Class
Pattern
Holds the needle and preprocessing data (depends on algorithm).
Pattern | |
 | |
Include Headers
seqan/find.h
Parameters
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). | |
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
Specializations
| Approximate Backward Nondeterministic Dawg Matching algorithm. Approximate string matching using bit parallelism. | |
| Multiple exact string matching using Aho-Corasick. | |
| Provides approximate string matching via backtracking on a substring index. | |
| Backward Factor Automaton Matching algorithm. | |
| Backward Nondeterministic Dawg Matching algorithm. Exact string matching using bit parallelism. | |
| A dynamic programming algorithm for approximate string-matching with a user-definable scoring function. | |
| A brute force online searching algorithm for approximate string matching with hamming distance. | |
| Exact string matching using Horspool's algorithm (1980). | |
| Multi-Pattern Backward Factor Automaton Matching. | |
| Multiple exact string matching using bit parallelism. The total size of the patterns should fit into a computer word. | |
| Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick. | |
| 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. | |
| 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. | |
| Multiple exact string matching using set horspool algorithm. | |
| Exact string matching using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet. | |
| Exact string matching using bit parallelism. The Shift-Or algorithm is applicable to search small patterns in texts using a small alphabet. | |
| A brute force online searching algorithm. | |
| 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. | |
| Exact string matching with wildcards using bit parallelism. The Shift-And algorithm is applicable to search small patterns in texts using a small alphabet. | |
| Online-algorithm for multi-pattern search. |
Metafunctions
| Type of the object a given object depends on. | |
| Returns the needle type of a Pattern type. | |
| Returns the scoring scheme of an approximate searching algorithm. |
Functions
| Search for a Pattern in a Finder object. | |
| Search the begin of an approximate match. | |
| The object a given object depends on. | |
| Returns the needle of a Pattern object (not implemented for some online-algorithms). | |
| Position of an iterator. | |
| The scoring scheme used for finding or aligning. | |
| Sets the needle of a Pattern object and optionally induces preprocessing. | |
| Sets the scoring scheme used for finding or aligning. |
SeqAn - Sequence Analysis Library - www.seqan.de