[Biojava-dev] DNASequence not being a bean

[PATERSON Trevor]

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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