[Biojava-dev] AbstractMethodError while enriching a sequence

[George Waldon]

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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