[Biococoa-dev] starting BCAlignment

Charles PARNOT charles.parnot at stanford.edu
Tue Mar 8 20:17:01 EST 2005

>I want to start with the BCAlignment stuff and there are many things to discuss:
>1. what exactly do we want an BCAlignment to be ?
>	A slim Datastructure for different Alignment algorithms
>	Or a comfortable datastructure, which is perhaps not very useful for programs concentrating on performance

In terms of design, we will probably need at least 2 types of classes, following the current structure of the project:
* some data objects with the results of alignement; I think there were some discussions about it before I joined, on what a sequence cluster might look like,...
* some tool objects that do the job

In the tools, you may have to transform the data structure for performance, if performance turns out to be an issue.

Now my 2 cents with maybe obvious things, but important to keep in mind.
It is probably a good idea to not focus too much on performance at first... and still leave some doors open for it, with some clean separation between the core functions and the rest. If you are familiar with Shark, it would be a good idea to use it after the first draft of your tools. If you are not familiar with it, it would still be a good idea!
I was just reading this piece today, linked from cocoadev.com, and it is a very interesting reading:

I suspect these considerations do not fully apply to scientific computing, where you can sometimes better predict performance bottleneck, but still, good reading.

>2. We need a BCMatrix (protocol or class) for substitution matrices
>3. A protocol for alignment generating algorithms
>5.. :-) i think it's enough for now

I am not an expert in alignments,  so I am listening to your ideas! Maybe you could present what you think the goals could be in more details, what kind of alignements you'd want to implement first, how far you want to go,...

You could also start putting some code, and I would look at it and make comments from the naive user's perspective. I am very good at making long emails with endless comments ;-)


Help science go fast forward:

Charles Parnot
charles.parnot at stanford.edu

Room  B157 in Beckman Center
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Stanford University
Stanford, CA 94305 (USA)

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