[BioRuby] bioruby documentation

[Toshiaki Katayama]

Resend: as this message seems not delivered according to
http://open-bio.org/pipermail/bioruby/2006-March/date.html

-k


Ryan,

Thank you for your very nice doc.

On 2006/03/07, at 0:14, Ryan Raaum wrote:
>    #   s = Bio::Sequence::Generic.new('atggaatga')

If you will utilize this documentation, please change
this example to use Bio::Sequence::NA.

Bio::Sequence::Generic is just for developers - to hold
gaps, spaces etc. intact - mainly for multiple alignment.


In that sense, the following mail you send me personally
should be fixed as:


Begin forwarded message:
> From: Ryan Raaum <rlr215 at nyu.edu>
> Date: 2006年3月7日 0:47:32:JST
> To: Toshiaki Katayama <ktym at hgc.jp>
> Cc: jan aerts (RI) <jan.aerts at bbsrc.ac.uk>
> Subject: BioRuby Sequence Documentation Patch
>
> Hello,
>
> I have begun work on some documentation (as you may have seen from the messages on the mailing list just this morning).  Here is what I've done.  All methods and attributes in the Bio::Sequence hierarchy should be documented.  A summary for each file is yet to be written, but if this documentation is acceptable, I will write those after these are applied.  I made two small code changes as well:
>
> 1. Added a whitespace stripping initialize method to Bio::Sequence::Generic to make it consistent with Bio::Sequence::AA and Bio::Sequence::NA in that respect.


The Bio::Sequence::Generic is not intended to strip.

In addition to this, why you made Bio::Sequence#guess method as :nodoc: ?
Seuence type guessing is not perfect so there need to be an interface
to change threshold etc.

Most of other parts seems to be acceptable - you really understood
the behind ideas!

On March 1, Jan also sent me a documented version of sequence.rb.
I'm sorry that I should post it on the list as soon as possible.

Anyway, could you contact him to merge your documentations?
If both of you are agreed, I'll commit your patch.


> 2. Modified the instance randomize method to start at length 0 IF a composition hash is given.  Otherwise, if there was an actual sequence AND a hash was given, odd things would happen.  (Of course, it was never meant to be called that way, but... as it CAN be called that way, I thought the behavior should be consistent.)


Thanks!


> I am happy to make modifications to this documentation,
>
> Best wishes,
>
> Ryan Raaum
>
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