflect.DelegatingMethodAccessorImpl.invoke 
> (DelegatingMethodAccessorImpl.java:25)
>    java.lang.reflect.Method.invoke(Method.java:585)
>    org.apache.catalina.security.SecurityUtil$1.run 
> (SecurityUtil.java:249)
>    java.security.AccessController.doPrivileged(Native Method)
>    javax.security.auth.Subject.doAsPrivileged(Subject.java:517)
>    org.apache.catalina.security.SecurityUtil.execute 
> (SecurityUtil.java:282)
>    org.apache.catalina.security.SecurityUtil.doAsPrivilege 
> (SecurityUtil.java:165)
>    java.security.AccessController.doPrivileged(Native Method)
>    com.sun.web.ui.util.UploadFilter.doFilter(UploadFilter.java:179)
>
>
> Any help would be appreciated!
> Thank you,
>
> Felix
>
>
> -- 
> Felix Dreher
> Max-Planck-Institute for Infection Biology
> Campus Charité Mitte
> Department of Immunology
> Mailing address: Schumannstraße 21/22
> Visitors: Virchowweg 12
> 10117 Berlin
> Germany
> Tel.: +49 (0)30 28460-254 / -494
> Mobile: +49 (0)163 7542426
>
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