[Biojava-dev] DNASequence not being a bean

[Scooter Willis]

We are seeing some differences as well and andy yates is reviewing. The features package was moved to the genome module so not sure how package deletes get propogated to the different repositories.

Can you make calls to static methods with your database mapping tool? If so we can have a helper class return the classes without an empty constructor.

Sent from G1

-----Original Message-----
From: PATERSON Trevor [trevor.paterson at roslin.ed.ac.uk]
Received: 5/12/10 6:20 AM
To: biojava-dev at lists.open-bio.org [biojava-dev at lists.open-bio.org]
Subject: Re: [Biojava-dev] DNASequence not being a bean



Thanks for your comments and ideas...

I am mulling things over

in the meantime - i haven't been able to connect to the SVN for a while...... there seems to be something  wrong with open-bio connections, does it still allow anonymous connections?

I can get the code tarred up from github....but it is missing a module so won't compile

>>org/biojava3/core/sequence/DNATests.java:[13,33] package org.biojava3.core.features does not exist

trevor



> -----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 10:10
> To: Scooter Willis
> Cc: 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/
>
>
>
>
>
> _______________________________________________
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> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
--
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