Re: [Seqan-dev] Time complexity of posGlobalize

[John Reid <j.reid@mail.cryst.bbk.ac.uk>]

On 27/07/11 12:31, John Reid wrote:
> On 26/07/11 07:17, Weese, David wrote:
> > Hi John,
> >
> > posGlobalize needs in either case constant time. posLocalize takes 
> > constant time only for pairs. Otherwise (for global positions = 
> > integers) it takes O(m log m) where m is the number of sequences.
> > And yes, global positions help to save memory. But you can configure 
> > the type used in the position tables by overloading SAValue for your 
> > index. With Packed Pairs you specify the number of bits used for 
> > seqno and seqofs.
> That sounds interesting. I'm not quite sure where in the documentation 
> I should look to see what how I should overload SAValue. Is there 
> documentation on this?
I think I worked it out by trial and error:

Index< string_set_t, IndexEsa< Pair< unsigned int, unsigned int, 
BitCompressed< 17, 13 > > > >

seems to be doing the job. I would like to know if it is just that I 
don't understand how the docs work or whether it is missing from the 
docs. Quite often I can't find things in the docs.