Class Specialization
ConcatDirect
A string set storing the concatenation of all strings within one string.
Include Headers
seqan/sequence.h
Parameters
The string type. Types: String |
Remarks
Specialization of
Metafunctions
| Returns the type of the concatenation sequence of all sequences in a StringSet. (StringSet) | |
| The default alphabet type of a suffix array, i.e. the type to store a position of a string or string set. (StringSet) |
Data Members
| The concatenation string. Concatenates all sequences of the StringSet without gaps. |
Functions
| Computes the pairwise similarity scores for a set of sequences (StringSet) | |
| Appends all sequences stored in files of directory to a StringSet. (StringSet) | |
| Appends a value to a container. (StringSet) | |
| Adds a new string to the StringSet and returns an id. (StringSet) | |
| Computes the best global pairwise alignment between two sequences given a non-empty seed chain. (StringSet) | |
| The begin of a container. (StringSet) | |
| Resets an object. (StringSet) | |
| Complement a sequence or a StringSet in-place. (StringSet) | |
| Concatenates the background frequency with the profile for the motif component. (StringSet) | |
| Returns the concatenation sequence of all sequences in a StringSet. (StringSet) | |
| Converts a pattern into a profile which consists of a set of frequency distributions. (StringSet) | |
| Converts a set of sequence patterns into a profile. (StringSet) | |
| Builds an index on a StringSet storing how often a q-gram occurs in each sequence. (StringSet) | |
| Creates the prefix sum table (StringSet) | |
| Determines the consensus pattern of a given profile. (StringSet) | |
| Displays a given set of strings. (StringSet) | |
| Represents the EM algorithm as used by MEME. (StringSet) | |
| The end of a container. (StringSet) | |
| Erases a part of a container (Owner) | |
| Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet) | |
| Represents the main function which is used to start the search for noticeable motif patterns. (StringSet) | |
| Search for repeats in a text. (StringSet) | |
| Generates random state and alphabet sequences of a given HMM. (StringSet) | |
| Retrieves a string from the StringSet given an id. (StringSet) | |
| Computes the best global pairwise alignment. (StringSet) | |
| Computes the best global pairwise alignment score. (StringSet) | |
| Retrieves the position of a string in the StringSet given an id. (StringSet) | |
| Creates infix object. (StringSet) | |
| Creates infix object. (StringSet) | |
| Iterator to item at given position. (StringSet) | |
| The number of items/characters. (StringSet) | |
| Loads contigs into fragment store. (StringSet) | |
| 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. (StringSet) | |
| Determines the normalized frequencies. (StringSet) | |
| Retrieves the id of a string in the StringSet given a position. (StringSet) | |
| Creates prefix object. (StringSet) | |
| Read all sequence records from a SequenceStream object. (StringSet) | |
| Read a given number of sequence records from SequenceStream. (StringSet) | |
| Removes a string from the StringSet given an id. (StringSet) | |
| 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. (StringSet) | |
| Loads the sequences of a stringset into an alignment. (StringSet) | |
| Divides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter. | |
| Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. (StringSet) | |
| Append a list of the words in the string, using sep as the delimiter string StringSet. (StringSet) | |
| Transform a String into a StringSet containing this String. (StringSet) | |
| Creates suffix object. (StringSet) | |
| Swaps the contents of two values. (StringSet) | |
| Convert characters in sequence or StringSet to lower case in-place. (StringSet) | |
| Convert characters in sequence or StringSet to lower case in-place. (StringSet) | |
| Reference to the value. (StringSet) | |
| Retrieves a string from the StringSet given an id. (StringSet) | |
| Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet) | |
| Write FASTA or FASTQ records. (StringSet) | |
| Write sequence records from to a SequenceStream object. (StringSet) | |
| Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel (StringSet) |
Shortcuts
| A sequence file mapped in memory as a StringSet of concatenated sequence file fragments. | |
| A sequence file mapped in memory as a StringSet of concatenated sequence file fragments. |
Example Programs
SeqAn - Sequence Analysis Library - www.seqan.de