[Biojava-dev] AbstractMethodError while enriching a sequence

George Waldon gwaldon at geneinfinity.org
Wed Mar 11 06:06:03 UTC 2009 

Ok for 1.7. I'll advertise on this list when the commit is done, probably in a few days.

Thanks again,
George


>----- ------- Original Message ------- -----
>From: mark.schreiber at novartis.com
>To: Andreas Prlic <andreas at sdsc.edu>
>Sent: Wed, 11 Mar 2009 10:20:12
>
>Adding methods to an interface will break any
>previous implementation of 
>that interface because it will no longer comply. In
>this case I think it 
>is OK as 'upgrading' any implementation would be
>pretty easy.
>
>I would also agree that it should be done before
>1.7 as it is a 
>reoccurring problem and will take ages to enter
>into an official release.
>
>- Mark
>
>biojava-dev-bounces at lists.open-bio.org wrote on
>03/11/2009 08:23:14 AM:
>
>> 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 geneinfini
>ty.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/RichAnnota
>tion;
>> >> >        at
>sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>
>Method)
>> >> >        at
>> >> 
>sun.reflect.NativeMethodAccessorImpl.invoke(NativeM
>ethodAccessorImpl.java:
>> >> 39)
>> >> >        at
>> >> 
>sun.reflect.DelegatingMethodAccessorImpl.invoke(Del
>egatingMethodAccessorIm
>> >> pl.java:25)
>> >> >        at
>java.lang.reflect.Method.invoke(Method.java:585)
>> >> >        at
>> >> 
>org.biojava.bio.seq.impl.TemplateUtils.populate(Tem
>plateUtils.java:125)
>> >> >        at
>> >> 
>org.biojava.bio.seq.impl.TemplateUtils.makeTemplate
>(TemplateUtils.java:135
>> >> )
>> >> >        at
>> >> 
>org.biojava.bio.seq.projection.ProjectedFeature.mak
>eTemplate(ProjectedFeat
>> >> ure.java:159)
>> >> >        at
>> >>
>org.biojavax.bio.seq.RichSequence$Tools.enrich(Rich
>Sequence.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 l
>ists.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.
>> > _______________________________________________
>
>> > biojava-dev mailing list
>> > biojava-dev at lists.open-bio.org
>> >
>http://lists.open-bio.org/mailman/listinfo/biojava-
>dev
>> >
>> 
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>>
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>dev
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