[Biojava-dev] AbstractMethodError while enriching a sequence

[Andreas Prlic]

Can you commit it before this release? otherwise it will take ages
again before this change is part of the main code base...
adding methods should not brake anything...
Andreas

On Tue, Mar 10, 2009 at 9:17 PM, George Waldon <gwaldon at geneinfinity.org> wrote:
> 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
>> >
>> > _______________________________________________
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> >
>>
>> --
>> Richard Holland, BSc MBCS
>> Finance Director, Eagle Genomics Ltd
>> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
>> http://www.
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