[Biojava-dev] DNASequence not being a bean

[Andy Yates]

Let us know what you think as soon as possible and how you're going to proceed.

I'm going through the code later on today and will attempt to clean up all of these problems. I'm sorry but for the moment the SVN will be broken. My only fix for the meanwhile is to ignore the GC tests which is the ones which will probably be causing you the problems

Andy

On 12 May 2010, at 10:37, PATERSON Trevor wrote:

> 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
>> 
> -- 
> The University of Edinburgh is a charitable body, registered in
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-- 
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/