Spec PigeonholePattern
Pigeonhole-based pattern. Must be used together with PigeonholeFinder.

Extends Pattern
All Extended Pattern
Defined in <seqan/index/find_pigeonhole.h>
Signature template <typename THaystack, typename TSpec> class Pattern<TIndex, Pigeonhole<TSpec> >;

Template Parameters

TSpec Specifies the type of pigeonhole filter.
TIndex A q-gram index of needle(s) that should be searched for. Types: IndexQGram

Interface Function Overview

Interface Functions Inherited From Pattern

Interface Metafunction Overview

Interface Metafunctions Inherited From Pattern

Member Variable Overview

Detailed Description

See PigeonholeFinder for more information on the algorithm.

See Also

Interface Functions Detail

TSize getMaxDeviationOfOrder(pattern);

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


pattern A PigeonholeFinder.


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.

void maskPatternSequence(pattern, seqNo, enable);


Disabling sequences in the pigeonhole filter requires the ONE_PER_DIAGONAL heuristic.

Mask and unmask pattern sequence.


pattern The PigeonholePattern to update.
seqNo Index of the sequence to disable/enable.
enable A bool that indicates whether hits are to be generated for the given sequence.

Member Variables Detail

PigeonholeParameters PigeonholePattern::parameters

The pigeonhole parameters to use for configuration.