Class
StringSet
A container class for a set of strings.
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Include Headers
sequence.h
Parameters
The string type. Types: String | |
The specializing type for the StringSet. Metafunctions: Spec Default: |
Specializations
| A string set storing references of the strings. | |
| A string set storing the strings as members. |
Metafunctions
| Returns the type of the concatenation sequence of all sequences in a StringSet. | |
| The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. |
Functions
| Appends all sequences stored in files of directory to a StringSet. | |
| Appends a value to a container. | |
| Adds a new string to the StringSet and returns an id. | |
| Adds a new string to the StringSet and returns an id. | |
| The begin of a container. | |
| Resets an object. | |
| Complement a sequence or a StringSet in-place. | |
| Concatenates the background frequency with the profile for the motif component. | |
| Returns the concatenation sequence of all sequences in a StringSet. | |
| Converts a pattern into a profile which consists of a set of frequency distributions. | |
| Converts a set of sequence patterns into a profile. | |
| Converts a set of sequence patterns into a profile. | |
| Builds an index on a StringSet storing how often a q-gram occurs in each sequence. | |
| Determines the consensus pattern of a given profile. | |
| Displays a given set of strings. | |
| Represents the EM algorithm as used by MEME. | |
| The end of a container. | |
| Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel | |
| Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel | |
| Represents the main function which is used to start the search for noticeable motif patterns. | |
| Generates random state and alphabet sequences of a given HMM. | |
| Generates random state and alphabet sequences of a given HMM. | |
| Retrieves a string from the StringSet given an id. | |
| Computes the best global alignment of the two sequences. | |
| Retrieves the position of a string in the StringSet given an id. | |
| Creates infix object. | |
| Creates infix object. | |
| Iterator to item at given position. | |
| The number of items/characters. | |
| Loads contigs into fragment store. | |
| Computes the best local alignment of two sequences. | |
| Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. | |
| Computes multiple local alignments of two sequences. | |
| Determines the normalized frequencies. | |
| Determines the normalized frequencies. | |
| Retrieves the id of a string in the StringSet given a position. | |
| Creates prefix object. | |
| Removes a string from the StringSet given an id. | |
| Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
| Reverse and complement a sequence or a StringSet in-place. | |
| Loads the sequences of a stringset into an alignment. | |
| Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. | |
| Creates suffix object. | |
| Swaps the contents of two values. | |
| Swaps the contents of two values. | |
| Convert characters in sequence or StringSet to lower case in-place. | |
| Convert characters in sequence or StringSet to lower case in-place. | |
| Reference to the value. | |
| Retrieves a string from the StringSet given an id. | |
| Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel | |
| Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel | |
| Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel | |
| Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de