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

Extends Pattern
All Extended Pattern
All Subcl's SwiftLocalPattern, SwiftSemiGlobalPattern
Defined in <seqan/index.h>
Signature template <typename TIndex, typename TSpec> class Pattern<TIndex, Swift<TSpec> >;

Template Parameters

TSpec Specifies the type of Swift filter.
TIndex A q-gram index of needle(s). Types: IndexQGram

Interface Function Overview

Interface Functions Inherited From Pattern

Interface Metafunction Overview

Interface Metafunctions Inherited From Pattern

Member Variable Overview

Detailed Description

The Pattern must be a IndexQGram over multiple patterns. The allowed error rate must be given when find or windowFindBegin is called.

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.

See Also

Interface Functions Detail

TPosition beginPosition(pattern);

Returns the begin position of the local match in the pattern.

Parameters

pattern The SwiftPattern to query.

Returns

TPosition The SA value of the pattern text.

Data Races

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

TPosition endPosition(pattern);

Returns the end position of the local match in the pattern.

Parameters

pattern The SwiftPattern to query.

Returns

TPosition The SA value of the pattern text.

Data Races

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

TSize getMaxDeviationOfOrder(pattern);

Returns the maximal out-of-order distance of adjacent hits.

Parameters

pattern A SwiftPattern.

Returns

TSize Returns the maximal distance two adjacent hits can have which are not in increasing order. TSize is the size type of the underlying index.

Data Races

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

TPair positionRange(pattern);

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

Parameters

pattern A Pattern 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(pattern)

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

Parameters

pattern SwiftPattern 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

void setMinThreshold(pattern, seqNo, thresh);

Set minimal threshold (t) for a given needle.

Parameters

pattern The SwiftPattern to modify.
seqNo The number to set the threshold for.
tresh The threshold to use.

This function can be used to make the filter allow less errors for a given needle.

Data Races

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

Member Variables Detail

SwiftParameters SwiftPattern::parameters

The SWIFT parameters to use for configuration.