Spec
SwiftPatternPattern for SWIFT search, must be used together with SwiftFinder.
Pattern for SWIFT search, must be used together with SwiftFinder.
Extends | Pattern |
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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. |
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TIndex |
A q-gram index of needle(s). Types: IndexQGram |
Interface Function Overview
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TPosition beginPosition(pattern);
Returns the begin position of the local match in the pattern. -
TPosition endPosition(pattern);
Returns the end position of the local match in the pattern. -
TSize getMaxDeviationOfOrder(pattern);
Returns the maximal out-of-order distance of adjacent hits. -
TPair positionRange(pattern);
Returns a pair of the begin and end position in the haystack or needle for the last hit found. -
TPair positionRangeNoClip(pattern)
Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found. -
void setMinThreshold(pattern, seqNo, thresh);
Set minimal threshold (t) for a given needle.
Interface Functions Inherited From Pattern
Interface Metafunction Overview
Interface Metafunctions Inherited From Pattern
Member Variable Overview
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SwiftParameters SwiftPattern::parameters
The SWIFT parameters to use for configuration.
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. |
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Returns
TPosition |
The SA value of the pattern text. |
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Data Races
Thread safety unknown!
TPosition endPosition(pattern);
Returns the end position of the local match in the pattern.
Parameters
pattern
|
The SwiftPattern to query. |
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Returns
TPosition |
The SA value of the pattern text. |
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Data Races
Thread safety unknown!
TSize getMaxDeviationOfOrder(pattern);
Returns the maximal out-of-order distance of adjacent hits.
Parameters
pattern
|
A SwiftPattern. |
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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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Data Races
Thread safety unknown!
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. |
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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. |
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Data Races
Thread safety unknown!
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. |
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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. |
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Data Races
Thread safety unknown!
See Also
void setMinThreshold(pattern, seqNo, thresh);
Set minimal threshold (t) for a given needle.
Parameters
pattern
|
The SwiftPattern to modify. |
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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
Thread safety unknown!
Member Variables Detail
SwiftParameters SwiftPattern::parameters
The SWIFT parameters to use for configuration.