Class
StringSet
A container class for a set of strings.

StringSet

Dependent | Owner

ConcatDirect

StringSet<TString, TSpec>
Include Headers
sequence.h
Parameters

TString | The string type. Types: String
TSpec | The specializing type for the StringSet. Metafunctions: Spec Default: Owner<Generous>.

Specializations

Dependent | A string set storing references of the strings.
Owner | A string set storing the strings as members.

Metafunctions

Concatenator | Returns the type of the concatenation sequence of all sequences in a StringSet.
SAValue | The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.

Functions

appendSeqs | Appends all sequences stored in files of directory to a StringSet.
appendValue | Appends a value to a container.
assignValueById | Adds a new string to the StringSet and returns an id.
assignValueById | Adds a new string to the StringSet and returns an id.
begin | The begin of a container.
clear | Resets an object.
complement | Complement a sequence or a StringSet in-place.
completeProfile | Concatenates the background frequency with the profile for the motif component.
concat | Returns the concatenation sequence of all sequences in a StringSet.
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.
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
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.
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.
infix | Creates infix object.
infixWithLength | Creates infix object.
iter | Iterator to item at given position.
length | The number of items/characters.
loadContigs | Loads contigs into fragment store.
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.
multiLocalAlignment | Computes multiple local alignments of two sequences.
normalize | Determines the normalized frequencies.
normalize | Determines the normalized frequencies.
positionToId | Retrieves the id of a string in the StringSet given a position.
prefix | Creates prefix object.
removeValueById | Removes a string from the StringSet given an id.
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
reverseComplement | Reverse and complement a sequence or a StringSet in-place.
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.
suffix | Creates suffix object.
swap | Swaps the contents of two values.
swap | Swaps the contents of two values.
toLower | Convert characters in sequence or StringSet to lower case in-place.
toUpper | Convert characters in sequence or StringSet to lower case in-place.
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
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
zscore | Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel

Example Programs
Mummy, Maximal Unique Matches, Index Finder StringSet
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:45