Model.hpp File Reference

Kmer management. More...

#include <gatb/system/api/Exception.hpp>
#include <gatb/kmer/api/IModel.hpp>
#include <gatb/tools/collections/api/Bag.hpp>
#include <gatb/tools/designpattern/api/Iterator.hpp>
#include <gatb/tools/designpattern/impl/IteratorHelpers.hpp>
#include <gatb/tools/misc/api/Data.hpp>
#include <gatb/tools/misc/api/Abundance.hpp>
#include <gatb/tools/math/Integer.hpp>
#include <gatb/tools/storage/impl/Storage.hpp>
#include <vector>
#include <algorithm>
#include <iostream>
#include <bitset>

Include dependency graph for Model.hpp:

Classes
struct	Kmer< span >
	Entry point for kmer management. More...
class	Kmer< span >::ModelMinimizer< ModelType, Comparator >
	Model that handles kmers of the Model type + a minimizer. More...
class	Kmer< span >::KmerDirect
	Kmer type for the ModelDirect class. More...
class	Kmer< span >::KmerCanonical
	Kmer type for the ModelCanonical class. More...
class	Kmer< span >::KmerMinimizer< Model, Comparator >
	Kmer type for the ModelMinimizer class. More...
class	Kmer< span >::ModelAbstract< ModelImpl, T >
class	Kmer< span >::ModelDirect
	Model that handles "direct" kmers, ie sequences of nucleotides. The associated value of such a kmer is computed as a polynom P(X) with X=4 and where the coefficients are in [0..3]. By convention, we use A=0, C=1, T=2 and G=3. More...
class	Kmer< span >::ModelCanonical
	Model that handles "canonical" kmers, ie the minimum value of the direct kmer and its reverse complement. More...
class	Kmer< span >::ModelMinimizer< ModelType, Comparator >
	Model that handles kmers of the Model type + a minimizer. More...
struct	Kmer< span >::Count
	Structure associating a kmer value with an abundance value. More...

Namespaces
	gatb::core
	Core package of the GATP project.
	gatb::core::kmer
	Package for genomic databases management.
	gatb::core::kmer::impl
	Implementation for genomic databases management.

Macros
#define	KMER_SPAN(n)   (boost::mpl::at<gatb::core::tools::math::IntegerList, boost::mpl::int_<n> >::type::value)
#define	KMER_DEFAULT_SPAN   KMER_SPAN(0)

Detailed Description

Kmer management.

Date

01/03/2013

Author

edrezen

Macro Definition Documentation

#define KMER_DEFAULT_SPAN   KMER_SPAN(0)

We get the first value in the kmer size list.

#define KMER_SPAN

(

n

)

(boost::mpl::at<gatb::core::tools::math::IntegerList, boost::mpl::int_<n> >::type::value)

We get the nth defined kmer size.