[BioRuby] restriction enzyme module

[Toshiaki Katayama]

Trevor,

Thank you for your reply.

> == 7 ==
>
>> And, you looks to have different strategies for RDoc documentation  
> on each file.
>> Which is the best practice?
>
> Thanks for catching a few mistakes of mine.  I think the README.DEV  
> is unclear or incorrect in how RDoc works in some circumstances.   
> This is something that I wanted to address in a larger document.   
> Since it seems like you're interested could you give me a few days to  
> put together a well thought-out guide for that, would that be okay?

Yes, please.

I'm not sure that the current README.DEV describes the best way
for RDoc documentation so if you could provide best practice,
I'm willing to wait for.

On 2007/04/05, at 6:48, Trevor Wennblom wrote:
> The only classes I'm primarily concerned about exposing and having  
> the API well documented at the moment are Bio::RestrictionEnzyme and  
> Bio::RestrictionEnzyme::Analysis which are both documented in the  
> Bio::RestrictionEnzyme RDoc. This could use some more examples and  
> I'm putting together improved documentation as Pjotr and I are using  
> this in some real-world tools.

I see.

> == 2 ==
> == 3 ==
> == 4 ==
> done

Thanks.

> == 5 ==
>
>> Why this empty class need to be present?
>
> Abstract base class - while not technically necessary I'm strongly in  
> favor of keeping it for clarity and further development.

OK.

> == 6 ==
>
>> Could you fold your RDoc documents less than 80 columns as long as  
> possible?
>> Or should I use larger terminal width...?
>
> Yes to both!  :D
>
> Sometimes I miss that since anytime I modify my comments I have to  
> reformat them to be 80 characters wide.  While I don't think it  
> should be a requirement, it is something that we should strive for -  
> perhaps a "strong suggestion."
>
>> Or should I use larger terminal width...?
>
> I use a mixture of TextMate and the terminal on OS X.  Just a quick  
> glance shows that I currently have terminals open with 147, 80, 175,  
> 230, and 122 columns wide.  I resize those little guys all the time.

I want to hear comments from others on this.

I have been used 'emacs -nw' on terminal sized 80x80 for long time
but now might be a time to resize it :)


> == 8 ==
>
>> def cut_with_enzyme(*args)
>>    Bio::RestrictionEnzyme::Analysis.cut(self, *args)
>> end
>> alias cut_with_enzymes cut_with_enzyme
>>
>> When do you plan to move this into lib/bio/sequence.rb?
>
> I wanted to get you're approval first.  Do you think that's the right  
> thing to do?  It would be nice since people wouldn't have to include  
> the analysis file directly.  Do you forsee any problems with me just  
> moving the four lines over to Bio::Sequence::NA?

As the restriction_enzyme/**/*.rb is autoloaded by default in the 
next release, there might be no problem to move this into Bio::Sequence::NA.

However, will it slow down the loading time?
When bio/sequence.rb is loaded, the above definition also loads
bio/restriction_enzyme.rb also? or the loading of bio/restriction_enzyme.rb
is delayed until the above method is called?


> == 9 ==
>
> Regarding to_re

I'll reply to the next mail.

Toshiaki