[BioRuby] Consensus sequence

[Naohisa GOTO]

Hi,

On Thu, 5 Aug 2010 09:28:04 +0900
Tomoaki NISHIYAMA <tomoakin at kenroku.kanazawa-u.ac.jp> wrote:

> Hi,
> 
> > 2) How can the count of the greatest residue (b[0][1]) be larger  
> > than or equal to the total number of residues?
> 
> 
> It is obvious that the count of the greatest residue is equal to the  
> total number of residues
> if all the residues are identical.
> 
> Presumably, the parameter threshold should be
> 0 <= threshold <= 1.0

In addition, the bahavior is undefined when the threshold is
out of the range.

> > 1) Why is it sorting? Shouldn't it use a linear search?

I forget what I was thinking when I wrote it in 2003.

> I really don't know.  So this is just my feeling,
> but this could be simplicity, readability, and extensibility...
> Did you compare the performance with linear search?

For simplicity and readability, using Enumerable#max (Array#max)
seems to be the straightforward way, though I don't know much
about the performance.

On Wed, 4 Aug 2010 15:32:02 -0400
James Keener <jimktrainslists at gmail.com> wrote:

> Also, there is a whole set of functions I am adding (group entropy and some book keeping/housecleaning things) and would like to commit them back.  What is the best way to commit them back?  

Please create your fork on GitHub and push them to the GitHub fork.

It seems http://github.com/fredrikj/bioruby also make some
modifications to the alignment classes (in lib/bio/appl/seala.rb
in the repository).

-- 
Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org