Class Specialization
Owner
A string set storing the strings as members.
StringSet<TString, Owner<> >
StringSet<TString, Owner<Default> >
Parameters
TString
The string type.
Types: String
Specialization of
Specializations
ConcatDirectA string set storing the concatenation of all strings within one string.
Metafunctions
SAValueThe default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. (StringSet)
Functions
appendValueAppends a value to a container. (StringSet)
assignValueByIdAdds a new string to the StringSet and returns an id. (StringSet)
clearResets an object. (StringSet)
completeProfileConcatenates the background frequency with the profile for the motif component. (StringSet)
convertPatternToProfileConverts a pattern into a profile which consists of a set of frequency distributions. (StringSet)
convertSetOfPatternsToProfileConverts a set of sequence patterns into a profile. (StringSet)
createCountArrayBuilds an index on a StringSet storing how often a q-gram occurs in each sequence. (StringSet)
determineConsensusSeqDetermines the consensus pattern of a given profile. (StringSet)
displayDisplays a given set of strings. (StringSet)
emRepresents the EM algorithm as used by MEME. (StringSet)
findMotifRepresents the main function which is used to start the search for noticeable motif patterns. (StringSet)
getValueByIdRetrieves a string from the StringSet given an id. (StringSet)
globalAlignmentComputes the best global alignment of the two sequences. (StringSet)
idToPositionRetrieves the position of a string in the StringSet given an id. (StringSet)
lengthThe number of items/characters. (StringSet)
localAlignmentComputes the best local alignment of two sequences. (StringSet)
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. (StringSet)
normalizeDetermines the normalized frequencies. (StringSet)
positionToIdRetrieves the id of a string in the StringSet given a position. (StringSet)
removeValueByIdRemoves a string from the StringSet given an id. (StringSet)
resizeChanges the length. (StringSet)
setStringsLoads the sequences of a stringset into an alignment. (StringSet)
stringSetLimitsRetrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. (StringSet)
subsetCreates a subset of a given StringSet. (StringSet)
valueReference to the value. (StringSet)
valueByIdRetrieves a string from the StringSet given an id. (StringSet)
Remarks
The strings are internally stored in a String<TString> object and the character position type is a Pair (seqNo,seqOfs) where seqNo identifies the string within the stringset and seqOfs identifies the position within this string.
The position type can be returned or modified by the meta-function SAValue called with the StringSet type.
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