gatb.core-API-1.4.2
Model.hpp File Reference

Kmer management. More...

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.