Class
String
General purpose container for sequences.
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String | |||||||
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Include Headers
seqan/sequence.h
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, static-size 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. | |
| String that is stored in external memory. Uses memory mapping. | |
| 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. | |
| The string type of the finder. | |
| 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. | |
| Concatenate two containers. | |
| Appends all sequences stored in files of directory to a StringSet. | |
| Assigns one object to another object. | |
| Assigns one object to another object. | |
| Extracts the sequence id up to the first whitespace of a sequence file fragment. | |
| Extracts the quality values of a sequence file fragment. | |
| Extracts the quality value id of a sequence file fragment. | |
| Extracts the sequence part of a sequence file fragment. | |
| Extracts the sequence part of a sequence file fragment. | |
| Extracts the sequence id of a sequence file fragment. | |
| Assigns value to item. (Container) | |
| Tests whether iterator is at nil position. | |
| The last item in container. (Container) | |
| The begin of a container. | |
| The begin of a container. | |
| The begin of a container. | |
| Begin position of object in host. | |
| Begin position of object in host. | |
| Test whether an automaton can parse a string completely. | |
| The maximal length. | |
| Resets an object. | |
| Returns all leaves underneath a given vertex. | |
| Complement a sequence or a StringSet in-place. | |
| Create an interval tree. | |
| Creates a factor oracle. | |
| Creates a factor oracle for the reversed string. | |
| Creates a trie of all suffixes of a text. | |
| 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. | |
| The end of a container. | |
| The end of a container. | |
| End position of object in host. | |
| End position of object in host. | |
| Erases a part of a container | |
| 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. | |
| Extends a seed. | |
| Extends a seed. | |
| Extension of seeds. | |
| Extension of seeds. | |
| Extends a seed and increases the score. | |
| Extends a seed and increases the score. | |
| Extension of seeds with score calculation. | |
| Extension of seeds with score calculation. | |
| :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. | |
| The first item in container. (Container) | |
| Constructs a alignment from a ChainedSeed. | |
| Constructs a alignment from a ChainedSeed. | |
| 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. | |
| Integrates an alignment into another by copying the gaps. | |
| Iterator to item at given position. | |
| The number of items/characters. | |
| The number of items/characters. | |
| The number of items/characters. | |
| Computes the longest common subsequence. | |
| Computes the longest common subsequence. | |
| Computes the longest increasing subsequence. | |
| Assigns value to item. (Container) | |
| 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. | |
| Replaces a part of a container with another container. | |
| Increases the capacity. | |
| Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
| Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
| Makes free space in container | |
| Makes free space in container | |
| Reverse and complement a sequence or a StringSet in-place. | |
| Calculates the score of a seed. | |
| Calculates the score of a seed. | |
| Sets the haystack of a Finder object. | |
| Sets the host of an object. | |
| Sets the needle of a Pattern object and optionally induces preprocessing. | |
| Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). | |
| 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. | |
| Swaps the contents of two values. | |
| Swaps the contents of two values. | |
| Access sequence as c-style string. | |
| Convert characters in sequence or StringSet to lower case in-place. | |
| Performs a topological sort on a directed acyclic graph (DAG). | |
| Convert characters in sequence or StringSet to lower case in-place. | |
| Computes a guide tree from a distance matrix. | |
| Reference to the value. |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de
