[Biojava-dev] AbstractMethodError while enriching a sequence

[George Waldon]

Thank you very much Richard for your input. I have opened bug #2787 on this question.  Since the addition of a new method could break some codes, I propose to implement this solution after the incoming release of biojava 1.7.

Thanks,
George

> -----Original Message-----
> From: Richard Holland [mailto:holland at eaglegenomics.com]
> Sent: Tuesday, March 10, 2009 9:09 AM
> To: George Waldon
> Cc: biojava-dev at biojava.org
> Subject: Re: [Biojava-dev] AbstractMethodError while enriching a sequence
> 
> My personal choice would be to change getAnnotation to return
> Annotation, and add a separate getRichAnnotation method which always
> returns RichAnnotation objects.
> 
> thanks,
> Richard
> 
> George Waldon wrote:
> > Hi,
> >
> > I got this problem again and needed to solve it. The culprit is the
> method 'public RichAnnotation getAnnotation()' in RichAnnotatable, which
> overrides 'Annotation getAnnotation()' in Annotatable and interferes with
> method invocation. Removal of this method solves the problem, nicely I
> would say, thanks for the folks who wrote the projection package. Biojava
> still builds without error and passes all tests.
> >
> > If it is ok, I'd like to commit the change. This is an interface change
> and comments are more than welcome. Maybe Richard Holland could comment
> his choice for this 'rich' method.
> >
> > Thanks,
> > George
> > ________________________________________
> > From: Mark Schreiber [markjschreiber at gmail.com]
> > Sent: Monday, March 02, 2009 9:41 PM
> > To: gwaldon at geneinfinity.org
> > Cc: biojava-dev at biojava.org
> > Subject: Re: [Biojava-dev] AbstractMethodError while enriching a
> sequence
> >
> > I seem to recall there is a subsequence method in RichSequence.Tools.
> This may remove the need for enrichment?
> >
> > - mark
> >
> > On 3 Mar 2009, 1:36 PM,
> <gwaldon at geneinfinity.org<mailto:gwaldon at geneinfinity.org>> wrote:
> >
> > Hi,
> >
> > I am catching this at:
> >
> > java.lang.AbstractMethodError:
> org.biojava.bio.seq.projection.TranslateFlipContext__org_biojavax_bio_seq_
> RichFeature.getAnnotation()Lorg/biojavax/RichAnnotation;
> >        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >        at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
> >        at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorIm
> pl.java:25)
> >        at java.lang.reflect.Method.invoke(Method.java:585)
> >        at
> org.biojava.bio.seq.impl.TemplateUtils.populate(TemplateUtils.java:125)
> >        at
> org.biojava.bio.seq.impl.TemplateUtils.makeTemplate(TemplateUtils.java:135
> )
> >        at
> org.biojava.bio.seq.projection.ProjectedFeature.makeTemplate(ProjectedFeat
> ure.java:159)
> >        at
> org.biojavax.bio.seq.RichSequence$Tools.enrich(RichSequence.java:588)
> >
> > while enriching a sequence, which was actually a
> SequenceTools.subsequence of a RichSequence.
> >
> > I am not sure what to do with this error. Has someone any suggestion?
> >
> > George
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org<mailto:biojava-dev at lists.open-bio.org>
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
> > _______________________________________________
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> > biojava-dev at lists.open-bio.org
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> >
> 
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.