On Thu, Dec 20, 2001 at 01:33:33PM -0800, Brian King wrote:
>
> Thomas,
>
> Yes, we'd be happy to see the BioJava AGAVE conversion code in the BioJava
> CVS tree soon. Please do the initial checkin, and then let Hanning and
> myself have an account so we can update it.
I've just done the chec
t: Re: [Biojava-l] AGAVE IO in BioJava
On Thu, Dec 20, 2001 at 01:33:33PM -0800, Brian King wrote:
> Yes, we'd be happy to see the BioJava AGAVE conversion code in the BioJava
> CVS tree soon. Please do the initial checkin, and then let Hanning and
> myself have an account so we
On Thu, Dec 20, 2001 at 01:33:33PM -0800, Brian King wrote:
> Yes, we'd be happy to see the BioJava AGAVE conversion code in the BioJava
> CVS tree soon. Please do the initial checkin, and then let Hanning and
> myself have an account so we can update it.
Hi...
I've now merged your contributio
On Thu, 20 Dec 2001, Thomas Down wrote:
> On Thu, Dec 20, 2001 at 01:06:12PM -0800, Brian King wrote:
> >
> > Thomas,
> >
> > I attached the code for BioJava AGAVE XML conversion. The code is similar
> > to the GAME IO package. The zip file has an ANT build.xml file, and there
> > is a JUnit
ED]]
> Sent: Thursday, December 20, 2001 1:22 PM
> To: Brian King
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] AGAVE IO in BioJava
>
>
> On Thu, Dec 20, 2001 at 01:06:12PM -0800, Brian King wrote:
> >
> > Thomas,
> >
> > I attached
On Thu, Dec 20, 2001 at 01:06:12PM -0800, Brian King wrote:
>
> Thomas,
>
> I attached the code for BioJava AGAVE XML conversion. The code is similar
> to the GAME IO package. The zip file has an ANT build.xml file, and there
> is a JUnit unit test called TestAgaveHandler.java. The unit test
>>SeqIOListener interface works quite a lot like the SAX
>>ContentHandler: You do something like:
>>
>> startFeature(container)
>> startFeature(child1);
>> endFeature();
>> startFeature(child2);
>> endFeature();
>> endFeature();
Thanks.
On Wed, Sep 12, 2001 at 12:32:36PM -0700, Brian King wrote:
>
> We'd like to add IO support for the AGAVE XML format
> (http://www.agavexml.org) into the BioJava library. Creating the output
> code in a SequenceFormat seems straightforward, but I'm confused about
> input. AGAVE and BioJava have
We'd like to add IO support for the AGAVE XML format
(http://www.agavexml.org) into the BioJava library. Creating the output
code in a SequenceFormat seems straightforward, but I'm confused about
input. AGAVE and BioJava have hierarchies of features and hierarchies of
sequences to represent ass
