String

Class

String

A sequence container with generic alphabet and many specializations.

String is at the heart of the SeqAn library (SeqAn is for SEQuence ANalaysis after all). There are various specializations with Alloc String being the default and most widely used one. Strings can be used to store arbitrary values and can be used for large biologicaly sequences as well as a generic, dynamic array and replace std::vector<>.



ContainerConcept

String

Concept Definition

Required Functions

endsWith	Check whether a sequence ends with a given suffix.
startsWith	Check whether a sequence starts with a given prefix.

String<TValue, TSpec>

Include Headers

seqan/sequence.h

Parameters

TValue	The value type, that is the type of the items/characters stored in the string. Metafunctions: Value
TSpec	The specializing type. Metafunctions: Spec Default: Alloc<>, see Alloc String.

Implements

ContainerConcept

Specializations

Alloc String	Expandable string that is stored on heap.
Array String	Fast, static-size string.
Block String	String optimized for push_back, top, and pop (Stack behaviour).
CStyle String	Allows adaption of strings to C-style strings.
External String	String that is stored in external memory.
File Reader String	Read sequence data from file.
Journaled String	Journaled versions of arbitrary underlying string.
MMap String	String that is stored in external memory. Uses memory mapping.
Packed String	A string that stores as many values in one machine word as possible.
Pizza & Chili String	String used by the Pizza & Chili indices.

Metafunctions

DefaultOverflowExplicit	The default overflow strategy for explicit resize.
DefaultOverflowImplicit	The default overflow strategy for implicit resize.
Infix	Infix sequence type.
IsSequence	Determines whether a container stores its elements in sequential order.
Motif	The string type of the finder.
Position	Type of an object that represents a position in a container.
Prefix	Prefix sequence type.
SAValue	The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.
Spec	The spec of a class.
Suffix	Suffix sequence type.
Value	Type of the items in the container or behind an iterator.

Functions

append	Concatenate two containers.
appendSeqs	Appends all sequences stored in files of directory to a StringSet.
assign	Assigns one object to another object.
assignCroppedSeqId	Extracts the sequence id up to the first whitespace of a sequence file fragment.
assignQual	Extracts the quality values of a sequence file fragment.
assignQualId	Extracts the quality value id of a sequence file fragment.
assignSeq	Extracts the sequence part of a sequence file fragment.
assignSeqId	Extracts the sequence id of a sequence file fragment.
assignValue	Assigns value to item. (ContainerConcept)
back	The last item in container. (ContainerConcept)
bamRecordToAlignment	Convert BamAlignmentRecord to an Align object.
begin	The begin of a container.
beginPosition	Begin position of object in host.
buildAlignmentGraph	Builds an Alignment Graph from a set of input alignments.
calculateCovariance	Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a background model.
calculateOverlapIndicator	Calculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p)
calculatePeriodicity	Calculate word periodicity (indicator for overlaps)
calculateProbability	Calculates the probability of a sequence given a Bernoulli model (String of background frequencies)
calculateVariance	Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background model.
canParseString	Test whether an automaton can parse a string completely.
capacity	The maximal length.
clear	Resets an object.
collectLeaves	Returns all leaves underneath a given vertex.
complement	Complement a sequence or a StringSet in-place.
countKmers	Counts kmers in a sequence. Optionally, a background model is returned.
createLfTable	Creates the LF table
createOracle	Creates a factor oracle.
createOracleOnReverse	Creates a factor oracle for the reversed string.
createPrefixSumTable	Creates the prefix sum table
createRankDictionary	This functions creates the dictionary.
createRightArrayBinaryTree	Computes the wavelet tree structure of a text.
createSentinelRankDictionary	This functions creates the dictionary structure.
createSuffixTrie	Creates a trie of all suffixes of a text.
createTrie	Creates a trie.
createTrieOnReverse	Creates a trie for all reversed keywords.
determineConsensusSeq	Determines the consensus pattern of a given profile.
empty	Test a container for being empty.
end	The end of a container.
endPosition	End position of object in host.
erase	Erases a part of a container
eraseBack	Deletes the last item of a container and reduces its size by 1. The container must have a size greater than or equal to 1.
extendSeed	Extends a seed.
findIntervals	Find all intervals that contain the query point or overlap with the query interval.
findIntervalsExcludeTouching	Find all intervals that contain the query point, exclude intervals that touch the query, i.e. where the query point equals the start or end point.
findRepeats	Search for repeats in a text.
front	The first item in container. (ContainerConcept)
getDistanceMatrix	Computes a pairwise distance matrix from an alignment graph.
getObjectId	A value that identifies the underlying sequence.
getSuccessor	Gets the successor for a given vertex and an edge label. For an automaton a single character is required whereas for a word graph getSuccessor takes a string.
getValue	Access to the value. (ContainerConcept)
globalAlignmentScore	Computes the best global pairwise alignment score.
goDown	Iterates down one edge or a path in a tree.
heaviestIncreasingSubsequence	Computes the heaviest increasing subsequence.
infix	Creates infix object.
infixWithLength	Creates infix object.
integrateAlign	Integrates an alignment into another by copying the gaps.
iter	Iterator to item at given position.
length	The number of items/characters.
longestCommonSubsequence	Computes the longest common subsequence.
longestIncreasingSubsequence	Computes the longest increasing subsequence.
moveValue	Assigns value to item. (ContainerConcept)
njTree	Computes a guide tree from a distance matrix.
parseString	Parses a string one character at a time and moves accordingly in the automaton.
position	Position of an iterator. (ContainerConcept)
prefix	Creates prefix object.
readFasta	Read first sequence from a FASTA file.
readRecord	Read the next sequence record from SequenceStream.
readRegion	Load the infix of a sequence from a FaiIndex.
readSequence	Load a whole sequence from an FaiIndex.
replace	Replaces a part of a container with another container.
reserve	Increases the capacity.
resize	Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
resizeSpace	Makes free space in container
reverseComplement	Reverse and complement a sequence or a StringSet in-place.
setHaystack	Sets the haystack of a Finder object.
setHost	Sets the host of an object.
setNeedle	Sets the needle of a Pattern object and optionally induces preprocessing.
shapeToString	Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position).
shareResources	Determines whether two sequences share the same resource.
stringSetLimits	Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
stringToShape	Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object.
stringToStringSet	Transform a String into a StringSet containing this String.
suffix	Creates suffix object.
swap	Swaps the contents of two values.
toCString	Access sequence as c-style string.
toLower	Convert characters in sequence or StringSet to lower case in-place.
topologicalSort	Performs a topological sort on a directed acyclic graph (DAG).
toUpper	Convert characters in sequence or StringSet to lower case in-place.
unhash	Inverse of the hash function; for ungapped shapes.
upgmaTree	Computes a guide tree from a distance matrix.
value	Reference to the value.
writeRecord	Write one sequence record from to a SequenceStream object.

Example Programs

ModView, ModReverse, Nested Modifiers