Class Specialization
Pizza & Chili String
String used by the Pizza & Chili indices.
Parameters
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 | |
Tag specifying the Pizza & Chili index library to use. Types: |
Specialization of
Implements
Metafunctions
| The default overflow strategy for explicit resize. (String) | |
| The default overflow strategy for implicit resize. (String) | |
| Infix sequence type. (String) | |
| Determines whether a container stores its elements in sequential order. (String) | |
| Type of iterator objects that are used to traverse the container. (String) | |
| Type of an object that represents a position in a container. (String) | |
| Prefix sequence type. (String) | |
| The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. (String) | |
| The spec of a class. (String) | |
| Suffix sequence type. (String) |
Functions
| Concatenate two containers. (String) | |
| Assigns one object to another object. (String) | |
| Assigns value to item. (Container) | |
| Tests whether iterator is at nil position. (String) | |
| The last item in container. (Container) | |
| The begin of a container. (String) | |
| Begin position of object in host. (String) | |
| Test whether an automaton can parse a string completely. (String) | |
| The maximal length. (String) | |
| Resets an object. (String) | |
| Returns all leaves underneath a given vertex. (String) | |
| Creates a factor oracle. (String) | |
| Creates a factor oracle for the reversed string. (String) | |
| Creates a trie of all suffixes of a text. (String) | |
| Creates a trie. (String) | |
| Creates a trie for all reversed keywords. (String) | |
| Determines the consensus pattern of a given profile. (String) | |
| Test a container for being empty. (String) | |
| The end of a container. (String) | |
| End position of object in host. (String) | |
| Erases a part of a container (String) | |
| Extends a seed. (String) | |
| Extenstion of seeds. (String) | |
| Resizes and fills a container. (String) | |
| The first item in container. (Container) | |
| Constructs a alignment from a ChainedSeed. (String) | |
| Computes a pairwise distance matrix from an alignment graph. (String) | |
| 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) | |
| Access to the value. (Container) | |
| Iterates down one edge or a path in a tree. (String) | |
| Moves iterator to nil position. (String) | |
| Computes the heaviest increasing subsequence. (String) | |
| A value that identifies the underlying sequence. (String) | |
| Creates infix object. (String) | |
| Creates infix object. (String) | |
| Iterator to item at given position. (String) | |
| The number of items/characters. (String) | |
| Computes the longest common subsequence. (String) | |
| Computes the longest increasing subsequence. (String) | |
| Assigns value to item. (Container) | |
| Parses a string one character at a time and moves accordingly in the automaton. (String) | |
| Position of an iterator. (Container) | |
| Creates prefix object. (String) | |
| Replaces a part of a container with another container. (String) | |
| Changes the length. (String) | |
| Makes free space in container (String) | |
| Calculates the score of a seed. (String) | |
| Sets the haystack of a Finder object. (String) | |
| Sets the needle of a Pattern object and optionally induces preprocessing. (String) | |
| Determines whether two sequences share the same resource. (String) | |
| Computes a guide tree from a distance matrix. (String) | |
| Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. (String) | |
| Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. (String) | |
| Creates suffix object. (String) | |
| Access sequence as c-style string. (String) | |
| Performs a topological sort on a directed acyclic graph (DAG). (String) | |
| Computes a guide tree from a distance matrix. (String) | |
| Reference to the value. (String) |
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.
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de