Re: [Seqan-dev] Time complexity of posGlobalize

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

On 28/07/11 12:26, Weese, David wrote:
> > I tend to look in the reference section of the documentation so I was 
> > here:
> > http://www.seqan.de/dddoc/html_devel/SPEC_Index_Esa.html
> >
> > I could see the definition
> > Index<TText, IndexEsa<> >
> >
> > but from this page I had no idea I could overload the SAValue, or 
> > indeed if I could whether it would be an argument to the IndexEsa 
> > template or to the Index template. Are you saying I need to 
> > specialise the metafunction SAValue to overload it for my index? 
> > Presumably this must be done in the seqan namespace? Is the SAValue 
> > for the index not a template argument to Index?
>
> Metafunctions shall not only be used by a user to determine a type of 
> a function or data structure. They are as well defining the types of 
> data structures, i.e. if you change the return type of a metafunction 
> you can change the behaviour and the types of data structures in the 
> library. This is a bit different to the STL, where types are defined 
> in a trait structure - an additional template argument.
>
> Changing the return type of a metafunction is only possible for a type 
> which is more special than the default type (it was already 
> specialized for). Of course there is a SAValue specialization done for 
> all Index classes of the form Index<TText, TSpec> which returns the 
> SAValue<TText>::Type. To be more special you can either specialize for 
> TText or TSpec. The example in my last mail did the latter. You will 
> find the list of metafunctions specialized for a certain type under 
> "Metafunction" on its documentation page.
>
> Yes, the specialization needs to be done in the seqan namespace. 
> SAValue is not an argument of the Index as there are many more 
> metafunctions (see Fibre, DefaultIndexCreator, ...) would blow the 
> interface. We intentionally left a single extra argument (TSpec) open 
> for enhancements. If you want to create a specialized index you can 
> define your own struct (MyIndex in the example) and give it as TSpec. 
> You can then change the behaviour of your index by specializing only 
> the types/tags you want to change like SAValue, Fibre, ... Just like 
> you would do it for functions in OOP.
OK, so if I've understood correctly I think the following should work. 
I'm trying to set up a ESA that uses a SAValue of type unsigned. I get a 
load of compile errors about No match for ‘getValueI2(unsigned int)’. 
Can you let me know what I'm doing wrong or if this is not possible.

#include <seqan/index.h>
#include <seqan/sequence.h>

using namespace seqan;

struct global {};

// specialise for our index
namespace seqan {

template< typename TText >
struct SAValue< Index< TText, IndexEsa< global > > >
{
typedef unsigned Type;
};

} // namespace seqan



typedef String< Dna5 > string_t; ///< A string of Dna5.
typedef StringSet< string_t > string_set_t; ///< StringSet type.
typedef Index< string_set_t, IndexEsa< global > > index_t;

int
main( int argc, char * argv[] ) {

string_set_t sequences;
index_t index( sequences );
Iterator< index_t, TopDown<> >::Type it( index );

return 0;
}