Class Specialization
Block String
String optimized for push_back, top, and pop (Stack behaviour).
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Block String | |||||||||||||
Include Headers
seqan/sequence.h
Parameters
The value type, that is the type of the items/characters stored in the string. Remarks: Use Value to get the value type for a given class. | |
A positive integer that specifies the number of values in each allocated block. Remarks: Size should be a power of 2, e.g., 1024. |
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. | |
| The string type of the finder. (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) | |
| Type of the items in the container or behind an iterator. (String) |
Functions
| Concatenate two containers. (String) | |
| Appends all sequences stored in files of directory to a StringSet. (String) | |
| Appends a value to a container. | |
| Assigns one object to another object. (String) | |
| Extracts the sequence id up to the first whitespace of a sequence file fragment. (String) | |
| Extracts the quality values of a sequence file fragment. (String) | |
| Extracts the quality value id of a sequence file fragment. (String) | |
| Extracts the sequence part of a sequence file fragment. (String) | |
| Extracts the sequence id of a sequence file fragment. (String) | |
| Assigns value to item. (ContainerConcept) | |
| The last item in container. (ContainerConcept) | |
| Convert BamAlignmentRecord to an Align object. (String) | |
| The begin of a container. (String) | |
| Begin position of object in host. (String) | |
| Builds an Alignment Graph from a set of input alignments. (String) | |
| Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a background model. (String) | |
| Calculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p) (String) | |
| Calculate word periodicity (indicator for overlaps) (String) | |
| Calculates the probability of a sequence given a Bernoulli model (String of background frequencies) (String) | |
| Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background model. (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) | |
| Complement a sequence or a StringSet in-place. (String) | |
| Counts kmers in a sequence. Optionally, a background model is returned. (String) | |
| Creates the LF table (String) | |
| Creates a factor oracle. (String) | |
| Creates a factor oracle for the reversed string. (String) | |
| Creates the prefix sum table (String) | |
| This functions creates the dictionary. (String) | |
| Computes the wavelet tree structure of a text. (String) | |
| This functions creates the dictionary structure. (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) | |
| 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) | |
| Extends a seed. (String) | |
| Find all intervals that contain the query point or overlap with the query interval. (String) | |
| 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) | |
| Search for repeats in a text. (String) | |
| The first item in container. (ContainerConcept) | |
| Computes a pairwise distance matrix from an alignment graph. (String) | |
| A value that identifies the underlying sequence. (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. (ContainerConcept) | |
| Computes the best global pairwise alignment score. (String) | |
| Iterates down one edge or a path in a tree. (String) | |
| Computes the heaviest increasing subsequence. (String) | |
| Creates infix object. (String) | |
| Creates infix object. (String) | |
| Integrates an alignment into another by copying the gaps. (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. (ContainerConcept) | |
| Computes a guide tree from a distance matrix. (String) | |
| Parses a string one character at a time and moves accordingly in the automaton. (String) | |
| Position of an iterator. (ContainerConcept) | |
| Creates prefix object. (String) | |
| Read first sequence from a FASTA file. (String) | |
| Read the next sequence record from SequenceStream. (String) | |
| Load the infix of a sequence from a FaiIndex. (String) | |
| Load a whole sequence from an FaiIndex. (String) | |
| Replaces a part of a container with another container. (String) | |
| Increases the capacity. | |
| Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
| Makes free space in container (String) | |
| Reverse and complement a sequence or a StringSet in-place. (String) | |
| Sets the haystack of a Finder object. (String) | |
| Sets the host of an object. (String) | |
| Sets the needle of a Pattern object and optionally induces preprocessing. (String) | |
| Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). (String) | |
| Determines whether two sequences share the same resource. (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) | |
| Transform a String into a StringSet containing this String. (String) | |
| Creates suffix object. (String) | |
| Swaps the contents of two values. (String) | |
| Access sequence as c-style string. (String) | |
| Convert characters in sequence or StringSet to lower case in-place. (String) | |
| Performs a topological sort on a directed acyclic graph (DAG). (String) | |
| Convert characters in sequence or StringSet to lower case in-place. (String) | |
| Inverse of the hash function; for ungapped shapes. (String) | |
| Computes a guide tree from a distance matrix. (String) | |
| Reference to the value. (String) | |
| Write one sequence record from to a SequenceStream object. (String) |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de