[Biojava-l] Problem with downloading Genbank-sequence

[Felix Dreher]

Hi Thomas,

I use "Java Studio Creator2 EarlyAccess2" as IDE, which runs with Java 
1.5 as platform.
Further I have an up-to-date bytecode.jar (it's in the cvs-library I 
just installed a few days ago).
When I ran the application with the additional line you sent, I got 
another exception. I hope this time maybe it's more useful ....:

java.lang.ExceptionInInitializerError

    org.biojava.bio.seq.FeatureFilter.(FeatureFilter.java:1813)
     java.lang.Class.forName0(Native Method)
     java.lang.Class.forName(Class.java:164)
    org.biojava.utils.walker.WalkerFactory.class$(WalkerFactory.java:40)
    org.biojava.utils.walker.WalkerFactory.getInstance(WalkerFactory.java:40)

    rnai.seq_input2.prerender(seq_input2.java:283)
    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)


Greetings,
Felix





Thomas Down wrote:

> 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
>>
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at biojava.org
>> http://biojava.org/mailman/listinfo/biojava-l
>
>


-- 
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