From gwaldon at geneinfinity.org  Tue Mar  3 00:27:55 2009
From: gwaldon at geneinfinity.org (gwaldon at geneinfinity.org)
Date: Tue, 03 Mar 2009 00:27:55 -0500
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090303052755.87019.qmail@mxw1102.verio-web.com>

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

From markjschreiber at gmail.com  Tue Mar  3 00:41:55 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 3 Mar 2009 13:41:55 +0800
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <93b45ca50903022139t2bc140e6k450db574f127c037@mail.gmail.com>
References: <20090303052755.87019.qmail@mxw1102.verio-web.com>
	<93b45ca50903022139t2bc140e6k450db574f127c037@mail.gmail.com>
Message-ID: <93b45ca50903022141o51c5a590h765f34006739049c@mail.gmail.com>

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

From gwaldon at geneinfinity.org  Tue Mar 10 02:13:42 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 10 Mar 2009 02:13:42 -0400
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090310061342.30095.qmail@mxw1102.verio-web.com>

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
_______________________________________________
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


From holland at eaglegenomics.com  Tue Mar 10 12:09:00 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 11 Mar 2009 00:09:00 +0800
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <20090310061342.30095.qmail@mxw1102.verio-web.com>
References: <20090310061342.30095.qmail@mxw1102.verio-web.com>
Message-ID: <49B6909C.7020803@eaglegenomics.com>

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
> _______________________________________________
> 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.eaglegenomics.com/

From gwaldon at geneinfinity.org  Tue Mar 10 17:17:33 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 10 Mar 2009 17:17:33 -0400
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090310211733.4546.qmail@mxw1102.verio-web.com>

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.

From andreas at sdsc.edu  Tue Mar 10 20:23:14 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 11 Mar 2009 00:23:14 +0000
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <20090310211733.4546.qmail@mxw1102.verio-web.com>
References: <20090310211733.4546.qmail@mxw1102.verio-web.com>
Message-ID: <59a41c430903101723r572b12d2xf0eb6a13413f8408@mail.gmail.com>

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
>


From mark.schreiber at novartis.com  Tue Mar 10 22:20:12 2009
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 11 Mar 2009 10:20:12 +0800
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <59a41c430903101723r572b12d2xf0eb6a13413f8408@mail.gmail.com>
Message-ID: <OFCFE00D62.83C2FF66-ON48257576.000CA58A-48257576.000CD650@ah.novartis.com>

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

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From gwaldon at geneinfinity.org  Wed Mar 11 02:06:03 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Wed, 11 Mar 2009 02:06:03 -0400
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090311060603.45334.qmail@mxw1102.verio-web.com>

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
>> >
>> 
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>>
>http://lists.open-bio.org/mailman/listinfo/biojava-
>dev
>
>_________________________
>
>CONFIDENTIALITY NOTICE
>
>The information contained in this e-mail message is
>intended only for the 
>exclusive use of the individual or entity named
>above and may contain 
>information that is privileged, confidential or
>exempt from disclosure 
>under applicable law. If the reader of this message
>is not the intended 
>recipient, or the employee or agent responsible for
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>message to the intended recipient, you are hereby
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From gwaldon at geneinfinity.org  Tue Mar 17 00:50:09 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 17 Mar 2009 00:50:09 -0400
Subject: [Biojava-dev] New method getRichAnnotation  in RichAnnotable
Message-ID: <20090317045009.50515.qmail@mxw1102.verio-web.com>

Hi all,

I just committed the new method getRichAnnotation returning RichAnnotation in RichAnnotatable. The interfaces RichFeature, BioEntry, CrossRef are consequently modified; make sure to adjust your code if necessary.

Thanks,
George Waldon

From bugzilla-daemon at portal.open-bio.org  Mon Mar 23 10:56:49 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 23 Mar 2009 10:56:49 -0400
Subject: [Biojava-dev] [Bug 2797] New:
	./tests/org/biojava/utils/process/AllTests.java is licenced
	under the GPL. Does it have consequences?
Message-ID: <bug-2797-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2797

           Summary: ./tests/org/biojava/utils/process/AllTests.java is
                    licenced under the GPL. Does it have consequences?
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Others
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: charles-debian-nospam at plessy.org


Dear BioJava developers,

first of all, the good news: BioJava is now available in the Debian operating
system: http://packages.debian.org/search?keywords=biojava

During the packaging, we realised that one of the distributed files,
./tests/org/biojava/utils/process/AllTests.java, is not licenced under the
LGPL, but under the GPL. I am unsure of how this file is used. In the "worst"
case, it would turn the whole BioJava under the GPL (as the LGPL allows
relicensing to the GPL). Can you clarify ?

Best regards,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

From bugzilla-daemon at portal.open-bio.org  Mon Mar 23 11:10:07 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 23 Mar 2009 11:10:07 -0400
Subject: [Biojava-dev] [Bug 2797]
	./tests/org/biojava/utils/process/AllTests.java is licenced
	under the GPL. Does it have consequences?
In-Reply-To: <bug-2797-485@http.bugzilla.open-bio.org/>
Message-ID: <200903231510.n2NFA70D002829@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2797


andreas at sdsc.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from andreas at sdsc.edu  2009-03-23 11:10 EST -------
This is a misleading header file. All of BioJava has been published under LGPL
for many years. As such I fixed the file header to provide the standard BioJava
LGPL text.

Andreas


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
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From holland at eaglegenomics.com  Tue Mar 24 06:56:18 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 24 Mar 2009 10:56:18 +0000
Subject: [Biojava-dev] Leadership
Message-ID: <49C8BC52.6010207@eaglegenomics.com>

A while back I indicated privately that I no longer really have the time
to dedicate to properly running and managing the BioJava project.
Recently Andreas Prlic has been doing a fantastic job in performing the
most important tasks such as monitoring bugzilla and making releases,
which has helped mask my absence.

Ideally I'd like to hand over to someone who can find time to put in
place a proper management structure with several people who each have
specific responsibilities, including someone who can create and sustain
a long-term vision and plan for the project (specifically completing
BioJava 3 based on the building blocks and example code that are already
in place). Whether that someone ends up leading the project or not I
don't think is relevant - what's relevant is that they can construct the
appropriate management structure and find the right people to do the
right jobs.

Would anyone like to volunteer? I'm asking the whole of biojava-dev in
the hope that this list reaches all our current contributors and
interested parties.

I think the best way to do this is to collect nominations, then place it
to the vote. Please email nominations to me by 31st March.

thanks,
Richard

-- 
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/

From andreas at sdsc.edu  Wed Mar 25 02:56:00 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Mar 2009 23:56:00 -0700
Subject: [Biojava-dev] Leadership
In-Reply-To: <49C8BC52.6010207@eaglegenomics.com>
References: <49C8BC52.6010207@eaglegenomics.com>
Message-ID: <59a41c430903242356m6fff07c8wec34fae203a12efb@mail.gmail.com>

Hi Richard,

Just to take this opportunity to say thanks for your BioJava
contributions in the last years. I understand you will not be gone
completely and you are just scaling back, right?

Andreas

On Tue, Mar 24, 2009 at 3:56 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> A while back I indicated privately that I no longer really have the time
> to dedicate to properly running and managing the BioJava project.
> Recently Andreas Prlic has been doing a fantastic job in performing the
> most important tasks such as monitoring bugzilla and making releases,
> which has helped mask my absence.
>
> Ideally I'd like to hand over to someone who can find time to put in
> place a proper management structure with several people who each have
> specific responsibilities, including someone who can create and sustain
> a long-term vision and plan for the project (specifically completing
> BioJava 3 based on the building blocks and example code that are already
> in place). Whether that someone ends up leading the project or not I
> don't think is relevant - what's relevant is that they can construct the
> appropriate management structure and find the right people to do the
> right jobs.
>
> Would anyone like to volunteer? I'm asking the whole of biojava-dev in
> the hope that this list reaches all our current contributors and
> interested parties.
>
> I think the best way to do this is to collect nominations, then place it
> to the vote. Please email nominations to me by 31st March.
>
> thanks,
> Richard
>
> --
> 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/
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

From holland at eaglegenomics.com  Wed Mar 25 04:45:23 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 25 Mar 2009 08:45:23 +0000
Subject: [Biojava-dev] Leadership
In-Reply-To: <59a41c430903242356m6fff07c8wec34fae203a12efb@mail.gmail.com>
References: <49C8BC52.6010207@eaglegenomics.com>
	<59a41c430903242356m6fff07c8wec34fae203a12efb@mail.gmail.com>
Message-ID: <49C9EF23.1010407@eaglegenomics.com>

That's right. I'll still code, contribute, bugfix, check, just I won't
be running the project per se.

Andreas Prlic wrote:
> Hi Richard,
> 
> Just to take this opportunity to say thanks for your BioJava
> contributions in the last years. I understand you will not be gone
> completely and you are just scaling back, right?
> 
> Andreas
> 
> On Tue, Mar 24, 2009 at 3:56 AM, Richard Holland
> <holland at eaglegenomics.com> wrote:
>> A while back I indicated privately that I no longer really have the time
>> to dedicate to properly running and managing the BioJava project.
>> Recently Andreas Prlic has been doing a fantastic job in performing the
>> most important tasks such as monitoring bugzilla and making releases,
>> which has helped mask my absence.
>>
>> Ideally I'd like to hand over to someone who can find time to put in
>> place a proper management structure with several people who each have
>> specific responsibilities, including someone who can create and sustain
>> a long-term vision and plan for the project (specifically completing
>> BioJava 3 based on the building blocks and example code that are already
>> in place). Whether that someone ends up leading the project or not I
>> don't think is relevant - what's relevant is that they can construct the
>> appropriate management structure and find the right people to do the
>> right jobs.
>>
>> Would anyone like to volunteer? I'm asking the whole of biojava-dev in
>> the hope that this list reaches all our current contributors and
>> interested parties.
>>
>> I think the best way to do this is to collect nominations, then place it
>> to the vote. Please email nominations to me by 31st March.
>>
>> thanks,
>> Richard
>>
>> --
>> 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/
>> _______________________________________________
>> 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.eaglegenomics.com/

From tallpaulinjax at yahoo.com  Fri Mar 27 11:52:45 2009
From: tallpaulinjax at yahoo.com (tallpaulinjax at yahoo.com)
Date: Fri, 27 Mar 2009 08:52:45 -0700 (PDT)
Subject: [Biojava-dev] Why is the Residue Number a String?
Message-ID: <603308.38301.qm@web30704.mail.mud.yahoo.com>


Hi,
?
I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
String residueNumber = line.substring(22,27).trim();
which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
?
Thanks!
?
Paul

From james at carmanconsulting.com  Fri Mar 27 12:05:03 2009
From: james at carmanconsulting.com (James Carman)
Date: Fri, 27 Mar 2009 12:05:03 -0400
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <603308.38301.qm@web30704.mail.mud.yahoo.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
Message-ID: <f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com>

Why would residueName's getter/setter be named getResidueNumber() and
setResidueNumber()?  Wouldn't it be better to have the getter/setter
as getResidueName() and setResidueName() or change the field to
residueNumber?

On Fri, Mar 27, 2009 at 11:52 AM,  <tallpaulinjax at yahoo.com> wrote:
>
> Hi,
>
> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
> String residueNumber = line.substring(22,27).trim();
> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>
> Thanks!
>
> Paul
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From andreas at sdsc.edu  Fri Mar 27 12:11:06 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 27 Mar 2009 09:11:06 -0700
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <603308.38301.qm@web30704.mail.mud.yahoo.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
Message-ID: <59a41c430903270911x6163f803u66146b2bc8996722@mail.gmail.com>

Hi Paul,

The reason is a simple one: Every amino acid in a PDB file is
identified uniquely by 3 things: The chain ID, the residue number and
the insertion code. To make sure one does not forget about the
insertion code, in BJ it is appended to the residue number.

To add to this, residue numbers can be negative, non-consecutive and
also non-sequential. As such it is often easiest, to treat them as
public identifiers and within your own code work with  the internal
atom or group positions...

Andreas



On Fri, Mar 27, 2009 at 8:52 AM,  <tallpaulinjax at yahoo.com> wrote:
>
> Hi,
>
> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
> String residueNumber = line.substring(22,27).trim();
> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>
> Thanks!
>
> Paul
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From james at carmanconsulting.com  Fri Mar 27 12:36:08 2009
From: james at carmanconsulting.com (James Carman)
Date: Fri, 27 Mar 2009 12:36:08 -0400
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <59a41c430903270931m298cff69ped6378298869a11@mail.gmail.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
	<f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com> 
	<59a41c430903270931m298cff69ped6378298869a11@mail.gmail.com>
Message-ID: <f2e8eedf0903270936p79d036bfnbfa0d7cdb32efd59@mail.gmail.com>

I assumed that.  My point was that the field name should match the
getter/setter name. :)

On Fri, Mar 27, 2009 at 12:31 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
> Hi James,
>
> Just to clarify, the names for the methods currently used in BJ are:
>
> group.getPDBCode() gives you the number + insertion code
> group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"
>
> If people think that these names are not clear, we can of course
> deprecate them and come up with more descriptive ones...
>
> Andreas
>
>
>
> On Fri, Mar 27, 2009 at 9:05 AM, James Carman
> <james at carmanconsulting.com> wrote:
>> Why would residueName's getter/setter be named getResidueNumber() and
>> setResidueNumber()? ?Wouldn't it be better to have the getter/setter
>> as getResidueName() and setResidueName() or change the field to
>> residueNumber?
>>
>> On Fri, Mar 27, 2009 at 11:52 AM, ?<tallpaulinjax at yahoo.com> wrote:
>>>
>>> Hi,
>>>
>>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>>> String residueNumber = line.substring(22,27).trim();
>>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>>
>>> Thanks!
>>>
>>> Paul
>>> _______________________________________________
>>> biojava-dev mailing list
>>> 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
>>
>


From andreas at sdsc.edu  Fri Mar 27 12:39:39 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 27 Mar 2009 09:39:39 -0700
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
	<f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com>
Message-ID: <59a41c430903270939g74fb1fdrd497237c62609e21@mail.gmail.com>

Hi James,

Just to clarify, the names for the methods currently used in BJ are:

group.getPDBCode() gives you the number + insertion code
group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"

If people think that these names are not clear, we can of course
deprecate them and come up with more descriptive ones...

Andreas


On Fri, Mar 27, 2009 at 9:05 AM, James Carman
<james at carmanconsulting.com> wrote:
> Why would residueName's getter/setter be named getResidueNumber() and
> setResidueNumber()? ?Wouldn't it be better to have the getter/setter
> as getResidueName() and setResidueName() or change the field to
> residueNumber?
>
> On Fri, Mar 27, 2009 at 11:52 AM, ?<tallpaulinjax at yahoo.com> wrote:
>>
>> Hi,
>>
>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>> String residueNumber = line.substring(22,27).trim();
>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>
>> Thanks!
>>
>> Paul
>> _______________________________________________
>> biojava-dev mailing list
>> 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
>


From tallpaulinjax at yahoo.com  Fri Mar 27 12:58:14 2009
From: tallpaulinjax at yahoo.com (Paul B)
Date: Fri, 27 Mar 2009 09:58:14 -0700 (PDT)
Subject: [Biojava-dev] Why is the Residue Number a String?
Message-ID: <389232.69110.qm@web30708.mail.mud.yahoo.com>

Ahhh! Gotcha! I hadn't even noticed the insertion code. Now I see you have included it in the substring() call. 

--- On Fri, 3/27/09, Andreas Prlic <andreas at sdsc.edu> wrote:


From: Andreas Prlic <andreas at sdsc.edu>
Subject: Re: [Biojava-dev] Why is the Residue Number a String?
To: tallpaulinjax at yahoo.com
Cc: biojava-dev at lists.open-bio.org
Date: Friday, March 27, 2009, 12:11 PM


Hi Paul,

The reason is a simple one: Every amino acid in a PDB file is
identified uniquely by 3 things: The chain ID, the residue number and
the insertion code. To make sure one does not forget about the
insertion code, in BJ it is appended to the residue number.

To add to this, residue numbers can be negative, non-consecutive and
also non-sequential. As such it is often easiest, to treat them as
public identifiers and within your own code work with? the internal
atom or group positions...

Andreas



On Fri, Mar 27, 2009 at 8:52 AM,? <tallpaulinjax at yahoo.com> wrote:
>
> Hi,
>
> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
> String residueNumber = line.substring(22,27).trim();
> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>
> Thanks!
>
> Paul
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From tallpaulinjax at yahoo.com  Fri Mar 27 13:19:25 2009
From: tallpaulinjax at yahoo.com (tallpaulinjax at yahoo.com)
Date: Fri, 27 Mar 2009 10:19:25 -0700 (PDT)
Subject: [Biojava-dev] Why is the Residue Number a String?
Message-ID: <539525.43639.qm@web30701.mail.mud.yahoo.com>



Andreas, that is actually confusing on my part, not James' part (I assume).?That might be perfectly clear to everyone else! I'm not asking that you change on my account. :-) However, if it stays the same perhaps you could add your explanation on the chain, residueNumber, and insertion code into the javaddocs? As well as what the getPDBCode() and getPDBName return?
?
James, sorry I had a typo in my original email on the field name, getter and setter.

--- On Fri, 3/27/09, Andreas Prlic <andreas.prlic at gmail.com> wrote:


From: Andreas Prlic <andreas.prlic at gmail.com>
Subject: Re: [Biojava-dev] Why is the Residue Number a String?
To: "James Carman" <james at carmanconsulting.com>
Cc: tallpaulinjax at yahoo.com, biojava-dev at lists.open-bio.org
Date: Friday, March 27, 2009, 12:31 PM


Hi James,

Just to clarify, the names for the methods currently used in BJ are:

group.getPDBCode() gives you the number + insertion code
group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"

If people think that these names are not clear, we can of course
deprecate them and come up with more descriptive ones...

Andreas



On Fri, Mar 27, 2009 at 9:05 AM, James Carman
<james at carmanconsulting.com> wrote:
> Why would residueName's getter/setter be named getResidueNumber() and
> setResidueNumber()? ?Wouldn't it be better to have the getter/setter
> as getResidueName() and setResidueName() or change the field to
> residueNumber?
>
> On Fri, Mar 27, 2009 at 11:52 AM, ?<tallpaulinjax at yahoo.com> wrote:
>>
>> Hi,
>>
>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>> String residueNumber = line.substring(22,27).trim();
>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>
>> Thanks!
>>
>> Paul
>> _______________________________________________
>> biojava-dev mailing list
>> 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
>


From valmik.desai at gmail.com  Sat Mar 28 16:14:45 2009
From: valmik.desai at gmail.com (Valmik Desai)
Date: Sat, 28 Mar 2009 16:14:45 -0400
Subject: [Biojava-dev] GEO data parsers
Message-ID: <dc22cb0903281314x3a5ee857g67c97767e92590df@mail.gmail.com>

Greetings!
I was wondering if GEO data parsers are already developed in BioJava?
http://www.biojava.org/wiki/BioJava_3_Use_Cases
I would like to contribute to it's development/testing.
Thanks,
Valmik

From gwaldon at geneinfinity.org  Tue Mar  3 05:27:55 2009
From: gwaldon at geneinfinity.org (gwaldon at geneinfinity.org)
Date: Tue, 03 Mar 2009 00:27:55 -0500
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090303052755.87019.qmail@mxw1102.verio-web.com>

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


From markjschreiber at gmail.com  Tue Mar  3 05:41:55 2009
From: markjschreiber at gmail.com (Mark Schreiber)
Date: Tue, 3 Mar 2009 13:41:55 +0800
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <93b45ca50903022139t2bc140e6k450db574f127c037@mail.gmail.com>
References: <20090303052755.87019.qmail@mxw1102.verio-web.com>
	<93b45ca50903022139t2bc140e6k450db574f127c037@mail.gmail.com>
Message-ID: <93b45ca50903022141o51c5a590h765f34006739049c@mail.gmail.com>

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


From gwaldon at geneinfinity.org  Tue Mar 10 06:13:42 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 10 Mar 2009 02:13:42 -0400
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090310061342.30095.qmail@mxw1102.verio-web.com>

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
_______________________________________________
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



From holland at eaglegenomics.com  Tue Mar 10 16:09:00 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 11 Mar 2009 00:09:00 +0800
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <20090310061342.30095.qmail@mxw1102.verio-web.com>
References: <20090310061342.30095.qmail@mxw1102.verio-web.com>
Message-ID: <49B6909C.7020803@eaglegenomics.com>

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
> _______________________________________________
> 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.eaglegenomics.com/


From gwaldon at geneinfinity.org  Tue Mar 10 21:17:33 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 10 Mar 2009 17:17:33 -0400
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090310211733.4546.qmail@mxw1102.verio-web.com>

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.


From andreas at sdsc.edu  Wed Mar 11 00:23:14 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Wed, 11 Mar 2009 00:23:14 +0000
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <20090310211733.4546.qmail@mxw1102.verio-web.com>
References: <20090310211733.4546.qmail@mxw1102.verio-web.com>
Message-ID: <59a41c430903101723r572b12d2xf0eb6a13413f8408@mail.gmail.com>

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
>



From mark.schreiber at novartis.com  Wed Mar 11 02:20:12 2009
From: mark.schreiber at novartis.com (mark.schreiber at novartis.com)
Date: Wed, 11 Mar 2009 10:20:12 +0800
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
In-Reply-To: <59a41c430903101723r572b12d2xf0eb6a13413f8408@mail.gmail.com>
Message-ID: <OFCFE00D62.83C2FF66-ON48257576.000CA58A-48257576.000CD650@ah.novartis.com>

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

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From gwaldon at geneinfinity.org  Wed Mar 11 06:06:03 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Wed, 11 Mar 2009 02:06:03 -0400
Subject: [Biojava-dev] AbstractMethodError while enriching a sequence
Message-ID: <20090311060603.45334.qmail@mxw1102.verio-web.com>

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
>> >
>> 
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>>
>http://lists.open-bio.org/mailman/listinfo/biojava-
>dev
>
>_________________________
>
>CONFIDENTIALITY NOTICE
>
>The information contained in this e-mail message is
>intended only for the 
>exclusive use of the individual or entity named
>above and may contain 
>information that is privileged, confidential or
>exempt from disclosure 
>under applicable law. If the reader of this message
>is not the intended 
>recipient, or the employee or agent responsible for
>delivery of the 
>message to the intended recipient, you are hereby
>notified that any 
>dissemination, distribution or copying of this
>communication is strictly 
>prohibited. If you have received this communication
>in error, please 
>notify the sender immediately by e-mail and delete
>the material from any 
>computer.  Thank you.


From gwaldon at geneinfinity.org  Tue Mar 17 04:50:09 2009
From: gwaldon at geneinfinity.org (George Waldon)
Date: Tue, 17 Mar 2009 00:50:09 -0400
Subject: [Biojava-dev] New method getRichAnnotation  in RichAnnotable
Message-ID: <20090317045009.50515.qmail@mxw1102.verio-web.com>

Hi all,

I just committed the new method getRichAnnotation returning RichAnnotation in RichAnnotatable. The interfaces RichFeature, BioEntry, CrossRef are consequently modified; make sure to adjust your code if necessary.

Thanks,
George Waldon


From bugzilla-daemon at portal.open-bio.org  Mon Mar 23 14:56:49 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 23 Mar 2009 10:56:49 -0400
Subject: [Biojava-dev] [Bug 2797] New:
	./tests/org/biojava/utils/process/AllTests.java is licenced
	under the GPL. Does it have consequences?
Message-ID: <bug-2797-485@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2797

           Summary: ./tests/org/biojava/utils/process/AllTests.java is
                    licenced under the GPL. Does it have consequences?
           Product: BioJava
           Version: live (CVS source)
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Others
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: charles-debian-nospam at plessy.org


Dear BioJava developers,

first of all, the good news: BioJava is now available in the Debian operating
system: http://packages.debian.org/search?keywords=biojava

During the packaging, we realised that one of the distributed files,
./tests/org/biojava/utils/process/AllTests.java, is not licenced under the
LGPL, but under the GPL. I am unsure of how this file is used. In the "worst"
case, it would turn the whole BioJava under the GPL (as the LGPL allows
relicensing to the GPL). Can you clarify ?

Best regards,

-- 
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.


From bugzilla-daemon at portal.open-bio.org  Mon Mar 23 15:10:07 2009
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 23 Mar 2009 11:10:07 -0400
Subject: [Biojava-dev] [Bug 2797]
	./tests/org/biojava/utils/process/AllTests.java is licenced
	under the GPL. Does it have consequences?
In-Reply-To: <bug-2797-485@http.bugzilla.open-bio.org/>
Message-ID: <200903231510.n2NFA70D002829@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2797


andreas at sdsc.edu changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #1 from andreas at sdsc.edu  2009-03-23 11:10 EST -------
This is a misleading header file. All of BioJava has been published under LGPL
for many years. As such I fixed the file header to provide the standard BioJava
LGPL text.

Andreas


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From holland at eaglegenomics.com  Tue Mar 24 10:56:18 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Tue, 24 Mar 2009 10:56:18 +0000
Subject: [Biojava-dev] Leadership
Message-ID: <49C8BC52.6010207@eaglegenomics.com>

A while back I indicated privately that I no longer really have the time
to dedicate to properly running and managing the BioJava project.
Recently Andreas Prlic has been doing a fantastic job in performing the
most important tasks such as monitoring bugzilla and making releases,
which has helped mask my absence.

Ideally I'd like to hand over to someone who can find time to put in
place a proper management structure with several people who each have
specific responsibilities, including someone who can create and sustain
a long-term vision and plan for the project (specifically completing
BioJava 3 based on the building blocks and example code that are already
in place). Whether that someone ends up leading the project or not I
don't think is relevant - what's relevant is that they can construct the
appropriate management structure and find the right people to do the
right jobs.

Would anyone like to volunteer? I'm asking the whole of biojava-dev in
the hope that this list reaches all our current contributors and
interested parties.

I think the best way to do this is to collect nominations, then place it
to the vote. Please email nominations to me by 31st March.

thanks,
Richard

-- 
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/


From andreas at sdsc.edu  Wed Mar 25 06:56:00 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Tue, 24 Mar 2009 23:56:00 -0700
Subject: [Biojava-dev] Leadership
In-Reply-To: <49C8BC52.6010207@eaglegenomics.com>
References: <49C8BC52.6010207@eaglegenomics.com>
Message-ID: <59a41c430903242356m6fff07c8wec34fae203a12efb@mail.gmail.com>

Hi Richard,

Just to take this opportunity to say thanks for your BioJava
contributions in the last years. I understand you will not be gone
completely and you are just scaling back, right?

Andreas

On Tue, Mar 24, 2009 at 3:56 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> A while back I indicated privately that I no longer really have the time
> to dedicate to properly running and managing the BioJava project.
> Recently Andreas Prlic has been doing a fantastic job in performing the
> most important tasks such as monitoring bugzilla and making releases,
> which has helped mask my absence.
>
> Ideally I'd like to hand over to someone who can find time to put in
> place a proper management structure with several people who each have
> specific responsibilities, including someone who can create and sustain
> a long-term vision and plan for the project (specifically completing
> BioJava 3 based on the building blocks and example code that are already
> in place). Whether that someone ends up leading the project or not I
> don't think is relevant - what's relevant is that they can construct the
> appropriate management structure and find the right people to do the
> right jobs.
>
> Would anyone like to volunteer? I'm asking the whole of biojava-dev in
> the hope that this list reaches all our current contributors and
> interested parties.
>
> I think the best way to do this is to collect nominations, then place it
> to the vote. Please email nominations to me by 31st March.
>
> thanks,
> Richard
>
> --
> 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/
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>


From holland at eaglegenomics.com  Wed Mar 25 08:45:23 2009
From: holland at eaglegenomics.com (Richard Holland)
Date: Wed, 25 Mar 2009 08:45:23 +0000
Subject: [Biojava-dev] Leadership
In-Reply-To: <59a41c430903242356m6fff07c8wec34fae203a12efb@mail.gmail.com>
References: <49C8BC52.6010207@eaglegenomics.com>
	<59a41c430903242356m6fff07c8wec34fae203a12efb@mail.gmail.com>
Message-ID: <49C9EF23.1010407@eaglegenomics.com>

That's right. I'll still code, contribute, bugfix, check, just I won't
be running the project per se.

Andreas Prlic wrote:
> Hi Richard,
> 
> Just to take this opportunity to say thanks for your BioJava
> contributions in the last years. I understand you will not be gone
> completely and you are just scaling back, right?
> 
> Andreas
> 
> On Tue, Mar 24, 2009 at 3:56 AM, Richard Holland
> <holland at eaglegenomics.com> wrote:
>> A while back I indicated privately that I no longer really have the time
>> to dedicate to properly running and managing the BioJava project.
>> Recently Andreas Prlic has been doing a fantastic job in performing the
>> most important tasks such as monitoring bugzilla and making releases,
>> which has helped mask my absence.
>>
>> Ideally I'd like to hand over to someone who can find time to put in
>> place a proper management structure with several people who each have
>> specific responsibilities, including someone who can create and sustain
>> a long-term vision and plan for the project (specifically completing
>> BioJava 3 based on the building blocks and example code that are already
>> in place). Whether that someone ends up leading the project or not I
>> don't think is relevant - what's relevant is that they can construct the
>> appropriate management structure and find the right people to do the
>> right jobs.
>>
>> Would anyone like to volunteer? I'm asking the whole of biojava-dev in
>> the hope that this list reaches all our current contributors and
>> interested parties.
>>
>> I think the best way to do this is to collect nominations, then place it
>> to the vote. Please email nominations to me by 31st March.
>>
>> thanks,
>> Richard
>>
>> --
>> 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/
>> _______________________________________________
>> 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.eaglegenomics.com/


From tallpaulinjax at yahoo.com  Fri Mar 27 15:52:45 2009
From: tallpaulinjax at yahoo.com (tallpaulinjax at yahoo.com)
Date: Fri, 27 Mar 2009 08:52:45 -0700 (PDT)
Subject: [Biojava-dev] Why is the Residue Number a String?
Message-ID: <603308.38301.qm@web30704.mail.mud.yahoo.com>


Hi,
?
I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
String residueNumber = line.substring(22,27).trim();
which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
?
Thanks!
?
Paul


From james at carmanconsulting.com  Fri Mar 27 16:05:03 2009
From: james at carmanconsulting.com (James Carman)
Date: Fri, 27 Mar 2009 12:05:03 -0400
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <603308.38301.qm@web30704.mail.mud.yahoo.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
Message-ID: <f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com>

Why would residueName's getter/setter be named getResidueNumber() and
setResidueNumber()?  Wouldn't it be better to have the getter/setter
as getResidueName() and setResidueName() or change the field to
residueNumber?

On Fri, Mar 27, 2009 at 11:52 AM,  <tallpaulinjax at yahoo.com> wrote:
>
> Hi,
>
> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
> String residueNumber = line.substring(22,27).trim();
> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>
> Thanks!
>
> Paul
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



From andreas at sdsc.edu  Fri Mar 27 16:11:06 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 27 Mar 2009 09:11:06 -0700
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <603308.38301.qm@web30704.mail.mud.yahoo.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
Message-ID: <59a41c430903270911x6163f803u66146b2bc8996722@mail.gmail.com>

Hi Paul,

The reason is a simple one: Every amino acid in a PDB file is
identified uniquely by 3 things: The chain ID, the residue number and
the insertion code. To make sure one does not forget about the
insertion code, in BJ it is appended to the residue number.

To add to this, residue numbers can be negative, non-consecutive and
also non-sequential. As such it is often easiest, to treat them as
public identifiers and within your own code work with  the internal
atom or group positions...

Andreas



On Fri, Mar 27, 2009 at 8:52 AM,  <tallpaulinjax at yahoo.com> wrote:
>
> Hi,
>
> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
> String residueNumber = line.substring(22,27).trim();
> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>
> Thanks!
>
> Paul
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



From james at carmanconsulting.com  Fri Mar 27 16:36:08 2009
From: james at carmanconsulting.com (James Carman)
Date: Fri, 27 Mar 2009 12:36:08 -0400
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <59a41c430903270931m298cff69ped6378298869a11@mail.gmail.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
	<f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com> 
	<59a41c430903270931m298cff69ped6378298869a11@mail.gmail.com>
Message-ID: <f2e8eedf0903270936p79d036bfnbfa0d7cdb32efd59@mail.gmail.com>

I assumed that.  My point was that the field name should match the
getter/setter name. :)

On Fri, Mar 27, 2009 at 12:31 PM, Andreas Prlic <andreas.prlic at gmail.com> wrote:
> Hi James,
>
> Just to clarify, the names for the methods currently used in BJ are:
>
> group.getPDBCode() gives you the number + insertion code
> group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"
>
> If people think that these names are not clear, we can of course
> deprecate them and come up with more descriptive ones...
>
> Andreas
>
>
>
> On Fri, Mar 27, 2009 at 9:05 AM, James Carman
> <james at carmanconsulting.com> wrote:
>> Why would residueName's getter/setter be named getResidueNumber() and
>> setResidueNumber()? ?Wouldn't it be better to have the getter/setter
>> as getResidueName() and setResidueName() or change the field to
>> residueNumber?
>>
>> On Fri, Mar 27, 2009 at 11:52 AM, ?<tallpaulinjax at yahoo.com> wrote:
>>>
>>> Hi,
>>>
>>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>>> String residueNumber = line.substring(22,27).trim();
>>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>>
>>> Thanks!
>>>
>>> Paul
>>> _______________________________________________
>>> biojava-dev mailing list
>>> 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
>>
>



From andreas at sdsc.edu  Fri Mar 27 16:39:39 2009
From: andreas at sdsc.edu (Andreas Prlic)
Date: Fri, 27 Mar 2009 09:39:39 -0700
Subject: [Biojava-dev] Why is the Residue Number a String?
In-Reply-To: <f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com>
References: <603308.38301.qm@web30704.mail.mud.yahoo.com>
	<f2e8eedf0903270905q4916dc9ema3e562b899a679aa@mail.gmail.com>
Message-ID: <59a41c430903270939g74fb1fdrd497237c62609e21@mail.gmail.com>

Hi James,

Just to clarify, the names for the methods currently used in BJ are:

group.getPDBCode() gives you the number + insertion code
group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"

If people think that these names are not clear, we can of course
deprecate them and come up with more descriptive ones...

Andreas


On Fri, Mar 27, 2009 at 9:05 AM, James Carman
<james at carmanconsulting.com> wrote:
> Why would residueName's getter/setter be named getResidueNumber() and
> setResidueNumber()? ?Wouldn't it be better to have the getter/setter
> as getResidueName() and setResidueName() or change the field to
> residueNumber?
>
> On Fri, Mar 27, 2009 at 11:52 AM, ?<tallpaulinjax at yahoo.com> wrote:
>>
>> Hi,
>>
>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>> String residueNumber = line.substring(22,27).trim();
>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>
>> Thanks!
>>
>> Paul
>> _______________________________________________
>> biojava-dev mailing list
>> 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
>



From tallpaulinjax at yahoo.com  Fri Mar 27 16:58:14 2009
From: tallpaulinjax at yahoo.com (Paul B)
Date: Fri, 27 Mar 2009 09:58:14 -0700 (PDT)
Subject: [Biojava-dev] Why is the Residue Number a String?
Message-ID: <389232.69110.qm@web30708.mail.mud.yahoo.com>

Ahhh! Gotcha! I hadn't even noticed the insertion code. Now I see you have included it in the substring() call. 

--- On Fri, 3/27/09, Andreas Prlic <andreas at sdsc.edu> wrote:


From: Andreas Prlic <andreas at sdsc.edu>
Subject: Re: [Biojava-dev] Why is the Residue Number a String?
To: tallpaulinjax at yahoo.com
Cc: biojava-dev at lists.open-bio.org
Date: Friday, March 27, 2009, 12:11 PM


Hi Paul,

The reason is a simple one: Every amino acid in a PDB file is
identified uniquely by 3 things: The chain ID, the residue number and
the insertion code. To make sure one does not forget about the
insertion code, in BJ it is appended to the residue number.

To add to this, residue numbers can be negative, non-consecutive and
also non-sequential. As such it is often easiest, to treat them as
public identifiers and within your own code work with? the internal
atom or group positions...

Andreas



On Fri, Mar 27, 2009 at 8:52 AM,? <tallpaulinjax at yahoo.com> wrote:
>
> Hi,
>
> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
> String residueNumber = line.substring(22,27).trim();
> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>
> Thanks!
>
> Paul
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>



From tallpaulinjax at yahoo.com  Fri Mar 27 17:19:25 2009
From: tallpaulinjax at yahoo.com (tallpaulinjax at yahoo.com)
Date: Fri, 27 Mar 2009 10:19:25 -0700 (PDT)
Subject: [Biojava-dev] Why is the Residue Number a String?
Message-ID: <539525.43639.qm@web30701.mail.mud.yahoo.com>



Andreas, that is actually confusing on my part, not James' part (I assume).?That might be perfectly clear to everyone else! I'm not asking that you change on my account. :-) However, if it stays the same perhaps you could add your explanation on the chain, residueNumber, and insertion code into the javaddocs? As well as what the getPDBCode() and getPDBName return?
?
James, sorry I had a typo in my original email on the field name, getter and setter.

--- On Fri, 3/27/09, Andreas Prlic <andreas.prlic at gmail.com> wrote:


From: Andreas Prlic <andreas.prlic at gmail.com>
Subject: Re: [Biojava-dev] Why is the Residue Number a String?
To: "James Carman" <james at carmanconsulting.com>
Cc: tallpaulinjax at yahoo.com, biojava-dev at lists.open-bio.org
Date: Friday, March 27, 2009, 12:31 PM


Hi James,

Just to clarify, the names for the methods currently used in BJ are:

group.getPDBCode() gives you the number + insertion code
group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"

If people think that these names are not clear, we can of course
deprecate them and come up with more descriptive ones...

Andreas



On Fri, Mar 27, 2009 at 9:05 AM, James Carman
<james at carmanconsulting.com> wrote:
> Why would residueName's getter/setter be named getResidueNumber() and
> setResidueNumber()? ?Wouldn't it be better to have the getter/setter
> as getResidueName() and setResidueName() or change the field to
> residueNumber?
>
> On Fri, Mar 27, 2009 at 11:52 AM, ?<tallpaulinjax at yahoo.com> wrote:
>>
>> Hi,
>>
>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>> String residueNumber = line.substring(22,27).trim();
>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>
>> Thanks!
>>
>> Paul
>> _______________________________________________
>> biojava-dev mailing list
>> 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
>



From valmik.desai at gmail.com  Sat Mar 28 20:14:45 2009
From: valmik.desai at gmail.com (Valmik Desai)
Date: Sat, 28 Mar 2009 16:14:45 -0400
Subject: [Biojava-dev] GEO data parsers
Message-ID: <dc22cb0903281314x3a5ee857g67c97767e92590df@mail.gmail.com>

Greetings!
I was wondering if GEO data parsers are already developed in BioJava?
http://www.biojava.org/wiki/BioJava_3_Use_Cases
I would like to contribute to it's development/testing.
Thanks,
Valmik