[Biojava-l] Parsing Code for Phylogenetic Trees

[Emig, Robin]

	Speaking as someone who started with pre1.0 biojava, I think you may
be changes with the following
Sequences (these were introduced close to the 1.1 release)
Gap symbols (I've been having problems with this implementation)
Alignments (When you create an alignment, is doesn't keep the order of the
sequences in the alignment because the current interface uses a
java.util.Map)
General parsing and converting to a String of symbol lists and symbols,
sequences. Matthew has been talking about changing the way this between 1.1
and 1.2.
	Having said that, even the changes that happened between pre1.0 and
1.1 were not too code obliterating, since the use of interfaces is
prevalent.

	However, It would be really great if you could mix and match
components of JalView in Biojava. ie if you have ever seen Vector NTI and
the way you can hide/rearrange the sequence view, the tree view, the plot
view etc. I would love it if jalview panes were generic enough to say create
an application which displays the alignment view and sequence logos, and the
messaging is generic enough that they could talk to eachother (ie I select a
position in the logo view and it selects it in the alignment view)
	I don't want take Jalview out of your hands, but I would love it if
all the code where in a cvs somewhere, where anyone who wanted to add to it
could. Esp if it gets biojava-sized, having a bunch of biojava people able
to add to it might be nice.
-Robin

-----Original Message-----
From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]On
Behalf Of Michele Clamp
Sent: Wednesday, March 14, 2001 3:35 PM
To: Emig, Robin
Cc: 'biojava-l@biojava.org'
Subject: RE: [Biojava-l] Parsing Code for Phylogenetic Trees


On Tue, 13 Mar 2001, Emig, Robin wrote:

>	Sounds good to me. Anyone else think a new version of Jalview would
>be a great show peice for Biojava?
>-Robin

I've been wanting to do this for a couple of years now.  Can I ask how
stable the code is? I've been burnt before when I used ensembl code for a
project and am now stuck with maintaining a year old version of it as
well as the latest one.

Myself and Steve Searle (from the EBI) are hacking away at jalview at the
moment.  Mostly its putting get/sets and interfaces in and moving the
event model to 1.1 (yes it was written that long ago :).  

M


-- 
And so as the stripey-winged owl's genome of Fate 
is decoded by the great sequencer of Time,
and as the big grep of Eternity uses all the cpu of Destiny
I come to the end of the mail.



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