Spec
PigeonholePatternPigeonhole-based pattern. Must be used together with PigeonholeFinder.
Pigeonhole-based pattern. Must be used together with PigeonholeFinder.
Extends | Pattern |
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All Extended | Pattern |
Defined in | <seqan/index/find_pigeonhole.h> |
Signature |
template <typename THaystack, typename TSpec>
class Pattern<TIndex, Pigeonhole<TSpec> >;
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Template Parameters
TSpec |
Specifies the type of pigeonhole filter. |
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TIndex |
A q-gram index of needle(s) that should be searched for. Types: IndexQGram |
Interface Function Overview
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TSize getMaxDeviationOfOrder(pattern);
Returns the maximal out-of-order distance of adjacent hits. -
void maskPatternSequence(pattern, seqNo, enable);
Mask and unmask pattern sequence.
Interface Functions Inherited From Pattern
Interface Metafunction Overview
Interface Metafunctions Inherited From Pattern
Member Variable Overview
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PigeonholeParameters PigeonholePattern::parameters
The pigeonhole parameters to use for configuration.
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.
Parameters
pattern
|
A PigeonholeFinder. |
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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. |
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void maskPatternSequence(pattern, seqNo, enable);
Note.
Disabling sequences in the pigeonhole filter requires the ONE_PER_DIAGONAL heuristic.
Mask and unmask pattern sequence.
Parameters
pattern
|
The PigeonholePattern to update. |
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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.