A container class for a set of strings.
StringSet<TString, TSpec>
The string type.
Types: String
The specializing type for the StringSet.
Metafunctions: Spec
Default: Generous.
DependentA string set storing references of the strings.
OwnerA string set storing the strings as members.
SAValueThe default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.
appendValueAppends a value to a container.
assignValueByIdAdds a new string to the StringSet and returns an id.
clearResets an object.
completeProfileConcatenates the background frequency with the profile for the motif component.
convertPatternToProfileConverts a pattern into a profile which consists of a set of frequency distributions.
convertSetOfPatternsToProfileConverts a set of sequence patterns into a profile.
createCountArrayBuilds an index on a StringSet storing how often a q-gram occurs in each sequence.
determineConsensusSeqDetermines the consensus pattern of a given profile.
displayDisplays a given set of strings.
emRepresents the EM algorithm as used by MEME.
findMotifRepresents the main function which is used to start the search for noticeable motif patterns.
getValueByIdRetrieves a string from the StringSet given an id.
globalAlignmentComputes the best global alignment of the two sequences.
idToPositionRetrieves the position of a string in the StringSet given an id.
lengthThe number of items/characters.
localAlignmentComputes the best local alignment of two sequences.
matchRefinementRefines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping.
normalizeDetermines the normalized frequencies.
positionToIdRetrieves the id of a string in the StringSet given a position.
removeValueByIdRemoves a string from the StringSet given an id.
resizeChanges the length.
stringSetLimitsRetrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
subsetCreates a subset of a given StringSet.
valueReference to the value.
valueByIdRetrieves a string from the StringSet given an id.
Include Headers
SeqAn - Sequence Analysis Library -