Spec
SwiftFinderFinder for SWIFT search, must be used together with SwiftPattern.
Finder for SWIFT search, must be used together with SwiftPattern.
Extends | Finder |
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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. |
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THaystack |
A haystack type. Types: Index, String, StringSet. |
Interface Function Overview
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THitString getWindowFindHits(finder);
Returns the string of hits from the finder. -
TPair positionRange(finder);
Returns a pair of the begin and end position in the haystack or needle for the last hit found. -
TPair positionRangeNoClip(finder);
Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found. -
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. -
void windowFindEnd(finder, pattern);
Flushes the finder. Used together with windowFindBegin and windowFindNext. -
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.
Interface Functions Inherited From Finder
Member Typedef Overview
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typedef (...) SwiftFinder::THitString;
The type to use for the hit string returned in getWindowFindHits.
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. |
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Returns
THitString |
String of hits, see THitString. |
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Data Races
Thread safety unknown!
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. |
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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. |
---|
Data Races
Thread safety unknown!
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. |
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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
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. |
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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. |
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Data Races
Thread safety unknown!
See Also
void windowFindEnd(finder, pattern);
Flushes the finder. Used together with windowFindBegin and windowFindNext.
Parameters
finder
|
A finder with window interface. |
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pattern
|
A pattern with window interface. Types: SwiftPattern |
Data Races
Thread safety unknown!
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. |
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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. |
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Data Races
Thread safety unknown!
See Also
Member Typedef Detail
typedef (...) SwiftFinder::THitString;
The type to use for the hit string returned in getWindowFindHits.