Class
String
General purpose container for sequences.

Container

String

Alloc String | Array String | Block String | CStyle String | External String | File Reader String
MMap String | Packed String | Pizza & Chili String

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
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

Page built @2012/03/14 16:34:45