General purpose container for sequences.
String<TValue, TSpec>
The value type, that is the type of the items/characters stored in the string.
Metafunctions: Value
The specializing type.
Metafunctions: Spec
Default: Alloc<>, see Alloc String.
Alloc StringExpandable string that is stored on heap.
Array StringFast but non-expandable string.
Block StringString optimized for push_back, top, and pop (Stack behaviour).
CStyle StringAllows adaption of strings to C-style strings.
External StringString that is stored in external memory.
File Reader StringRead sequence data from file.
Packed StringA string that stores as many values in one machine word as possible.
Pizza & Chili StringString used by the Pizza & Chili indices.
DefaultOverflowExplicitThe default overflow strategy for explicit resize.
DefaultOverflowImplicitThe default overflow strategy for implicit resize.
InfixInfix sequence type.
IsSequenceDetermines whether a container stores its elements in sequential order.
IteratorType of iterator objects that are used to traverse the container.
PositionType of an object that represents a position in a container.
PrefixPrefix sequence type.
SAValueThe default alphabet type of a suffix array, i.e. the type to store a position of a string or string set.
SpecThe spec of a class.
SuffixSuffix sequence type.
appendConcatenate two containers.
assignAssigns one object to another object.
assignValueAssigns value to item. (Container)
atNilTests whether iterator is at nil position.
backThe last item in container. (Container)
beginThe begin of a container.
beginPositionBegin position of object in host.
capacityThe maximal length.
clearResets an object.
createOracleCreates a factor oracle.
createOracleOnReverseCreates a factor oracle for the reversed string.
createTrieCreates a trie.
createTrieOnReverseCreates a trie for all reversed keywords.
determineConsensusSeqDetermines the consensus pattern of a given profile.
emptyTest a container for being empty.
endThe end of a container.
endPositionEnd position of object in host.
eraseErases a part of a container
extendSeed Extends a seed.
extendSeeds Extenstion of seeds.
fillResizes and fills a container.
frontThe first item in container. (Container)
getAlignment Constructs a alignment from a MultiSeed.
getDistanceMatrixComputes a pairwise distance matrix from an alignment graph.
getSuccessorGets 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.
getValueAccess to the value. (Container)
goDownIterates down one edge or a path in a tree.
goNilMoves iterator to nil position.
heaviestIncreasingSubsequenceComputes the heaviest increasing subsequence.
idA value that identifies the underlying sequence.
infixCreates infix object.
infixWithLengthCreates infix object.
iterIterator to item at given position.
lengthThe number of items/characters.
longestCommonSubsequenceComputes the longest common subsequence.
longestIncreasingSubsequenceComputes the longest increasing subsequence.
moveValueAssigns value to item. (Container)
parseStringParses a string one character at a time and moves accordingly in the automaton.
positionPosition of an iterator. (Container)
prefixCreates prefix object.
replaceReplaces a part of a container with another container.
resizeChanges the length.
resizeSpaceMakes free space in container
scoreSeed Calculates the score of a seed.
setHaystackSets the haystack of a Finder object.
setNeedleSets the needle of a Pattern object and optionally induces preprocessing.
shareResourcesDetermines whether two sequences share the same resource.
slowNjTreeComputes a guide tree from a distance matrix.
stringSetLimitsRetrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
stringToShapeTakes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object.
suffixCreates suffix object.
toCStringAccess sequence as c-style string.
topological_sortPerforms a topological sort on a directed acyclic graph (DAG).
upgmaTreeComputes a guide tree from a distance matrix.
valueReference to the value.
Include Headers
SeqAn - Sequence Analysis Library -