[Bioperl-l] Bio::Tools::Seg: zero documentation

[Allen Smith]

On Sep 21,  5:12pm, Hilmar Lapp wrote:
> Hi Balamurugan, we appreciate your submission, but is it OK with you 
> to ask you to please add standard documentation and tests as soon as 
> possible?

Agreed - speaking of documentation, does anyone know of a good reference
source for the various matrix file formats in use? I have most of the alpha
coding of Bio::Matrix::Substitution done (not Bio::Matrix::SubstitutionI
yet, I'm afraid; the implementation/interface distinction in this particular 
case is rather unclear to me, at least), and am working on documentation and 
then tests (e.g., using some reasonably common matrix file formats - making
sure they can be read in properly, if at all possible).

> Confer other modules for examples about how to do that. We 
> also do have programming conventions posted at 
> http://www.bioperl.org/wiki/html/BioPerl/BioperlProgrammingConventions.html.

One nit in that regard:

	"* Create lists using '==over N / ==item / ==back syntax. Always add 
	the number of items as an argument to ==over."

The argument to '==over' is how far over one wishes indentation to take
place (although some formatters don't use this, and just add 8 spaces,
BTW). I'm afraid I can't see quite what the relationship is between this and 
the number of items.

> Seg.pm and Tmhmm.pm both have literally zero lines of documentation 
> or comment, it looks like they've been stripped of comments.

Urk!

	-Allen

-- 
Allen Smith			http://cesario.rutgers.edu/easmith/
September 11, 2001		A Day That Shall Live In Infamy II
"They that can give up essential liberty to obtain a little temporary
safety deserve neither liberty nor safety." - Benjamin Franklin