[Biojava-dev] JAXB plugin dependencies in sequence-blastxml module

[trevor paterson (RI)]

Personally I think that the code should be independent of any IDE quirks - not tailored to work with every possible IDE. As we know what the issue is and how to avoid it I think the dependency should be left as it is.

It looks like netbeans is supplying something equivalent to jaxb 2.0 which lacks the Marshaller.marshall(Object, File) method signature - found since version 2.1.  - the sequence-blastxml BlastXMLTYools object uses this convenience method.

Trevor Paterson PhD
new email trevor.paterson at roslin.ed.ac.uk

Bioinformatics 
The Roslin Institute
Edinburgh University
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-----Original Message-----
From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
Sent: 04 September 2009 22:50
To: trevor paterson (RI)
Cc: biojava-dev at biojava.org; andy law (RI)
Subject: Re: [Biojava-dev] JAXB plugin dependencies in sequence-blastxml module

Hi Trevor and Andy,

Thanks for the detailed feedback. To make sure nothing gets lost I
added a todo list to the wiki. Feel free to add other action items...
http://biojava.org/wiki/BioJava:MavenMigration

* I understand the jaxb problem is mainly related to netbeans. I think
we should support easy setup on all popular IDEs. Would it be of
advantage to change the dependency to a different jaxb package? Seems
there are many available...

Richard, do you as the module lead have an opinion which version of
jaxb to depend on? - I suppose you will say the latest... :-)

Andreas