Class
String
General purpose container for sequences.
String | |||||||
Parameters
The value type, that is the type of the items/characters stored in the string. Metafunctions: Value | |
The specializing type. Metafunctions: Spec |
Implements
Specializations
Expandable string that is stored on heap. | |
Fast but non-expandable string. | |
String optimized for push_back, top, and pop (Stack behaviour). | |
Allows adaption of strings to C-style strings. | |
String that is stored in external memory. | |
Read sequence data from file. | |
A string that stores as many values in one machine word as possible. | |
String used by the Pizza & Chili indices. |
Metafunctions
The default overflow strategy for explicit resize. | |
The default overflow strategy for implicit resize. | |
Infix sequence type. | |
Determines whether a container stores its elements in sequential order. | |
Type of iterator objects that are used to traverse the container. | |
Type of an object that represents a position in a container. | |
Prefix sequence type. | |
The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. | |
The spec of a class. | |
Suffix sequence type. |
Functions
Concatenate two containers. | |
Assigns one object to another object. | |
Assigns value to item. (Container) | |
Tests whether iterator is at nil position. | |
The last item in container. (Container) | |
The begin of a container. | |
Begin position of object in host. | |
The maximal length. | |
Resets an object. | |
Creates a factor oracle. | |
Creates a factor oracle for the reversed string. | |
Creates a trie. | |
Creates a trie for all reversed keywords. | |
Determines the consensus pattern of a given profile. | |
Test a container for being empty. | |
The end of a container. | |
End position of object in host. | |
Erases a part of a container | |
Extends a seed. | |
Extenstion of seeds. | |
Resizes and fills a container. | |
The first item in container. (Container) | |
Constructs a alignment from a MultiSeed. | |
Computes a pairwise distance matrix from an alignment graph. | |
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. | |
Access to the value. (Container) | |
Iterates down one edge or a path in a tree. | |
Moves iterator to nil position. | |
Computes the heaviest increasing subsequence. | |
A value that identifies the underlying sequence. | |
Creates infix object. | |
Creates infix object. | |
Iterator to item at given position. | |
The number of items/characters. | |
Computes the longest common subsequence. | |
Computes the longest increasing subsequence. | |
Assigns value to item. (Container) | |
Parses a string one character at a time and moves accordingly in the automaton. | |
Position of an iterator. (Container) | |
Creates prefix object. | |
Replaces a part of a container with another container. | |
Changes the length. | |
Makes free space in container | |
Calculates the score of a seed. | |
Sets the haystack of a Finder object. | |
Sets the needle of a Pattern object and optionally induces preprocessing. | |
Determines whether two sequences share the same resource. | |
Computes a guide tree from a distance matrix. | |
Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. | |
Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. | |
Creates suffix object. | |
Access sequence as c-style string. | |
Performs a topological sort on a directed acyclic graph (DAG). | |
Computes a guide tree from a distance matrix. | |
Reference to the value. |
Example Programs
Include Headers
sequence.h
SeqAn - Sequence Analysis Library - www.seqan.de