[Biojava-l] Problem with downloading Genbank-sequence

[Felix Dreher]

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