DBGraph.hpp File Reference

#include <iostream>
#include "Integer.hpp"
#include <bitset>
#include <unordered_map>
#include <unordered_set>
#include <algo/gnomon/gnomon_model.hpp>
#include <atomic>

Include dependency graph for DBGraph.hpp:

Go to the source code of this file.

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Classes
class	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::find_kmer
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::reserve
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::container_size
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::container_capacity
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::element_size
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::clear
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::push_back
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::push_back_elements
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::merge_sorted
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::update_count
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::get_count
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::get_kmer_count
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::container_sort
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::swap_with_other
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::uniq
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::extract_uniq
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::save
struct	DeBruijn::CKmerCountTemplate< T1, T2, T3, T4, T5 >::load
class	DeBruijn::CKmerMapTemplate< T1, T2, T3, T4, T5, V >
struct	DeBruijn::CKmerMapTemplate< T1, T2, T3, T4, T5, V >::kmer_hash
struct	DeBruijn::CKmerMapTemplate< T1, T2, T3, T4, T5, V >::container_size
struct	DeBruijn::CKmerMapTemplate< T1, T2, T3, T4, T5, V >::reserve
struct	DeBruijn::CKmerMapTemplate< T1, T2, T3, T4, T5, V >::mapper
struct	DeBruijn::CKmerMapTemplate< T1, T2, T3, T4, T5, V >::find
struct	DeBruijn::SAtomic< T >
class	DeBruijn::CDBGraph
struct	DeBruijn::CDBGraph::Successor
class	DeBruijn::CReadHolder
class	DeBruijn::CReadHolder::kmer_iterator
class	DeBruijn::CReadHolder::string_iterator
class	DeBruijn::CDBGraphDigger
struct	DeBruijn::CDBGraphDigger::SElement
struct	DeBruijn::CDBGraphDigger::SContig

Namespaces
	DeBruijn

Typedefs
typedef CKmerCountTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 > >	DeBruijn::TKmerCount
template<typename V >
using	DeBruijn::TKmerMap = CKmerMapTemplate< LargeInt< 1 >, LargeInt< 2 >, LargeInt< 4 >, LargeInt< 8 >, LargeInt< 16 >, V >
typedef vector< pair< int, size_t > >	DeBruijn::TBins

Functions
	USING_SCOPE (gnomon)
	USING_SCOPE (boost)
	USING_SCOPE (std)
int	DeBruijn::FindValleyAndPeak (const TBins &bins, int rlimit)
pair< int, int >	DeBruijn::HistogramRange (const TBins &bins)

Variables
	USING_NCBI_SCOPE

Function Documentation

USING_SCOPE() [1/3]

USING_SCOPE

(

boost

)

USING_SCOPE() [2/3]

USING_SCOPE

(

gnomon

)

USING_SCOPE() [3/3]

USING_SCOPE

(

std

)

Variable Documentation

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 12 of file DBGraph.hpp.