String

Class

String

General purpose container for sequences.



Container

String

String<TValue, TSpec>

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

Container

Specializations

Alloc String	Expandable string that is stored on heap.
Array String	Fast but non-expandable 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.
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.
Iterator	Type of iterator objects that are used to traverse the container.
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.

Functions

append	Concatenate two containers.
assign	Assigns one object to another object.
assignValue	Assigns value to item. (Container)
atNil	Tests whether iterator is at nil position.
back	The last item in container. (Container)
begin	The begin of a container.
beginPosition	Begin position of object in host.
capacity	The maximal length.
clear	Resets an object.
createOracle	Creates a factor oracle.
createOracleOnReverse	Creates a factor oracle for the reversed string.
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
extendSeed	Extends a seed.
extendSeeds	Extenstion of seeds.
fill	Resizes and fills a container.
front	The first item in container. (Container)
getAlignment	Constructs a alignment from a MultiSeed.
getDistanceMatrix	Computes a pairwise distance matrix from an alignment graph.
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. (Container)
goDown	Iterates down one edge or a path in a tree.
goNil	Moves iterator to nil position.
heaviestIncreasingSubsequence	Computes the heaviest increasing subsequence.
id	A value that identifies the underlying sequence.
infix	Creates infix object.
infixWithLength	Creates infix object.
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. (Container)
parseString	Parses a string one character at a time and moves accordingly in the automaton.
position	Position of an iterator. (Container)
prefix	Creates prefix object.
replace	Replaces a part of a container with another container.
resize	Changes the length.
resizeSpace	Makes free space in container
scoreSeed	Calculates the score of a seed.
setHaystack	Sets the haystack of a Finder object.
setNeedle	Sets the needle of a Pattern object and optionally induces preprocessing.
shareResources	Determines whether two sequences share the same resource.
slowNjTree	Computes a guide tree from a distance matrix.
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.
suffix	Creates suffix object.
toCString	Access sequence as c-style string.
topological_sort	Performs a topological sort on a directed acyclic graph (DAG).
upgmaTree	Computes a guide tree from a distance matrix.
value	Reference to the value.

Example Programs

ModReverse, ModView, Nested Modifiers, String Basics

Include Headers

sequence.h

SeqAn - Sequence Analysis Library - www.seqan.de