String

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, 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.
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.
Iterator	Type of iterator objects that are used to traverse the container.
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.

Functions

append	Concatenate two containers.
append	Concatenate two containers.
appendSeqs	Appends all sequences stored in files of directory to a StringSet.
assign	Assigns one object to another object.
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.
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. (Container)
atNil	Tests whether iterator is at nil position.
back	The last item in container. (Container)
begin	The begin of a container.
begin	The begin of a container.
begin	The begin of a container.
beginPosition	Begin position of object in host.
beginPosition	Begin position of object in host.
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.
createIntervalTree	Create an interval tree.
createOracle	Creates a factor oracle.
createOracleOnReverse	Creates a factor oracle for the reversed string.
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.
end	The end of a container.
end	The end of a container.
endPosition	End position of object in host.
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.
extendSeed	Extends a seed.
extendSeeds	Extension of seeds.
extendSeeds	Extension of seeds.
extendSeedScore	Extends a seed and increases the score.
extendSeedScore	Extends a seed and increases the score.
extendSeedsScore	Extension of seeds with score calculation.
extendSeedsScore	Extension of seeds with score calculation.
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.
front	The first item in container. (Container)
getAlignment	Constructs a alignment from a ChainedSeed.
getAlignment	Constructs a alignment from a ChainedSeed.
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.
integrateAlign	Integrates an alignment into another by copying the gaps.
iter	Iterator to item at given position.
length	The number of items/characters.
length	The number of items/characters.
length	The number of items/characters.
longestCommonSubsequence	Computes the longest common subsequence.
longestCommonSubsequence	Computes the longest common subsequence.
longestIncreasingSubsequence	Computes the longest increasing subsequence.
moveValue	Assigns value to item. (Container)
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.
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.
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
resizeSpace	Makes free space in container
reverseComplement	Reverse and complement a sequence or a StringSet in-place.
scoreSeed	Calculates the score of a seed.
scoreSeed	Calculates the score of a seed.
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.
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.
swap	Swaps the contents of two values.
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.
upgmaTree	Computes a guide tree from a distance matrix.
value	Reference to the value.

Example Programs

ModView, ModReverse, Nested Modifiers

SeqAn - Sequence Analysis Library - www.seqan.de