[Biopython-dev] [biopython] pairwise2: Allow insertion after deletion and performance improvements (#782)

[PD Dr. Markus Piotrowski]

Dear Michiel,

I'm happy to work further on the module in the future. E.g. I think 
there are still some performance gains possible when using *score_only* 
(and I wonder if I will be able to implement Miller and Myers algorithm 
which works in linear space).
Also, some of the interesting parameters like *penalize_end_gaps* and 
*score_only* should really be mentioned in the doctest part.
I also agree that the user interface is quite unpythonic (I'm still not 
sure if I have understood how the decoding is going on...).
Regarding the cpairwise2module.c I have to say that this is the first 
time I coded in C (it took me 2 days to until I was able to compile it 
under Windows, with at least one day 
installing/de-installing/re-installing Microsofts Visual Studio), thus I 
tried to introduce as few changes as possible. Suggestions are very welcome.

Markus

Am 16.03.2016 um 05:41 schrieb mdehoon:
>
> @peterjc <https://github.com/peterjc> , @MarkusPiotrowski 
> <https://github.com/MarkusPiotrowski> : Thanks for your contribution.
> I think that the pairwise2 code has not had a dedicated maintainer 
> since 2005, and while we have done some maintenance on it in the past, 
> I don't think we currently have a real expert for this code among the 
> Biopython developers. So I would suggest to accept the changes by 
> @MarkusPiotrowski <https://github.com/MarkusPiotrowski> as is, as he 
> has looked at the code in much detail and is likely the most familiar 
> with the code now.
>
> I also think that the user interface to pairwise2 is rather 
> unpythonic, with arguments encoded in the function names, and it 
> currently lacks documentation. I would be in favor of a further 
> revision of this module (after accepting the current changes) to make 
> it more intuitive and pythonic to users. @MarkusPiotrowski 
> <https://github.com/MarkusPiotrowski> if you'd like to further revise 
> this module, let's discuss on the mailing list.
>
> The only comment on the submitted code is that some functions in 
> cpairwise2module.c (for example calc_affine_penalty) could be declared 
> static if they are not used outside of this file.
>
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