Functions
This section lists the functions implemented in SeqAn.
Note that SeqAn uses global functions to access data types,
e.g. the length of a string str is determined by calling length(str) and not by calling a member function str.length() .
Functions
Access function returning the distance dependent |
Alignments
Assigns the source to a new value. | |
Remove blanks from a gapped sequence. | |
A column in an alignment. | |
The container of columns in an alignment. | |
Count blanks at a specific position in a gapped sequence. | |
Creates a new source. | |
Test if object depends from it's source. | |
Makes an object independent from other objects. | |
Test if there is a source. | |
Returns reference to a value that is used as gap character. | |
Computes the best global alignment of the two sequences. | |
Computes the heaviest increasing subsequence. | |
Insert one blank into a gapped sequence. | |
Insert blanks into a gapped sequence. | |
Test a gapped sequence for gaps at a specific position. | |
Computes the best local alignment of two sequences. | |
Computes the longest common subsequence. | |
Computes the longest increasing subsequence. | |
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. | |
Moves the source to a new value. | |
Computes multiple local alignments of two sequences. | |
Removes one blank from a gapped sequence. | |
Removes blanks from a gapped sequence. | |
A row in an alignment. | |
The container of rows in an alignment. | |
Score for gaps. | |
Score for extending gaps. | |
Score for opening a gap. | |
Match score. | |
Mismatch score. | |
Let an external object be the source. | |
Loads the sequences of a stringset into an alignment. | |
Computes the best local alignment of the (two) sequences given in align. | |
Computes next best local alignment. | |
The source of an object. | |
Begin of the source segment. | |
End of the source segment. | |
Length of the source. | |
The used part of the source. |
Alphabets
Converts a value into another value. | |
Returns reference to a value that is used as gap character. | |
Infimum for a given type. | |
Maps an alphabet 1-to-1 to the interval [0..ValueSize). | |
Supremum for a given type. |
Array Handling
Destroys the begin of an array and keeps the rest. | |
Construct objects in a given memory buffer. | |
Copy constructs an array of objects into in a given memory buffer. | |
Move constructs an array of objects into in a given memory buffer. | |
Copies a range of objects into another range of objects. | |
Copies a range of objects into another range of objects starting from the last element. | |
Copies a range of objects into another range of objects starting from the first element. | |
Destroys an array of objects. | |
Assigns one object to each element of a range. | |
Moves a range of objects into another range of objects. | |
Moves a range of objects into another range of objects starting from the last element. | |
Moves a range of objects into another range of objects starting from the first element. |
Blast
Determines whether an iterator is at the beginning position. | |
Determines whether an iterator is at the beginning position. | |
Determines whether an iterator is at the end position. | |
Determines whether an iterator is at the end position. | |
Determines whether an iterator is at the end position. | |
Reference to the name (identifier) of the database in a Blast report. | |
Orientation of the database sequence within a Blast HSP alignment. | |
Turns a HSP from a Blast search into an Alignment object. | |
Turns a HSP from a Blast search into an Alignment object. | |
The bit score associated with a Blast HSP. | |
The begin position of the HSP on the database sequence. | |
The end position of the HSP on the database sequence. | |
The name (identifier) of the database in a Blast report. | |
The e-value associated with a Blast HSP. | |
The Expect-Value cutoff parsed from a Blast report. | |
The gapped kappa value parsed from a Blast report. | |
The lambda value parsed from a Blast report. | |
The gap extension penalty parsed from a Blast report. | |
The gap open penalty parsed from a Blast report. | |
The kappa value parsed from a Blast report. | |
The lambda value parsed from a Blast report. | |
Get next Blast report from a file containing multiple Blast reports. | |
The number of gaps within a Blast HSP alignment. | |
The begin position of the HSP on the query sequence. | |
The end position of the HSP on the query sequence. | |
The name (identifier) of the query in a Blast report. | |
The Smith-Waterman score associated with a Blast HSP. | |
Access to the value. | |
Access to the value. | |
Iterates to the first position of a container. | |
Iterates to the first position of a container. | |
Iterates to the last position of a container. | |
Iterates to next position. | |
Iterates to next position. | |
Iterates to pevious position. | |
The BlastHit this iterator is working on. | |
The BlastReport this iterator is working on. | |
The number of items/characters. | |
The total number of hits in a Blast report. | |
The number of HSPs for an entire Blast report or for one Blast hit. | |
Reference to the name (identifier) of the query in a Blast report. | |
Orientation of the query sequence within a Blast HSP alignment. | |
Loads records from a file. | |
Reference to the value. | |
Reference to the value. |
Chaining
Computes the chain on a set of fragments. |
Comparisons
Compares two objects. | |
Test whether a sequence is prefix of another sequence. | |
Operator "==". | |
Operator ">". | |
Operator ">=". | |
Operator "<". | |
Operator "<=". | |
Operator "!=". | |
Test whether a sequence is prefix of another sequence. | |
Length of longest common prefix. |
Containers
The last item in container. | |
The begin of a container. | |
Begin position of object in host. | |
The maximal length. | |
Resets an object. | |
Test a container for being empty. | |
The end of a container. | |
End position of object in host. | |
Erases a part of a container | |
Resizes and fills a container. | |
The first item in container. | |
Access to the value. | |
Creates infix object. | |
Creates infix object. | |
Iterator to item at given position. | |
The number of items/characters. | |
Creates prefix object. | |
Increases the capacity. | |
Changes the length. | |
Makes free space in container | |
Resizes container to minimum capacity | |
Creates suffix object. | |
Access sequence as c-style string. | |
Reference to the value. |
Content Manipulation
Concatenate two containers. | |
Appends a value to a container. | |
Assigns one object to another object. | |
Assigns value to item. | |
Access to the value. | |
Inserts a single value into a container. | |
Hands over content from one container to another container. | |
Assigns value to item. | |
Deletes item with the highest priority and adjusts the priority queue. | |
Inserts a new item and adjusts the priority queue if necessary. | |
Replaces a part of a container with another container. | |
Assigns one object to another object avoiding to copy contents. | |
Makes holder dependent. | |
Reference to the item with the highest priority. | |
Constructs an object at specified position. | |
Move constructs an object at specified position. | |
Destoys an object at specified position. |
Dependent Objects
Called when dependency is added. | |
Makes an object to owner of its content. | |
Test whether object depends on other objects. | |
Makes an object independent from other objects. | |
The object a given object depends on. | |
Called when dependency is released. | |
Sets begin of object in host. | |
Sets begin position of object in host. | |
Sets end of object in host. | |
Sets begin position of object in host. | |
Sets the host of an object. |
Graph
Adds a new edge to the graph, either with or without cargo. | |
Shortcut to add multiple edges at once. Creates vertices implicitly. | |
Adds a new vertex to the graph. | |
Given a multiple alignment, this function calculates all kinds of alignment statistics. | |
Finds shortest paths between all pairs of vertices in a graph. | |
Assigns a new cargo to the edge. | |
Assigns another EdgeStump to the next source pointer. | |
Assigns another EdgeStump to the next target pointer. | |
Assigns a property to an item in the property map. | |
Assigns a source vertex to an edge. | |
Assigns a target vertex to an edge. | |
Determines whether an iterator is at the beginning position. | |
Determines whether an iterator is at the end position. | |
Computes shortest paths from a single source in a graph. | |
Implements a breadth-first search on a graph. | |
Access to the cargo. | |
Resets an object. | |
Removes all edges in a graph. | |
Removes all vertices in a graph. | |
Combines multiple alignment graphs into one single graph. | |
Decomposes an undirected graph into its connected components. | |
Computes shortest paths from a single source in a directed acyclic graph (DAG). | |
Number of incident edges for a given vertex. | |
Implements a depth-first search on a graph. | |
Computes shortest paths from a single source in a graph. | |
Test a container for being empty. | |
Finds an edge. | |
Finds shortest paths between all pairs of vertices in a graph. | |
Computes a maximum flow in a directed graph. | |
Returns an adjacency matrix representation of the graph. | |
Get method for the edge cargo. | |
Computes a pairwise distance matrix from an alignment graph. | |
Returns the smallest distributed id. That is, the return value is guaranteed to be the smallest id obtained so far. | |
Returns the largest distributed id plus 1. That is, the return value is guaranteed to be an upper bound on all distributed ids. | |
Get method for the next source pointer. | |
Get method for the next target pointer. | |
Utility function returning a value that represents nil. Useful for various graph algorithms, e.g., missing predecessors, vertices that have not been visited, etc. | |
Get method for an item's property. | |
Get method for the source. | |
Get method for the target. | |
Access to the value. | |
Iterates to the first position of a container. | |
Iterates to the last position of a container. | |
Iterates to next position. | |
Iterates to pevious position. | |
The graph this iterator is working on. | |
Determines the number of ids that were obtained. | |
Checks whether the given id is in use or not. | |
Number of incoming edges for a given vertex. | |
Computes a minimum spanning tree on a graph. | |
Accesses the next source pointer. | |
Accesses the next target pointer. | |
Number of edges in a graph. | |
Number of vertices in a graph. | |
Obtains a new id from the id manager. | |
Number of outgoing edges for a given vertex. | |
Computes a minimum spanning tree on a graph. | |
Performs a progressive alignment. | |
Accesses the property of an item in the property map. | |
Releases all ids handled by this id manager at once. | |
Releases a given id so it can be redistributed later on. | |
Removes an edge from the graph. For automatons a label is required. | |
Removes the incoming edges of a given vertex. | |
Removes the outgoing edges of a given vertex. | |
Removes a vertex. | |
Initializes an edge map | |
Initializes a vertex map. | |
Computes a guide tree from a distance matrix. | |
Returns the source vertex of an edge. | |
Decomposes a directed graph into its strongly connected components. | |
Given a multiple alignment, this function calculates the sum-of-pairs score. | |
Accesses the target of an EdgeStump. | |
Returns the target vertex of an edge. | |
Performs a topological sort on a directed acyclic graph (DAG). | |
Determines whether there is a path between any two given vertices or not. | |
Transposes a graph, either in-place or from source to dest. | |
Performs the consistency extension proposed in T-Coffee. | |
Computes a guide tree from a distance matrix. | |
Reference to the value. |
Graph: Alignment Graph
Assigns a new string set to an alignment graph. | |
Converts an alignment graph into an alignment matrix. | |
Finds a vertex given a sequence id and a position. | |
Gets the begin position for this vertex descriptor in the sequence. | |
Gets the length of the label of a given vertex descriptor in the sequence. | |
Finds the first position in a sequence that is not assigned to a nil vertex. | |
Finds the last position in a sequence that is not assigned to a nil vertex. | |
Gets the string set of an alignment graph. | |
Gets the label that is associated with this vertex descriptor. | |
Gets the sequence id that is associated with this vertex descriptor. | |
Gets the string set of an alignment graph. |
Graph: Automaton
Assigns a new root vertex to the automaton. | |
Creates the root in a tree or an automaton. | |
Get method for the root of a tree or an automaton. | |
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. | |
Tests whether a given vertex is the root or not. | |
Returns the label of the out-edge this iterator points to. | |
Parses a string one character at a time and moves accordingly in the automaton. | |
Gets a reference to the root of the tree. |
Graph: Hmm
Assigns a begin state. | |
Assigns a new emission probability. | |
Assigns an end state. | |
Assigns a new transition probability. | |
Implements the backward algorithm. | |
Returns a reference to the begin state. | |
Returns a reference to the emission probability. | |
Returns a reference to the end state. | |
Implements the forward algorithm. | |
Returns the begin state. | |
Returns the emission probability. | |
Returns the end state. | |
Returns the transition probability. | |
Returns a reference to the transition probability. | |
Implements the viterbi algorithm. |
Graph: Oracle
Creates a factor oracle. | |
Creates a factor oracle for the reversed string. |
Graph: Tree
Adds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge. | |
Assigns a new root vertex to the automaton. | |
Returns the child vertex of an edge. | |
Returns all leaves underneath a given vertex. | |
Creates the root in a tree or an automaton. | |
Get method for the root of a tree or an automaton. | |
Tests whether a given vertex is a leaf or not. | |
Tests whether a given vertex is the root or not. | |
Number of children of a given tree vertex. | |
Number of tree edges. | |
Returns the parent vertex of an edge. | |
Removes all children from the tree given a parent. | |
Removes a child from the tree given a parent. | |
Gets a reference to the root of the tree. |
Graph: Trie
Creates a trie. | |
Creates a trie for all reversed keywords. |
Graph: Word 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. | |
Parses a string one character at a time and moves accordingly in the automaton. |
Index
Returns an alignment of the occurences of the representative substring in the index text. | |
Shortcut for | |
Shortcut for | |
Test whether iterator points to a node with only leaf-children. | |
Count the number of children of a tree node. | |
Returns the number of occurences of representative in the index text. | |
Creates a Burrows-Wheeler table from a given text and suffix array. | |
Creates a child table from a given lcp table. | |
Builds an index on a StringSet storing how often a q-gram occurs in each sequence. | |
Creates a lcp table from a given text and suffix array. | |
Builds a q-gram index on a sequence. | |
Builds the directory of a q-gram index on a sequence. | |
Builds the suffix array of a q-gram index on a sequence. | |
Creates a suffix array from a given text. | |
Builds a q-gram index on a sequence. | |
Shortcut for | |
Returns | |
Returns a specific Fibre of an Index object. | |
Returns the number of sequences, which contain the representative as a substring. | |
Returns an occurence of the representative substring in the index text. | |
Returns all occurences of the representative substring in the index text. | |
Returns the characters left beside all occurence of the representative substring in the index text. | |
Iterates down one edge or a path in a tree. | |
Iterates to the next sibling in a tree. | |
Iterates up one edge to the parent in a tree. | |
Computes a (lower) hash value for a shape applied to a sequence. | |
Computes a unique hash value of a shape, even if it is shorter than its span. | |
Computes a unique hash value for the adjacent shape, even if it is shorter than q. | |
Computes the hash value for the adjacent shape. | |
Computes an upper hash value for a shape applied to a sequence. | |
Shortcut for | |
Shortcut for | |
Creates a specific Fibre. | |
Shortcut for | |
Shortcut for | |
Shortcut for | |
Shortcut for | |
Shortcut for | |
On-demand creation of a specific Fibre. | |
Shortcut for | |
Shortcut for | |
Returns whether a specific Fibre is present. | |
Shortcut for | |
Test whether iterator points to a leaf. | |
Test whether the occurences of an iterator's representative mutually differ in the character left of the hits. | |
Test whether the characters left of the two occurences of representative are equal. | |
Test whether iterator points to a suffix. | |
Test whether iterator points to the root node. | |
Test whether the representative occurs only once in every sequence. | |
Returns the last common ancestor of two tree nodes. | |
Returns the length of the longest-common-prefix of two Suffix Tree nodes. | |
Shortcut for | |
Shortcut for | |
If | |
If | |
Sorts a string of occurrences. | |
Returns the first character of the edge from an | |
Returns a substring representing the edge from an | |
Returns the length of the edge from the | |
Returns the length of the substring representing the path from root to | |
Shortcut for | |
Returns the length of the substring representing the path from root to | |
Returns a substring representing the path from root to | |
Shortcut for | |
Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. | |
Number of relevant positions in a shape. |
Input/Output
Asynchronously loads records from a specific position in a file. | |
Asynchronously saves records to a specific position in a file. | |
Cancels an asynchronous request. | |
Closes a file. | |
Waits for all open requests to complete. | |
Iterates to next position. | |
Tries to determine the format of a file. | |
The number of items/characters. | |
Opens a file. | |
Opens a temporary file. | |
Loads a record from file. | |
Loads records from a file. | |
Loads records from a specific position in a file. | |
Finds the first feature specified by 'key' starting from position 'start' in the feature table (the feature table can be obtained by calling readLineType with the two-character code "FT"). | |
Reads the information belonging to the two-character line code specified. | |
Read meta information from file. | |
Changes the length. | |
Sets the current file pointer to the beginning. | |
Changes the current file pointer. | |
Sets the file end to the current pointer. | |
Gets the file size. | |
Gets the current file pointer. | |
Waits for an asynchronous request to complete. | |
Writes to stream. | |
Saves records to a file. | |
Saves records to a specific position in a file. |
Iteration
Assigns value to item. | |
Determines whether an iterator is at the beginning position. | |
Determines whether an iterator is at the end position. | |
Tests whether iterator is at nil position. | |
The begin of a container. | |
Container of an iterator. | |
The difference between two iterators. | |
The end of a container. | |
Access to the value. | |
Iterates to the first position of a container. | |
Iterates to the last position of a container. | |
Iterates some steps further. | |
Iterates to next position. | |
Moves iterator to nil position. | |
Iterates to pevious position. | |
Assigns value to item. | |
Position of an iterator. | |
Reference to the value. |
Map
Insert another value into a multi map. | |
Returns a cargo given a key. | |
Removes a value from a map. | |
Removes a value from a map. | |
Find a value in a map. | |
Determines whether a map contains a value given key. | |
Insert new value into map. | |
Subscript operator | |
Returns a value given a key. |
Memory
Allocates memory from heap. | |
Deallocates all memory blocks. | |
Deallocates memory. |
Miscellaneous
adds an instance of CommandLineOption to the CommandLineParser | |
Adjusts the priority of the first item. | |
adds a line of text to the help output of the CommandLineParser | |
Returns the count of passed arguments. | |
Fills the passed variable | |
Fills the passed variable | |
Returns true if the there is an option registered in the parser, that has the passed optionIdentifier | |
Prints the complete help message for your parser to the stream. | |
Returns the help text associated with the CommandLineOption object | |
A value that identifies the underlying sequence. | |
Returns true if the option was set on the parsed command line. | |
Computes logarithm of base 2 for integer types | |
Returns the long option name of a CommandLineOption object | |
Returns true if the option was set on the parsed command line. | |
using this option you can define how many non parameterized options are required by your program. | |
Sets the help text associated with the CommandLineOption object | |
Sets the long option name of a CommandLineOption object | |
Sets the short option name of a CommandLineOption object | |
Determines whether two sequences share the same resource. | |
Prints a short help message for your parser to the stream | |
Returns the short option name of a CommandLineOption object |
Motif Search
Counts the number of times each residue of a fixed sequence alphabet occurs in a given sequence. | |
Counts the number of times each residue of a fixed sequence alphabet occurs in a given set of sequences. | |
Adds a value of a specific type to each element of a given FrequencyDistribution object. | |
Determines the background letter frequencies in a given dataset | |
Calculates the binomial coefficient C(n,k). | |
Concatenates the background frequency with the profile for the motif component. | |
Converts a pattern into a profile which consists of a set of frequency distributions. | |
Coverts a residue to a frequency distribution (profile). | |
Converts a set of sequence patterns into a profile. | |
Determines the consensus pattern of a given profile. | |
Displays a given set of strings. | |
Displays all found motif candidates. In the case of the Projection Motif Finder the function displays the consensus pattern of the found motif candidate. | |
Represents the EM algorithm as used by MEME. | |
Calculates the factorial value of any integer number. | |
Represents the main function which is used to start the search for noticeable motif patterns. | |
Determines the Hamming distance between two sequences. | |
Determines the corresponding sequence pattern given the hash value. | |
Logarithmizes each element of a given FrequencyDistribution object. | |
Determines the normalized frequencies. | |
Determines the residue position in a given FrequencyDistribution object with the maximum frequency. | |
Determines the sum of all frequencies in a given FrequencyDistribution object. |
Pipelining
Initiates a read process. | |
Initiates a write process. | |
Returns a bundle of two objects. | |
Returns a bundle of three objects. | |
Returns a bundle of five objects. | |
Terminates a read process. | |
Terminates a write process. | |
Gets the first element of the remaining stream. | |
Pops the first element of the remaining stream. | |
Appends an item at the end of an input stream. |
Scoring
Coordinates computation by invokating extrapolation, alphabet extension, rounding, scaling, type conversion and symmetrization. | |
returns the distance on which PAM matrix computation is based. | |
returns entropy of the PAM matrix. | |
The score for aligning two values according to a scoring scheme. |
Searching
Search for a Pattern in a Finder object. | |
Score of the last found match in approximate searching. | |
Returns the haystack of a Finder object. | |
Returns the needle of a Pattern object (not implemented for some online-algorithms). | |
The minimal score a match must reach in approximate searching. | |
The scoring scheme used for finding or aligning. | |
Sets the haystack of a Finder object. | |
Sets the needle of a Pattern object and optionally induces preprocessing. | |
Sets the position of a finder. | |
Sets the minimal score a match must reach in approximate searching. | |
Sets the scoring scheme used for finding or aligning. |
Seed Handling
Adds a seed to an existing set. | |
Adds several seeds to an existing set. If a merging or chaining algorithm is used seeds are added if the merging or chaining fails. | |
Adds diagonal to the seed. | |
Calculates a banded alignment around a Seed. | |
Calculates a banded alignment around a chain of seeds. | |
Returns the diagonal of the end point. | |
Extends a seed. | |
Extenstion of seeds. | |
Constructs a alignment from a MultiSeed. | |
Calculates the best global chain using the Gusfield-Algorithm with scores (ManhattanDistance) and without. | |
Returns the most left diagonal of the seed (maximum diagonal value). | |
Returns the first position of the seed in the query. | |
Returns the first position of the seed in the database. | |
Sets the maximal distance between two seed during a chaining process. | |
btains a new id from the id manager. | |
Sets the minimum length for a seed to be saved permanently. | |
Releases a given id so it can be redistributed later on. | |
Returns the most right diagonal of the seed (minimum diagonal value). | |
Returns the last position of the seed in the query. | |
Returns the last position of the seed in the database. | |
Calculates the score of a seed. | |
Returns the score of a seed. | |
Sets a new value for the most left diagonal. | |
Updates the start point of the seed. | |
Updates the start point of the seed. | |
Sets the maximal distance between two seed during a chaining process. | |
Sets the minimum length for a seed to be saved permanently. | |
Sets a new value for the most right diagonal. | |
Updates the end point of the seed. | |
Updates the end point of the seed. | |
Returns the diagonal of the start point. |
Sequences
Adds a new string to the StringSet and returns an id. | |
Returns the sequence number of a position. | |
Returns the local sequence offset of a position. | |
Retrieves a string from the StringSet given an id. | |
Retrieves the position of a string in the StringSet given an id. | |
Converts a local/global to a global position. | |
Converts a local/global to a local position. | |
Retrieves the id of a string in the StringSet given a position. | |
Removes a string from the StringSet given an id. | |
Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. | |
Creates a subset of a given StringSet. | |
Retrieves a string from the StringSet given an id. |
SeqAn - Sequence Analysis Library - www.seqan.de