[Biojava-dev] Biojava3-Core

[Andy Yates]

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/