[Biojava-l] Re: the current discussion

Mark Schreiber mark_s@sanger.otago.ac.nz
Tue, 25 Jan 2000 09:26:20 +1300 (NZDT)

Good to see more code around. I should have mine up in a couple of days.
Probably most use will be the ever expanding CodonToolKit which implements
methods such as translate() backTranslate() calcCAI() calcRSCU() etc. It
is designed to be a sort of plug in.

On Sun, 23 Jan 2000, Mike Marsh wrote:

> My code is not yet javadoc'd.  And won't be before next weekend.  But you
> can have a look at a UML diagram of my protein classes.  It communicates a
> lot.  

Prehaps as a standard all classes should have atleast javadoc or better,
what do others think?
> On GUIS:  agree with most of what's been said.  Should definitely keep the
> GUI isolated from the implementation of the model, in accordance with
> Model-View-Contoller paradigm

I agree completely. But if people can design GUI's that can easily be used
with several packages or that fit really well with a package I think they
would be great. Things like a sequence viewer could fit with many
implementations of a sequence class. Also for those interested in HMMs I
have often thought it would be great to have a GUI that lets you perform
model surgery graphically. (Oh to have the time!)

> On String implementation of Sequences:
> Ewan says that the Sequence class should implement the internal data as a
> string.  I really have to disagree with this.  It makes much more sense to
> model the data structure like the real thing.  For example,
> ProteinSequence is a linear sequence of Amino Acids.  In my
> implementation, I do exactly this.  ProteinSequence is a linear list of
> Objects which implement ProteinChar interface.  The ProteinChar interface
> defines all of the state properties we have for amino acids (e.g. charge,
> aromaticity).  
> Because all of my ProteinChar objects are smart (i.e. they know their
> internal state), I can write some simple methods really easily.

This maybe a matter of person utility. For my work I have no need at the
moment for anything other than strings however those doing protein
modelling will benefit more from Mikes strategy. Lets have both! and
why not have some kind of class to convert between the two.

Mark Schreiber			Ph: 64 3 4797875
Rm 218				email mark_s@sanger.otago.ac.nz
Department of Biochemistry	email m.schreiber@clear.net.nz
University of Otago		
PO Box 56
New Zealand