Class Specialization
Dependent
A string set storing references of the strings.
StringSet
Dependent
StringSet<TString, Dependent<TSpec> >
Parameters
TString
The string type.
Types: String
TSpec
The specializing type for the dependent string set.
Remarks: Possible values are Tight or Generous
Tight is very space efficient whereas Generous provides fast access to the strings in the container via ids.
Specialization of
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)
beginThe begin of a container. (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)
endThe end of a container. (StringSet)
expectationComputes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet)
findMotifRepresents the main function which is used to start the search for noticeable motif patterns. (StringSet)
generateSequenceGenerates random state and alphabet sequences of a given HMM. (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)
iterIterator to item at given position. (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. Refines (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)
multiLocalAlignmentComputes multiple local alignments of two sequences. (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)
valueReference to the value. (StringSet)
valueByIdRetrieves a string from the StringSet given an id. (StringSet)
varianceComputes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet)
zscoreComputes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet)
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