[Biojava-dev] AbstractMethodError while enriching a sequence

Wed Mar 11 02:20:12 UTC 2009

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 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.
> > _______________________________________________
> > biojava-dev mailing list
> > biojava-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> >
> 
> _______________________________________________
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> http://lists.open-bio.org/mailman/listinfo/biojava-dev

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