Extended Aho-Corasick algorithm capable of matching ambiguous amino acids in the pattern (i.e. proteins). More...

#include <OpenMS/ANALYSIS/ID/AhoCorasickAmbiguous.h>

Collaboration diagram for AhoCorasickAmbiguous:

Public Types
typedef ::seqan::StringSet<::seqan::AAString >	PeptideDB

typedef ::seqan::Pattern< PeptideDB, ::seqan::FuzzyAC >	FuzzyACPattern

Public Member Functions
	AhoCorasickAmbiguous ()
	Default Ctor; call setProtein() before using findNext(). More...

	AhoCorasickAmbiguous (const String &protein_sequence)
	Prepare to start searching for hits in a new protein sequence. More...

void	setProtein (const String &protein_sequence)
	Reset to new protein sequence. All previous data is forgotten. More...

bool	findNext (const FuzzyACPattern &pattern)
	Enumerate hits. More...

Size	getHitDBIndex ()
	Get index of hit into peptide database of the pattern. More...

Int	getHitProteinPosition ()
	Offset into protein sequence where hit was found. More...

Static Public Member Functions
static void	initPattern (const PeptideDB &pep_db, const int aaa_max, const int mm_max, FuzzyACPattern &pattern)
	Construct a trie from a set of peptide sequences (which are to be found in a protein). More...

Private Types
typedef FuzzyACPattern::KeyWordLengthType	KeyWordLengthType

Private Attributes
::seqan::Finder< seqan::AAString >	finder_
	locate the next peptide hit in protein More...

::seqan::AAString	protein_
	the protein sequence - we need to store it since the finder only keeps a pointer to protein when constructed More...

::seqan::PatternAuxData< PeptideDB >	dh_
	auxiliary data to hold a state after searching More...

Detailed Description

Extended Aho-Corasick algorithm capable of matching ambiguous amino acids in the pattern (i.e. proteins).

... Features: + blazingly fast + low memory usage + number of allowed ambAA's can be capped by user (default 3).

This implementation is based on the original AC in SeqAn.

Member Typedef Documentation

◆ FuzzyACPattern

typedef ::seqan::Pattern<PeptideDB, ::seqan::FuzzyAC> FuzzyACPattern

◆ KeyWordLengthType

typedef FuzzyACPattern::KeyWordLengthType KeyWordLengthType

private

◆ PeptideDB

typedef ::seqan::StringSet<::seqan::AAString> PeptideDB

Constructor & Destructor Documentation

◆ AhoCorasickAmbiguous() [1/2]

AhoCorasickAmbiguous ( )

inline

Default Ctor; call setProtein() before using findNext().

◆ AhoCorasickAmbiguous() [2/2]

AhoCorasickAmbiguous ( const String & protein_sequence )

inline

Prepare to start searching for hits in a new protein sequence.

This only sets the sequence. No computation is performed. Use findNext() to enumerate the hits.

Parameters

protein_sequence Sequence (ambiguous characters allowed)

References AhoCorasickAmbiguous::setProtein().

Member Function Documentation

◆ findNext()

bool findNext ( const FuzzyACPattern & pattern )

inline

Enumerate hits.

Parameters

pattern The pattern (i.e. trie) created with initPattern().

Returns: False if end of protein is reached. True if a hit is found.

References AhoCorasickAmbiguous::dh_, seqan::find(), and AhoCorasickAmbiguous::finder_.

Referenced by PeptideIndexing::addHits_().

◆ getHitDBIndex()

Size getHitDBIndex ( )

inline

Get index of hit into peptide database of the pattern.

Only valid if findNext() returned true before.

References AhoCorasickAmbiguous::dh_, and seqan::position().

Referenced by PeptideIndexing::addHits_().

◆ getHitProteinPosition()

Int getHitProteinPosition ( )

inline

Offset into protein sequence where hit was found.

Only valid if findNext() returned true before.

References AhoCorasickAmbiguous::finder_, and seqan::position().

Referenced by PeptideIndexing::addHits_().

◆ initPattern()

static void initPattern	(	const PeptideDB &	pep_db,
		const int	aaa_max,
		const int	mm_max,
		FuzzyACPattern &	pattern
	)

inlinestatic

Construct a trie from a set of peptide sequences (which are to be found in a protein).

Peptides must not contain ambiguous characters (exception thrown otherwise) or unknown characters (such as J or U). Ambiguous characters are only allowed in protein sequences.

Usage: Build the pattern only once and use it multiple times when running findNext().

Parameters

pep_db	Set of peptides
aaa_max	Maximum allowed ambiguous characters in the matching protein sequence
mm_max	Maximum allowed mismatches in the matching protein sequence
pattern	The pattern to be created

Exceptions

Exception::InvalidValue if a peptide contains an unknown (U,J,...) or ambiguous character

Referenced by PeptideIndexing::run().