Class
Pattern
Holds the needle and preprocessing data (depends on algorithm).

Pattern

AbndmAlgo | AhoCorasick | Backtracking | Bfam | BndmAlgo | DPSearch

Bfam<Oracle>
Bfam<Trie>

HammingSimpleFinder | Horspool | MultiBfam | MultipleShiftAnd | Myers | Pex

MultiBfam<Oracle>

Hierarchical
NonHierarchical

Pigeonhole | SetHorspool | ShiftAnd | ShiftOr | Simple Finder | Swift

SwiftLocal
SwiftSemiGlobal

WildShiftAnd | WuManber

Pattern<TNeedle[, TSpec]>
Include Headers
seqan/find.h
Parameters

TSpec | The online-algorithm to search with. Types: AbndmAlgo, AhoCorasick, Backtracking, Bfam, BndmAlgo, HammingSimpleFinder, Horspool, MultiBfam, MultipleShiftAnd, Myers, Pex, Pigeonhole, Score, SetHorspool, ShiftAnd, ShiftOr, Simple Finder, Swift, WildShiftAnd, WuManber Default: The result of DefaultPattern Remarks: Leave empty for index-based pattern matching (see Index).
TNeedle | The needle type. Types: String

Remarks
If TNeedle is a set of strings, then position(pattern) returns the index of the currently matching needle.
Member of
HammingSimpleFinder, BndmAlgo
Specializations

AbndmAlgo | Approximate Backward Nondeterministic Dawg Matching algorithm. Approximate string matching using bit parallelism.
AhoCorasick | Multiple exact string matching using Aho-Corasick.
Backtracking | Provides approximate string matching via backtracking on a substring index.
Bfam | Backward Factor Automaton Matching algorithm.
BndmAlgo | Backward Nondeterministic Dawg Matching algorithm. Exact string matching using bit parallelism.
DPSearch | A dynamic programming algorithm for approximate string-matching with a user-definable scoring function.
HammingSimpleFinder | A brute force online searching algorithm for approximate string matching with hamming distance.
Horspool | Exact string matching using Horspool's algorithm (1980).
MultiBfam | Multi-Pattern Backward Factor Automaton Matching.
MultipleShiftAnd | Multiple exact string matching using bit parallelism. The total size of the patterns should fit into a computer word.
Myers | Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick.
Pex | Provides a fast approximate string matching filter that splits the needle into several pieces that are searched with a multiple exact string matching algorithm and later verified.
Pigeonhole | Provides a fast filter alogrithm that uses the pigeonhole lemma, i.e. if a pattern matches with k errors in the text, every partition into k+1 parts contains one part that matches without error.
SetHorspool | Multiple exact string matching using set horspool algorithm.
ShiftAnd | Exact string matching using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
ShiftOr | Exact string matching using bit parallelism. The Shift-Or algorithm is applicable to search small patterns in texts using a small alphabet.
Simple Finder | A brute force online searching algorithm.
Swift | Provides a fast filter alogrithm that guarantees to find all regions overlapping with potential ε-matches. An ε-match is a matching region of minimal length and an error rate of at most ε.
WildShiftAnd | Exact string matching with wildcards using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet.
WuManber | Online-algorithm for multi-pattern search.

Metafunctions

Host | Type of the object a given object depends on.
Needle | Returns the needle type of a Pattern type.
ScoringScheme | Returns the scoring scheme of an approximate searching algorithm.

Functions

find | Search for a Pattern in a Finder object.
findBegin | Search the begin of an approximate match.
host | The object a given object depends on.
needle | Returns the needle of a Pattern object (not implemented for some online-algorithms).
position | Position of an iterator.
scoringScheme | The scoring scheme used for finding or aligning.
setNeedle | Sets the needle of a Pattern object and optionally induces preprocessing.
setScoringScheme | Sets the scoring scheme used for finding or aligning.

SeqAn - Sequence Analysis Library - www.seqan.de

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