Spec SwiftFinder
Finder for SWIFT search, must be used together with SwiftPattern.

Extends Finder
All Extended Finder
All Subcl's SwiftLocalFinder, SwiftSemiGlobalFinder
Defined in <seqan/index.h>
Signature template <typename THaystack, typename TSpec> class Finder<THaystack, Swift<TSpec> >;

Template Parameters

TSpec Specifies the type of Swift filter.
THaystack A haystack type. Types: Index, String, StringSet.

Member Function Overview

Member Functions Inherited From Finder

Interface Function Overview

Interface Functions Inherited From Finder

Member Typedef Overview

Interface Metafunction Overview

Interface Metafunctions Inherited From Finder

Detailed Description

See SwiftPattern for an overview of the SWIFT algorithm.

See Also

Interface Functions Detail

THitString getWindowFindHits(finder);

Returns the string of hits from the finder.

Parameters

finder A finder with window interface.

Returns

THitString String of hits, see THitString.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

TPair positionRange(finder);

Returns a pair of the begin and end position in the haystack or needle for the last hit found.

Parameters

finder A Finder object.

Returns

TPair A Pair of the begin and end position in the haystack or needle for the last hit found. The return type is Pair<typename SAValue<THost&g;::Type> if THost is the type of haystack or needle.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

TPair positionRangeNoClip(finder);

Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.

Parameters

finder A SwiftFinder object to query.

Returns

TPair A pair of the begin and end position in the haystack or needle for the last hit found. These positions could be negative or beyond the end of finder or pattern when using filter algorithms. The return type is Pair<typename SAValue<THost>::Type> if THost is the type of haystack or needle.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

bool windowFindBegin(finder, pattern, errorRate);

Initializes the pattern. Sets the finder on the begin position. Gets the first non-repeat range and sets it in the finder. Used together with windowFindEnd.

Parameters

finder A finder with window interface.
pattern A pattern with window interface. Types: SwiftPattern.
errorRate Error rate that is allowed between reads and reference. Should be the same in as in windowFindNext. Types: double

Returns

bool true if there were bases to be scanned and false otherwise.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

void windowFindEnd(finder, pattern);

Flushes the finder. Used together with windowFindBegin and windowFindNext.

Parameters

finder A finder with window interface.
pattern A pattern with window interface. Types: SwiftPattern

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

bool windowFindNext(finder, pattern, finderWindowLength)

Searches over the next window with the finder. The found hits can be retrieved with getWindowFindHits. Used together with windowFindBegin and windowFindEnd.

Parameters

finder A SwiftFinder.
pattern A SwiftPattern.
finderWindowLength Number of bases that are scanned beginning from the position the finder is at. Including bases that are marked as repeats and that are skipped. Types: nolink:unsigned int

Returns

bool true, if there are bases that can be scanned, false otherwise.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

See Also

Member Typedef Detail

typedef (...) SwiftFinder::THitString;

The type to use for the hit string returned in getWindowFindHits.