Class Specialization
Owner
A string set storing the strings as members.

StringSet

Owner

ConcatDirect

StringSet<TString, Owner<> >
StringSet<TString, Owner<Default> >
Include Headers
seqan/sequence.h
Parameters

TString | The string type. Types: String

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.
Specialization of
StringSet
Specializations

ConcatDirect | A string set storing the concatenation of all strings within one string.

Metafunctions

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

Functions

alignmentFreeComparison | Computes the pairwise similarity scores for a set of sequences (StringSet)
appendSeqs | Appends all sequences stored in files of directory to a StringSet. (StringSet)
appendValue | Appends a value to a container. (StringSet)
assignValueById | Adds a new string to the StringSet and returns an id. (StringSet)
bandedChainAlignment | Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (StringSet)
begin | The begin of a container. (StringSet)
clear | Resets an object. (StringSet)
complement | Complement a sequence or a StringSet in-place. (StringSet)
completeProfile | Concatenates the background frequency with the profile for the motif component. (StringSet)
concat | Returns the concatenation sequence of all sequences in a StringSet. (StringSet)
convertPatternToProfile | Converts a pattern into a profile which consists of a set of frequency distributions. (StringSet)
convertSetOfPatternsToProfile | Converts a set of sequence patterns into a profile. (StringSet)
createCountArray | Builds an index on a StringSet storing how often a q-gram occurs in each sequence. (StringSet)
createPrefixSumTable | Creates the prefix sum table (StringSet)
determineConsensusSeq | Determines the consensus pattern of a given profile. (StringSet)
display | Displays a given set of strings. (StringSet)
em | Represents the EM algorithm as used by MEME. (StringSet)
end | The end of a container. (StringSet)
erase | Erases a part of a container
expectation | Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet)
findMotif | Represents the main function which is used to start the search for noticeable motif patterns. (StringSet)
findRepeats | Search for repeats in a text. (StringSet)
generateSequence | Generates random state and alphabet sequences of a given HMM. (StringSet)
getValueById | Retrieves a string from the StringSet given an id. (StringSet)
globalAlignment | Computes the best global pairwise alignment. (StringSet)
globalAlignmentScore | Computes the best global pairwise alignment score. (StringSet)
idToPosition | Retrieves the position of a string in the StringSet given an id. (StringSet)
infix | Creates infix object. (StringSet)
infixWithLength | Creates infix object. (StringSet)
iter | Iterator to item at given position. (StringSet)
length | The number of items/characters. (StringSet)
loadContigs | Loads contigs into fragment store. (StringSet)
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. (StringSet)
normalize | Determines the normalized frequencies. (StringSet)
positionToId | Retrieves the id of a string in the StringSet given a position. (StringSet)
prefix | Creates prefix object. (StringSet)
readAll | Read all sequence records from a SequenceStream object. (StringSet)
readBatch | Read a given number of sequence records from SequenceStream. (StringSet)
removeValueById | Removes a string from the StringSet given an id. (StringSet)
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value. (StringSet)
reverseComplement | Reverse and complement a sequence or a StringSet in-place. (StringSet)
setStrings | Loads the sequences of a stringset into an alignment. (StringSet)
stringSetLimits | Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. (StringSet)
stringSplit | Append a list of the words in the string, using sep as the delimiter string StringSet. (StringSet)
stringToStringSet | Transform a String into a StringSet containing this String. (StringSet)
suffix | Creates suffix object. (StringSet)
toLower | Convert characters in sequence or StringSet to lower case in-place. (StringSet)
toUpper | Convert characters in sequence or StringSet to lower case in-place. (StringSet)
value | Reference to the value. (StringSet)
valueById | Retrieves a string from the StringSet given an id. (StringSet)
variance | Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet)
write2 | Write FASTA or FASTQ records. (StringSet)
writeAll | Write sequence records from to a SequenceStream object. (StringSet)
zscore | Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet)

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

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