[Biojava-l] Parsing Code for Phylogenetic Trees

[Phillip Lord]

>>>>> "Robin" == Emig, Robin <Robin.Emig@maxygen.com> writes:

  Robin>         However, It would be really great if you could mix
  Robin> and match components of JalView in Biojava. ie if you have
  Robin> ever seen Vector NTI and the way you can hide/rearrange the
  Robin> sequence view, the tree view, the plot view etc. I would love
  Robin> it if jalview panes were generic enough to say create an
  Robin> application which displays the alignment view and sequence
  Robin> logos, and the messaging is generic enough that they could
  Robin> talk to eachother 


        I sent a message to the biojava list yesterday but it appears
not to have got through. Apologies if the same thing gets through
twice. 

       I've been working on upgrading the Cinema alignment editor 
for a while now. It's been around for a while now, and we have ended
up re-writing it totally. It's now written in 1.2, and using the Swing
gui set. Its highly modular and the modules all communicate in an
event driven way. Tying together a sequence alignment view and a tree
view would be relatively trivial. We also have several generic Swing
gui components which we had to develop to get the thing working (most
importantly a JAlignmentViewer class). 

        At the moment it does not use biojava, but our own sequence
API. We found out about biojava after we had designed and done some
implementation of our API, but at the time biojava had only immutable
sequences which made it difficult to use for us. I have thought about
adding biojava support but have not got around to it yet.

       Anyway if people are interested the code is on the web. If
jalview is also being rewritten it seems likely that there will be
common code which could be used across the two apps, so feel free to
take a look.

     Phil

-- 
Phillip Lord,				Phone: +44 (0) 161 275 5980
PostDoctoral Research Associate,        Email: p.lord@hgmp.mrc.ac.uk
School of Biological Sciences,          http://www.bioinf.man.ac.uk/~lord/home.html
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The University of Manchester,
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