Class Specialization
Pizza & Chili String
String used by the Pizza & Chili indices.

Container

String

Pizza & Chili String

String<TValue, PizzaChili<TSpec> >
Include Headers
seqan/index.h
Parameters

TValue | The value type, that is the type of them items/characters stored in the string. Remarks: This type must be a simple type and it must hold that sizeof(TValue) == 1.
TSpec | Tag specifying the Pizza & Chili index library to use. Types: Pizza & Chili Index Tags

Remarks
The string is lazy in the sense that it holds a reference to the compressed index structure it is associated with. Only when the text is actually read, the index is queried for the text. If only a substring is needed, this string tries to query only a substring.
Specialization of
String
Implements
Container
Metafunctions

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

Functions

append | Concatenate two containers. (String)
append | Concatenate two containers. (String)
appendSeqs | Appends all sequences stored in files of directory to a StringSet. (String)
assign | Assigns one object to another object. (String)
assign | Assigns one object to another object. (String)
assignCroppedSeqId | Extracts the sequence id up to the first whitespace of a sequence file fragment. (String)
assignQual | Extracts the quality values of a sequence file fragment. (String)
assignQualId | Extracts the quality value id of a sequence file fragment. (String)
assignSeq | Extracts the sequence part of a sequence file fragment. (String)
assignSeq | Extracts the sequence part of a sequence file fragment. (String)
assignSeqId | Extracts the sequence id of a sequence file fragment. (String)
assignValue | Assigns value to item. (Container)
atNil | Tests whether iterator is at nil position. (String)
back | The last item in container. (Container)
begin | The begin of a container. (String)
begin | The begin of a container. (String)
begin | The begin of a container. (String)
beginPosition | Begin position of object in host. (String)
beginPosition | Begin position of object in host. (String)
canParseString | Test whether an automaton can parse a string completely. (String)
capacity | The maximal length. (String)
clear | Resets an object. (String)
collectLeaves | Returns all leaves underneath a given vertex. (String)
complement | Complement a sequence or a StringSet in-place. (String)
createIntervalTree | Create an interval tree. (String)
createOracle | Creates a factor oracle. (String)
createOracleOnReverse | Creates a factor oracle for the reversed string. (String)
createSuffixTrie | Creates a trie of all suffixes of a text. (String)
createTrie | Creates a trie. (String)
createTrieOnReverse | Creates a trie for all reversed keywords. (String)
determineConsensusSeq | Determines the consensus pattern of a given profile. (String)
empty | Test a container for being empty. (String)
end | The end of a container. (String)
end | The end of a container. (String)
end | The end of a container. (String)
endPosition | End position of object in host. (String)
endPosition | End position of object in host. (String)
erase | Erases a part of a container (String)
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. (String)
extendSeed | Extends a seed. (String)
extendSeed | Extends a seed. (String)
extendSeeds | Extension of seeds. (String)
extendSeeds | Extension of seeds. (String)
extendSeedScore | Extends a seed and increases the score. (String)
extendSeedScore | Extends a seed and increases the score. (String)
extendSeedsScore | Extension of seeds with score calculation. (String)
extendSeedsScore | Extension of seeds with score calculation. (String)
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. (String)
front | The first item in container. (Container)
getAlignment | Constructs a alignment from a ChainedSeed. (String)
getAlignment | Constructs a alignment from a ChainedSeed. (String)
getDistanceMatrix | Computes a pairwise distance matrix from an alignment graph. (String)
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. (String)
getValue | Access to the value. (Container)
goDown | Iterates down one edge or a path in a tree. (String)
goNil | Moves iterator to nil position. (String)
heaviestIncreasingSubsequence | Computes the heaviest increasing subsequence. (String)
id | A value that identifies the underlying sequence. (String)
infix | Creates infix object. (String)
infixWithLength | Creates infix object. (String)
integrateAlign | Integrates an alignment into another by copying the gaps. (String)
iter | Iterator to item at given position. (String)
length | The number of items/characters. (String)
length | The number of items/characters. (String)
length | The number of items/characters. (String)
longestCommonSubsequence | Computes the longest common subsequence. (String)
longestCommonSubsequence | Computes the longest common subsequence. (String)
longestIncreasingSubsequence | Computes the longest increasing subsequence. (String)
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. (String)
position | Position of an iterator. (Container)
prefix | Creates prefix object. (String)
replace | Replaces a part of a container with another container. (String)
replace | Replaces a part of a container with another container. (String)
reserve | Increases the capacity. (String)
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value. (String)
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value. (String)
resizeSpace | Makes free space in container (String)
resizeSpace | Makes free space in container (String)
reverseComplement | Reverse and complement a sequence or a StringSet in-place. (String)
scoreSeed | Calculates the score of a seed. (String)
scoreSeed | Calculates the score of a seed. (String)
setHaystack | Sets the haystack of a Finder object. (String)
setHost | Sets the host of an object. (String)
setNeedle | Sets the needle of a Pattern object and optionally induces preprocessing. (String)
shapeToString | Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). (String)
shareResources | Determines whether two sequences share the same resource. (String)
slowNjTree | Computes a guide tree from a distance matrix. (String)
stringSetLimits | Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. (String)
stringToShape | Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. (String)
suffix | Creates suffix object. (String)
swap | Swaps the contents of two values. (String)
swap | Swaps the contents of two values. (String)
toCString | Access sequence as c-style string. (String)
toLower | Convert characters in sequence or StringSet to lower case in-place. (String)
topologicalSort | Performs a topological sort on a directed acyclic graph (DAG). (String)
toUpper | Convert characters in sequence or StringSet to lower case in-place. (String)
upgmaTree | Computes a guide tree from a distance matrix. (String)
value | Reference to the value. (String)

Example Programs
ModView, Pizza & Chili Index, ModReverse, Nested Modifiers
See Also
Pizza & Chili Index, Pizza & Chili Index Tags
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:51