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
| Returns the number of occurences of a q-gram for every sequence of a StringSet . | |
| Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel | |
| Find all intervals that contain the query point or overlap with the query interval. | |
| Apply the journal to the underlying string, destructively on the underlying string. | |
| Projects a position of one sequence taking part in a pairwise match onto the other sequence. | |
| Returns true if the segment match is in reverse orientation. | |
| Return a random number between 0 and 1 using mtRand. | |
| Prepend a value to a container. | |
| Perform realignment similar to Anson-Myers algorithm. | |
| 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 |
Alignments
| Assigns the source to a new value. | |
| Remove blanks from a gapped sequence. | |
| Begin position of the source segment. | |
| Position of the end of the source segment. | |
| A column in an alignment. | |
| The container of columns in an alignment. | |
| Count characters at a specific position in a gapped sequence. | |
| 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 a global multiple alignment. | |
| Computes the heaviest increasing subsequence. | |
| Insert one blank into a gapped sequence. | |
| Insert blanks into a gapped sequence. | |
| Integrates an alignment into another by copying the gaps. | |
| Test a gapped sequence for gaps at a specific position. | |
| Computes the best local alignment of two sequences. | |
| 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. | |
| Set gap opening and extension score. | |
| Set gap extension score. | |
| Set gap opening score. | |
| Set match score. | |
| Set mismatch score. | |
| Let an external object be the source. | |
| Loads the sequences of a stringset into an 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. | |
| Transforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned. | |
| Transforms source to view position. |
Alphabets
| Assign quality value between strings. | |
| Assign quality to a character from an alphabet with integrated quality. | |
| Converts a value into another value. | |
| Returns reference to a value that is used as gap character. | |
| Supremum for a given type. | |
| Infimum for a given type. | |
| Maps an alphabet 1-to-1 to the interval [0..ValueSize). |
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. |
Atomic Operations
| Atomically add an integer to another integer. | |
| Compare-and-Swap operation. | |
| Atomically decrement an integer. | |
| Atomically increment an integer. | |
| Lock-free implementation of | |
| Lock-free implementation of | |
| Atomically combine two integers with | |
| Atomically combine wto integers with |
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 Smith-Waterman 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. | |
| 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. |
Class: Align
| Integrates an alignment into another by copying the gaps. | |
| Computes the best local alignment of two sequences. |
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 | |
| 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. | |
| 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. | |
| Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
| 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 sequence into a container. | |
| 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. | |
| Swaps the contents of two values. | |
| 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
| 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. | |
| 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. |
Fragment Store
| Appends an aligned read entry to a fragment store. | |
| Appends two paired-end reads to a fragment store. | |
| Appends a name to a name store. | |
| Appends a read to a fragment store. | |
| Calculates a string with insert sizes for each pair match. | |
| Calculates a string that maps the | |
| Removes all reads from a fragment store. | |
| Removes invalid aligned reads and rename | |
| Renames | |
| Converts all matches to a multiple global alignment in gap-space. | |
| Converts pair-wise alignments to a multiple global alignment. | |
| Appends a name to a name store. | |
| Returns the mate number of read for a given | |
| Returns the read with the given | |
| Calculates a visible layout of aligned reads. | |
| Manually loads a contig sequence. | |
| Loads contigs into fragment store. | |
| Loads reads into fragment store. | |
| Locks a contig sequence from being removed. | |
| Locks all contig sequences from being removed. | |
| Performs a binary lower bound search on the aligned reads. | |
| Prints a window of the visible layout of reads into a outstream. | |
| Loads records from a file. | |
| Recreate a name store cache. | |
| Stably sort aligned reads. | |
| Removes a previous contig lock and clears sequence no further lock exist. | |
| Removes a previous lock for all contigs and clears sequences without lock. | |
| Removes a previous contig lock. | |
| Removes a previous lock for all contigs. | |
| Performs a binary upper bound search on the aligned reads. | |
| Saves records to a file. | |
| Write contigs from fragment store into file. |
Graph
| Adds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge. | |
| 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 begin state. | |
| Assigns a new cargo to the edge. | |
| Assigns a new emission probability. | |
| Assigns an end state. | |
| 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 new root vertex to the graph. | |
| Assigns a silent status to a state. | |
| Assigns a source vertex to an edge. | |
| Assigns a new string set to an alignment graph. | |
| Assigns a target vertex to an edge. | |
| Assigns a new transition probability. | |
| Determines whether an iterator is at the beginning position. | |
| Determines whether an iterator is at the end position. | |
| Implements the backward algorithm. | |
| Returns a reference to the begin state. | |
| Computes shortest paths from a single source in a directed graph. | |
| Implements a breadth-first search on a graph. | |
| Test whether an automaton can parse a string completely. | |
| Access to the cargo. | |
| Returns the child vertex of an edge. | |
| Resets an object. | |
| Removes all edges in a graph. | |
| Removes all vertices in a graph. | |
| Returns all leaves underneath a given vertex. | |
| Decomposes an undirected graph into its connected components. | |
| Converts an alignment graph into an alignment matrix. | |
| Creates a factor oracle. | |
| Creates a factor oracle for the reversed string. | |
| Creates the root in a tree or an automaton. | |
| Creates a trie of all suffixes of a text. | |
| Creates a trie. | |
| Creates a trie for all reversed keywords. | |
| 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. | |
| Returns a reference to the emission probability. | |
| Test a container for being empty. | |
| Returns a reference to the end state. | |
| Finds an edge. | |
| Finds a vertex given a sequence id and a position. | |
| Finds shortest paths between all pairs of vertices in a graph. | |
| Computes a maximum flow in a directed graph. | |
| Implements the forward algorithm. | |
| Gets the begin position for this fragment or this vertex descriptor in the sequence. | |
| Gets the length of the label of a given vertex descriptor in the sequence. | |
| Generates random state and alphabet sequences of a given HMM. | |
| Returns an adjacency matrix representation of the graph. | |
| Returns the begin state. | |
| Get method for the edge cargo. | |
| Computes a pairwise distance matrix from an alignment graph. | |
| Returns the emission probability. | |
| Returns the end state. | |
| Finds the first position in a sequence that is not assigned to a nil vertex. | |
| 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. | |
| Finds the last position in a sequence that is not assigned to a nil vertex. | |
| 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 root of a tree or an automaton. | |
| Get method for the source. | |
| Gets the string set of 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. | |
| Get method for the target. | |
| Returns the transition probability. | |
| 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. | |
| Tests whether a given vertex is a leaf or not. | |
| Tests whether a given vertex is the root or not. | |
| Indicates whether a state is silent or not. | |
| Computes a minimum spanning tree on a graph. | |
| Returns the label of the out-edge this iterator points to (for automatons). | |
| Gets the label that is associated with this vertex descriptor or the sequence that is associated with a fragment. | |
| Accesses the next source pointer. | |
| Accesses the next target pointer. | |
| Number of children of a given tree vertex. | |
| Number of edges in a graph. | |
| Number of tree edges. | |
| Number of vertices in a graph. | |
| Obtains a new id from the id manager. | |
| Number of outgoing edges for a given vertex. | |
| Returns the parent vertex of an edge. | |
| Parses a string one character at a time and moves accordingly in the automaton. | |
| 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 all children from the tree given a parent. | |
| Removes a child from the tree given a parent. | |
| 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. | |
| Gets a reference to the root of the tree. | |
| Gets the sequence id that is associated with this vertex descriptor or with a sequence of a fragment. | |
| Reference to the silent status of a state. | |
| Computes a guide tree from a distance matrix. | |
| Returns the source vertex of an edge. | |
| Gets the string set of an alignment graph. | |
| 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). | |
| Returns a reference to the transition probability. | |
| 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 a full or group-based consistency extension. | |
| Computes a guide tree from a distance matrix. | |
| Reference to the value. | |
| Implements the viterbi algorithm. |
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 substring or a q-gram 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. | |
| Creates a matrix storing the number of common q-grams between all pairs of sequences. | |
| Returns an occurence of the representative substring or a q-gram in the index text. | |
| Returns all occurences of the representative substring or a q-gram in the index text. | |
| Returns the characters left beside all occurence of the representative substring in the index text. | |
| Return the q-gram step size used for index creation. | |
| Iterates down one edge or a path in a tree. | |
| Iterates to the next sibling in a tree. | |
| Move iterator to the root node. | |
| Iterates up one edge to the parent in a tree. | |
| Computes a (lower) hash value for a shape applied to a sequence. | |
| Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span | |
| Computes a unique hash value for the adjacent shape, even if it is shorter than q. | |
| Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span. | |
| Computes the hash value for the adjacent shape. | |
| Computes an upper hash value for a shape applied to a sequence. | |
| Shortcut for | |
| Shortcut for | |
| Shortcut for | |
| 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 | |
| Returns the zero-based node depth of the | |
| If | |
| If | |
| Returns the vertex descriptor of the parent node. | |
| 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 | |
| Returns the suffix array interval borders of occurences of representative substring or a q-gram in the index text. | |
| Shortcut for | |
| Shortcut for | |
| Returns the length of the substring representing the path from root to | |
| Returns a substring representing the path from root to | |
| Initializes a vertex map. | |
| Shortcut for | |
| Change the q-gram step size used for index creation. | |
| Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position). | |
| Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object. | |
| Shortcut for | |
| Number of relevant positions in a shape. |
Input/Output
| Appends all sequences stored in files of directory to a StringSet. | |
| 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 id of a sequence file fragment. | |
| 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. | |
| Guesses a file format from the contents of a sequence file. | |
| Guesses a file format from a sequence file name. | |
| The number of items/characters. | |
| Load a score matrix from a file. | |
| 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. | |
| Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
| 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. | |
| Divides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter. | |
| Gets the current file pointer. | |
| Waits for an asynchronous request to complete. | |
| Writes to stream. | |
| Saves records to a file. | |
| Saves records to a file. | |
| 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. | |
| Get the the key of the element. | |
| Subscript operator | |
| Returns a value given a key. |
Memory
| Allocates memory from heap. | |
| Deallocates all memory blocks. | |
| Deallocates memory. |
Misc
| Returns the cpu time in seconds. | |
| Return a Mersenne-Twister random number. | |
| Initialize the Mersenne-Twister random number generator. | |
| Returns the system time in seconds. |
Miscellaneous
| Return a CommandLineOption object extended by an argument text. | |
| Adds an extra line of text below the help text of an option. | |
| Adds an interval to an interval tree. | |
| Adds a line of text to the help output of the CommandLineParser. | |
| Adds a CommandLineOption object to the CommandLineParser. | |
| Adds a new section the help output of the CommandLineParser. | |
| Adds a line of text to the title output of the CommandLineParser. | |
| Adds a line of text to the usage output of the CommandLineParser. | |
| Adds a line of text to the version output of the CommandLineParser. | |
| Adjusts the priority of the first item. | |
| Returns the count of passed arguments. | |
| Returns the argument text of a CommandLineOption object. | |
| Create an interval tree. | |
| :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. | |
| Returns an argument set on the command line. | |
| Returns all arguments set on the command line. | |
| Get method for the left boundary. | |
| Retrieves the value of a long-name option given on the command line. | |
| Retrieves the value of a short-name option given on the command line. | |
| Returns all values of a long-name option given on the command line. | |
| Returns all values of a short-name option given on the command line. | |
| Get method for the right boundary. | |
| Returns whether a certain long-name option is registered in the parser. | |
| Returns whether a certain short-name option is registered in the parser. | |
| Prints the complete help message for the parser to a stream. | |
| Returns the help text associated with the CommandLineOption object. | |
| A value that identifies the underlying sequence. | |
| Returns whether option is a switch. | |
| Returns whether option argument can be a double. | |
| Returns whether option is hidden on the help screen. | |
| Returns whether option argument can be an integer. | |
| Returns whether an option label should be printed on the help screen. | |
| Returns whether the option can be given multiple times. | |
| Returns whether option is mandatory. | |
| Returns whether a long-name option was set on the parsed command line. | |
| Returns whether a short-name option was set on the parsed command line. | |
| Returns whether option argument can be a string. | |
| Access to the right boundary. | |
| Computes logarithm of base 2 for integer types | |
| Returns the long-name of a CommandLineOption object. | |
| Parses the command line. | |
| Sets the number of arguments (non-parameterized options) are required by the program. | |
| Access to the right boundary. | |
| Sets the help text associated with the CommandLineOption object. | |
| Sets the long-name of a CommandLineOption object. | |
| Set the option type. | |
| Sets the short-name of a CommandLineOption object. | |
| Determines whether two sequences share the same resource. | |
| Prints a short help message for the parser to a stream | |
| Returns the short-name of a CommandLineOption object. | |
| Prints a version text to a stream. |
Miscellaneous:
| Print the current SeqAn debug level and the compiler flags to the given stream. |
Modifier
| Complement a sequence or a StringSet in-place. | |
| Reverse and complement a sequence or a StringSet in-place. | |
| Convert characters in sequence or StringSet to lower case in-place. | |
| Convert characters in sequence or StringSet to lower case in-place. |
Modifiers
| Reverse an object/container in-place. |
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. | |
| Gets the motif out of a MotifFinder. If pos is given, the pos-th motif is returned, otherwise the first motif is returned. | |
| Determines the Hamming distance between two sequences. | |
| Determines the corresponding sequence pattern given the hash value. | |
| Logarithmizes each element of a given FrequencyDistribution object. | |
| Gets number of motifs in the MotifFinder. | |
| 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. |
Random
| Pick a random number using a random number generator object, possibly following the given distribution. | |
| Shuffle the given container. |
Scoring
| Returns the score for aligning the characters | |
| Returns the score for aligning the characters | |
| Returns the score for extending a horizontal gap after | |
| Returns the score for extending a vertical gap after | |
| Returns the score for a horizontal gap after | |
| Returns the score for opening a horizontal gap after | |
| Returns the score for opening a vertical gap after | |
| Returns the score for a vertical gap after | |
| Set the value of the given matrix to the default value. | |
| Set the substitution score between two values. |
Searching
| Search for a Pattern in a Finder object. | |
| Search the begin of an approximate match. | |
| Score of the last match found by findBegin during approximate searching. | |
| Score of the last found match in approximate searching. | |
| Gets the string of hits from the finder | |
| Returns the haystack of a Finder object. | |
| Returns the needle of a Pattern object (not implemented for some online-algorithms). | |
| Returns a pair of the begin and end position in the haystack or needle for the last hit found. | |
| Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found. | |
| 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. | |
| Initializes the pattern. Sets the finder on the begin position. Gets the first non-repeat range and sets it in the finder. Used together with windowFindBegin and windowFindEnd. | |
| Flushes the pattern. Used together with windowFindBegin and windowFindNext. | |
| Searches over the next window with the finder. The found hits can be retrieved with getSwiftHits Used together with windowFindBegin and windowFindEnd. |
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. | |
| Dimension of a seed. | |
| Returns the diagonal of the end point. | |
| Extends a seed. | |
| Extends a seed and increases the score. | |
| Extension of seeds. | |
| Extension of seeds with score calculation. | |
| Constructs a alignment from a ChainedSeed. | |
| 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. | |
| The begin position of segment in a seed. | |
| 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. | |
| The end position of segment in a seed. | |
| 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 begin position of segment in a 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. | |
| Sets end position of segment in a seed. | |
| Returns the diagonal of the start point. |
Sequences
| Adds a new string to the StringSet and returns an id. | |
| Returns the concatenation sequence of all sequences in a StringSet. | |
| 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 to a local/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. | |
| Retrieves a string from the StringSet given an id. |
sequences
| Returns true if the iterator is at the end of a sequence. |
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