Class Specialization
Swift
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.
Include Headers
seqan/index.h
Parameters
A q-gram index of needle(s). Types: IndexQGram | |
Specifies the type of Swift filter. |
Specializations
The specialization for the general swift filter that finds epsilon matches between haystack and needle. | |
The specialization for the semi-global swift filter that finds regions of the haystack where a needle matches with an error rate less than ε. |
Metafunctions
Type of the container given an iterator. (Finder) | |
Type of an object that stores the difference between two iterators. (Finder) | |
Returns the haystack type of a Finder type. (Finder) | |
Type of the object a given object depends on. (Pattern) | |
Type of the object a given object depends on. (Pattern) | |
Type of iterator objects that are used to traverse the container. (Finder) | |
Returns the needle type of a Pattern type. (Pattern) | |
Returns the scoring scheme of an approximate searching algorithm. (Pattern) | |
Type of the items in the container. (Finder) |
Functions
The begin of a container. (Finder) | |
Begin position of object in host. (Finder) | |
Resets an object. (Finder) | |
The end of a container. (Finder) | |
End position of object in host. (Finder) | |
Search for a Pattern in a Finder object. (Pattern) | |
Search for a Pattern in a Finder object. (Pattern) | |
Search the begin of an approximate match. (Pattern) | |
Search the begin of an approximate match. (Pattern) | |
Returns the haystack of a Finder object. (Finder) | |
The object a given object depends on. (Pattern) | |
Creates infix object. | |
Creates infix object. | |
The number of items/characters. (Finder) | |
Returns the needle of a Pattern object (not implemented for some online-algorithms). (Pattern) | |
Position of an iterator. (Pattern) | |
Position of an iterator. (Pattern) | |
Returns a pair of the begin and end position in the haystack or needle for the last hit found. | |
Returns a pair of the begin and end position in the haystack or needle for the last hit found. | |
Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found. | |
Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found. | |
The scoring scheme used for finding or aligning. (Pattern) | |
Sets the haystack of a Finder object. (Finder) | |
Sets the needle of a Pattern object and optionally induces preprocessing. (Pattern) | |
Sets the scoring scheme used for finding or aligning. (Pattern) |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de