[Biojava-dev] AbstractMethodError while enriching a sequence

[Richard Holland]

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(DelegatingMethodAccessorImpl.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(ProjectedFeature.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
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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.eaglegenomics.com/