[Biojava-dev] Biojava3-Core

Wed May 12 11:04:30 UTC 2010

i was a netbeans die-hard until i had to delve into the perl ensembl-api.........
where eclipse certainly wins over emacs :)

> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org 
> [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of 
> Andy Yates
> Sent: 12 May 2010 11:59
> To: Scooter Willis
> Cc: LAW Andrew; biojava-dev at lists.open-bio.org
> Subject: Re: [Biojava-dev] Biojava3-Core
> 
> I'll still be an Eclipse boy at heart; after all it's where 
> my Perl editor with working debugger lives
> 
> On 12 May 2010, at 11:58, Scooter Willis wrote:
> 
> > You will never go back to the dark side once you see the light!
> > 
> > Sent from G1
> > 
> > -----Original Message-----
> > From: Andy Yates [ayates at ebi.ac.uk]
> > Received: 5/12/10 6:46 AM
> > To: LAW Andrew [andy.law at roslin.ed.ac.uk]
> > CC: Scooter Willis [HWillis at scripps.edu]; 
> > biojava-dev at lists.open-bio.org [biojava-dev at lists.open-bio.org]
> > Subject: Re: [Biojava-dev] Biojava3-Core
> > 
> > 
> > I'm an Eclipse man but I'm more than happy to switch to 
> Netbeans for BioJava.
> > 
> > On 12 May 2010, at 11:23, LAW Andrew wrote:
> > 
> > > We use NetBeans too.
> > >
> > > And I *like* the NetBeans conventions :o}
> > >
> > >
> > > On 12 May 2010, at 11:17, Scooter Willis wrote:
> > >
> > >> Using the default netbeans profile. I will extract the 
> details. If I am the only netbeans user then I can use 
> eclipse setup if you provide details. The only thing that I 
> have a personal preference for is using a full line versus 
> breaking a method call into multiple lines. I understand the 
> need for short lines in a VI world.
> > >>
> > >> Scooter
> > >>
> > >> Sent from G1
> > >>
> > >> -----Original Message-----
> > >> From: Andy Yates [ayates at ebi.ac.uk]
> > >> Received: 5/12/10 5:10 AM
> > >> To: Scooter Willis [HWillis at scripps.edu]
> > >> CC: biojava-dev at lists.open-bio.org 
> [biojava-dev at lists.open-bio.org]
> > >> Subject: Re: [Biojava-dev] Biojava3-Core
> > >>
> > >>
> > >>
> > >> One thing as a co-contributor that I've noticed is there 
> is a difference in coding style. I'm happy to adopt any 
> coding style the majority agree with but I'd rather not do a 
> huge commit changing 2 spaced tabs into 4 spaced tabs :). Can 
> you send around your netbeans coding profile?
> > >>
> > >> Andy
> > >>
> > >> On 12 May 2010, at 02:39, Scooter Willis wrote:
> > >>
> > >>>
> > >>> I just committed a fairly significant number of changes 
> into BioJava3-core. If you don't have any code changes in 
> core then probably better to delete the core package and 
> check out again o avoid resolving lots of conflicts.
> > >>>
> > >>> I also checked in the beginning of biojava3-genome 
> which makes significant use of biojava3-core. The code is 
> being used to take gene predictions from GeneMarkHMM, GeneID 
> and GeneMark which all have their own version of gff, gff3 
> and gtf output. The code will take features from the 
> predictions and maps them onto DNASequences and allows you to 
> get ProteinSequence for each prediction. It is very much a 
> work in progress and will be adding additional features in 
> the next 30 days for a gene annotation project that is part 
> of the day job.
> > >>>
> > >>> Let me know if you have any comments or suggestions. I 
> promise better java docs, test cases and wiki overview soon.
> > >>>
> > >>> Scooter
> > >>> _______________________________________________
> > >>> biojava-dev mailing list
> > >>> biojava-dev at lists.open-bio.org
> > >>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > >>
> > >> --
> > >> Andrew Yates                   Ensembl Genomes Engineer
> > >> EMBL-EBI                       Tel: +44-(0)1223-492538
> > >> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> > >> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> > >>
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
> > >> biojava-dev mailing list
> > >> biojava-dev at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > >
> > > Later,
> > >
> > > Andy
> > > --------
> > > Yada, yada, yada...
> > > The University of Edinburgh is a charitable body, registered in 
> > > Scotland, with registration number SC005336
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> > >
> > >
> > > --
> > > The University of Edinburgh is a charitable body, registered in 
> > > Scotland, with registration number SC005336.
> > >
> > >
> > > _______________________________________________
> > > biojava-dev mailing list
> > > biojava-dev at lists.open-bio.org
> > > http://lists.open-bio.org/mailman/listinfo/biojava-dev
> > 
> > --
> > Andrew Yates                   Ensembl Genomes Engineer
> > EMBL-EBI                       Tel: +44-(0)1223-492538
> > Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> > Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> > 
> > 
> > 
> > 
> > 
> 
> -- 
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 
> 
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> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 
-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.