| Class StringSet A container class for a set of strings.
StringSet
Dependent | Owner
ConcatDirect
StringSet<TString, TSpec> Parameters
TString | The string type. Types: String
TSpec | The specializing type for the StringSet. Metafunctions: Spec Default: Generous.
Specializations
Dependent | A string set storing references of the strings.
Owner | A string set storing the strings as members.
Metafunctions
SAValue | The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.
Functions
appendValue | Appends a value to a container.
assignValueById | Adds a new string to the StringSet and returns an id.
begin | The begin of a container.
clear | Resets an object.
completeProfile | Concatenates the background frequency with the profile for the motif component.
convertPatternToProfile | Converts a pattern into a profile which consists of a set of frequency distributions.
convertSetOfPatternsToProfile | Converts a set of sequence patterns into a profile.
createCountArray | Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
determineConsensusSeq | Determines the consensus pattern of a given profile.
display | Displays a given set of strings.
em | Represents the EM algorithm as used by MEME.
end | The end of a container.
expectation | Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel
findMotif | Represents the main function which is used to start the search for noticeable motif patterns.
generateSequence | Generates random state and alphabet sequences of a given HMM.
getValueById | Retrieves a string from the StringSet given an id.
globalAlignment | Computes the best global alignment of the two sequences.
idToPosition | Retrieves the position of a string in the StringSet given an id.
iter | Iterator to item at given position.
length | The number of items/characters.
localAlignment | Computes the best local alignment of two sequences.
matchRefinement | 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. 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.
multiLocalAlignment | Computes multiple local alignments of two sequences.
normalize | Determines the normalized frequencies.
positionToId | Retrieves the id of a string in the StringSet given a position.
removeValueById | Removes a string from the StringSet given an id.
resize | Changes the length.
setStrings | Loads the sequences of a stringset into an alignment.
stringSetLimits | Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
value | Reference to the value.
valueById | Retrieves a string from the StringSet given an id.
variance | Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel
zscore | Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel
Example Programs Index Finder StringSet, Maximal Unique Matches, Mummy Include Headers sequence.h SeqAn - Sequence Analysis Library - www.seqan.de