[BioRuby] bioruby documentation

[Toshiaki Katayama]

Ryan,

Thank you for your quick fix.
I quote your mail as it was not posted to the list.

> Also, in the last round of editing, I made a small change to the Bio::Sequence#guess function.

Thanks. This bug was introduced when I added length and index arguments...

Toshiaki


On 2006/03/08, at 0:56, Ryan Raaum wrote:

> Hi All,
>
>
>>
>> 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.
>>
>
> Done. (For this and all other examples using Bio::Sequence::Generic)
>
>> Bio::Sequence::Generic is just for developers - to hold
>> gaps, spaces etc. intact - mainly for multiple alignment.
>>
>
> Made Bio::Sequence::Generic :nodoc:
>
>>>
>>> 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.
>
> Removed the added method.
>
>>
>> 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.
>
> Documented the guess methods.
>
>> 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.
>
> If Jan will send me his sequence.rb, I can merge it with mine and send the merged file back to Jan.  After he's edited the merge to his liking, we can put it all together and send it in as a unified patch.
>
>
> Also, in the last round of editing, I made a small change to the Bio::Sequence#guess function.  In the line where the "total" is calculated, the original version used the length of the @seq as the starting length, but for the length and index parameters to work properly with the threshold value, the length of the guess string (`str` is the local method variable) is what should be the base length.
>
> Best,
>
> -Ryan
>