AhoCorasickAmbiguous.h File Reference

#include <OpenMS/CONCEPT/Macros.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <cassert>
#include <functional>
#include <limits>
#include <queue>
#include <string>
#include <unordered_map>
#include <vector>

Include dependency graph for AhoCorasickAmbiguous.h:

Go to the source code of this file.

Classes
struct	Hit
struct	AA
class	Index
struct	hash< OpenMS::Index >
struct	ACNode
struct	ACNode::DepthHits
	internal struct to steal one bit from depth to use as hit indicator More...
struct	ACSpawn
	a spin-off search path through the trie, which can deal with ambiguous AAs and mismatches More...
struct	ACTrieState
class	ACTrie
	An Aho Corasick trie (a set of nodes with suffix links mainly) More...

Namespaces
	OpenMS
	Main OpenMS namespace.

Functions
AA	nextValidAA (const std::string::const_iterator end, std::string::const_iterator &it_q)

Variables
constexpr char const	AAtoChar [28]
constexpr char const	CharToAA [128]
	Conversion table from 7-bit ASCII char to internal value representation for an amino acid (AA) More...