Class Specialization
Myers
Provides fast approximate searching of one string in another using Myer's fast bit-parallel algorithm with application of the Ukkonen-trick.

Pattern

Myers

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

TNeedle | The needle type. Types: String
TSpec | Specialization tag. Default: Tag.FindInfix Remarks: This could be FindInfix for infix search or FindPrefix for prefix search.
TFindBeginPatternSpec | Specialization of Pattern used to find the begin of matches. Default: DefaultFindBeginPatternSpec Remarks: This must be a finder for prefix search, e.g. DPSearch<TScore, FindPrefix> or Myers<FindPrefix>. Specify void to suppress prefix searching.

Remarks
The needle-length must be smaller than the highest number that can be stored in an unsigned int.
Specialization of
Pattern
Metafunctions

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

Functions

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

Shortcuts

MyersUkkonen | Semin-global (query-global, text-local) pattern matching without findBegin() support.
MyersUkkonenBanded | Semin-global (query-global, text-local) pattern matching without findBegin() support.
MyersUkkonenGlobal | Global (query-global, text-global) pattern matching without findBegin() support.
MyersUkkonenGlobalBanded | global (query-global, text-global) pattern matching without findBegin() support.

See Also
FindInfix, MyersUkkonen, MyersUkkonenGlobal, MyersUkkonenBanded, MyersUkkonenGlobalBanded, FindPrefix
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:51