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
Add to the default values of an option of an ArgumentParser. | |
Check whether a BamStream object is at end when reading. | |
Check whether a SequenceStream is at the end of the file. | |
Returns a reference to the last seed diagonal. | |
Returns an iterator to the beginning of the seed digonals. | |
Return the clipping begin position as a source position. | |
Create FaiIndex from FASTA file. | |
Global chaining of seeds. | |
Clears the LF table. | |
Clears the prefix sum table. | |
Clears the rank dictionary. | |
Clears the dictionary. | |
Return the begin position of the clipping in the unclipped gapped sequence. | |
Return the end position of the clipping in the unclipped gapped sequence. | |
Close BamStream object's underlying file. | |
Close the SequenceStream. | |
Returns the number of occurrences of a specified character from the start to a specified position. | |
This functions creates a compressed suffix array with a specified compression factor. | |
Creates the LF table | |
Creates the prefix sum table | |
This functions creates the dictionary. | |
Computes the wavelet tree structure of a text. | |
This functions creates the dictionary structure. | |
Clears the LF table. | |
Returns whether or not the rank dictionary is empty. | |
Returns whether or not the dictionary is empty. | |
Returns an iterator to the end of the seed diagonals. | |
Return the clipping end position as a source position. | |
Find a tag by its key for a BamTagsDict object. | |
Flush output when writing. | |
Write all data from SequenceStream to disk. | |
Returns a reference to the first seed diagonal. | |
Returns the number of different characters in the prefix sum table. | |
Returns | |
Returns the character of a given position within the prefix sum table. | |
This function returns the pivot character of the node the iterator currently points to. | |
Returns the position of a given character within the prefix sum table. | |
Returns file format extensions given a format tag. | |
Returns the position in RightArrayBinaryTree of the left child vertex. | |
Returns the position of the iterator in the host. | |
Returns the prefix sum of a given position. | |
Returns the rank (the number of bits set from the start of the bit string) of a specified position. | |
Returns the position in RightArrayBinaryTree of the right child vertex. | |
Returns the character used to substitute the sentinel sign. | |
Returns the number of vertices in the subtree starting at the position an iterator points to. | |
Returns the character of a specified position. | |
Returns the character of a specified position. | |
Returns the prefix sum of a given position. | |
Sets the iterator to the left child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false. | |
Sets the iterator to the right child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false. | |
Translates position in host to virtual (view) position. | |
Creates a specific Fibre. | |
Returns whether a specific Fibre is present. | |
Returns the segment of the last found match in haystack. | |
Check whether the BamStream object has is in the failure state. | |
Check whether a SequenceStream object is ready for reading. | |
Returns whether the bit with the given index is set to 1. | |
Returns the number of diagonals in the chained seed. | |
Returns the number of different characters in the prefix-sum table. | |
Open a BamStream object for reading/writing. | |
This functions loads a dictionary from disk. | |
This functions loads a LF table from disk. | |
This functions loads a prefix-sum table from disk. | |
This functions loads a dictionary from disk. | |
This functions loads a RightArrayBinaryTree from disk. | |
This functions loads a dictionary from disk. | |
Open or re-open a file using a SequenceStream. | |
Returns a reference to the entry of the prefix sum table of a given position. | |
Read all sequence records from a SequenceStream object. | |
Read a given number of sequence records from SequenceStream. | |
Read one BamAlignmentRecord from a BamStream. | |
Read the next sequence record from SequenceStream. | |
Reset BamStream object to status after construction. | |
Resize the prefix sum table to be able to store more or less characters. | |
This functions saves a compressed suffix array to disk. | |
This functions saves an index to disk. | |
This functions saves a LF table to disk. | |
This functions saves a prefix-sum table to disk. | |
This functions saves a dictionary to disk. | |
This functions saves a RankSupportBitString to disk. | |
This functions saves a RightArrayBinaryTree to disk. | |
This functions saves a dictionary to disk. | |
This functions saves a sparse string to disk. | |
Returns the number of matches and mismatches of the seed. This is the longest true diagonal fitting into its dimensions. | |
Returns whether a specified position is a sentinel position. | |
Set the begin position of the clipped gapped sequence, given a source position. | |
Sets the begin position of the clipping. | |
Sets the end position of the clipping. | |
Set default value of an option of an ArgumentParser. | |
Set the end position of the clipped gapped sequence, given a source position. | |
Set help text of argument parser. | |
Set the LfTable of the compressed suffix array. | |
Set largest allowed value for an option or argument of an ArgumentParser. | |
Set smallest allowed value for an option or argument of an ArgumentParser. | |
Returns a reference to the entry of the prefix-sum table of a given position. | |
Sets the sentinel position.. | |
Sets the character used to substitute the sentinel sign. | |
Set valid values for an argument or option of an ArgumentParser. | |
Compute split alignments. | |
This function computes the position of a specified position in the suffix array (additionally containing entries for the sentinels. The returned position correspond to the suffix array of the original text without sentinels. | |
Transposes matrix | |
Returns the value stored at a specified position in the compressed suffix-array. | |
Translates virtual (view) position to position in host. | |
Write FASTA or FASTQ records. | |
Write sequence records from to a SequenceStream object. | |
Write one BamAlignmentRecord to a BamStream. | |
Write one FASTA or FASTQ record. | |
Write one sequence record from to a SequenceStream object. |
Alignment Free
Computes the pairwise similarity scores for a set of sequences | |
Calculates the covariance for the number of word occurrences for two words in a sequence of length n, given a background model. | |
Calculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p) | |
Calculate word periodicity (indicator for overlaps) | |
Calculates the probability of a sequence given a Bernoulli model (String of background frequencies) | |
Calculates the variance for the number of word occurrences of a word in a sequence of length n given a background model. | |
Counts kmers in a sequence. Optionally, a background model is returned. | |
Cut out all masked sequences from a Dna5String. | |
Transform a String into a StringSet containing this String. |
Alignments
Assign the source of a Gaps object, copying data. | |
Computes the best global pairwise alignment between two sequences given a non-empty seed chain. | |
Clear clipping from Gaps object. | |
Clear gaps and clipping from Gaps object. | |
A column in an alignment. | |
The container of columns in an alignment. | |
Reports number of continues gaps right of current iterator position. | |
Return the "gap" value from an alphabet. | |
Projects a position of one sequence taking part in a pairwise match onto the other sequence. | |
Compute next suboptimal local alignment. | |
Computes the best global pairwise alignment. | |
Computes the best global pairwise alignment score. | |
Computes a global multiple alignment. | |
Computes the heaviest common subsequence between two strings using the match information given in an alignment graph. | |
Computes the heaviest increasing subsequence. | |
Returns reference to sequence from entry. | |
Insert one gap into a gapped sequence. | |
Insert multiple gaps into a gapped sequence. | |
Integrates an alignment into another by copying the gaps. | |
Query whether a given clipped view position is a gap. | |
Returns true if the segment match is in reverse orientation. | |
Return length of the gapped sequence. | |
Computes the best pairwise local alignment using the Smith-Waterman algorithm. | |
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. | |
Compute next suboptimal local alignment. | |
Returns position stored in | |
Remove one gap from a gapped sequence. | |
Remove multiple gaps 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. | |
Helper function for element access, depending on score type. | |
Set gap opening and extension score. | |
Set gap extension score. | |
Set gap opening score. | |
Set match score. | |
Set mismatch score. | |
Set the source of a Gaps object, do not copy if possible. | |
Loads the sequences of a stringset into an alignment. | |
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. | |
Return length of the gapped sequence without clipping. | |
Returns value of character referenced by |
Alphabets
Assign quality values between strings. | |
Assigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a sequence. | |
Converts a value into another value. | |
Convert an integer quality value into its ASCII representation for FASTQ (Phred scale). | |
Return the "gap" value from an alphabet. | |
Returns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with a specified element from a sequence. | |
Supremum for a given type. | |
Infimum for a given type. | |
Maps an alphabet 1-to-1 to the interval [0..ValueSize). | |
Return the "unknown" value from an alphabet. | |
Returns size of an alphabet. |
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 |
BAM I/O
Assign tags in BAM format to tags in SAM format. | |
Assign tags in SAM format to tags in BAM format. | |
Convert BamAlignmentRecord to an Align object. | |
Erase tag from BamTagsDict. | |
Extract and cast "atomic" value from tags string with index | |
Find a tag's key of a BamHeaderRecord. | |
Returns length of BamAlignmentRecord's projection in reference. | |
Return char identifying the type of the atomic argument. | |
Return size of the type identified by | |
Return key of a tag by index. | |
Get key of a tag by index. | |
Return tag value from a BamHeaderRecord or BamTagsDict. | |
Return the value of a tag by its index in the BamTagsDict. | |
Query index for number of unaligned reads. | |
Return true if a BamAlignmentRecord has the "all properly aligned" flag set. | |
Return true if a BamAlignmentRecord has the "PCR or optical duplicate" flag set. | |
Return true if a BamAlignmentRecord has the "first fragment of template" flag set. | |
Return true if a BamAlignmentRecord has the "last fragment of template" flag set. | |
Return true if a BamAlignmentRecord has the "multiple" flag set. | |
Return true if a BamAlignmentRecord has the "next fragment reverse-complemented" flag set. | |
Return true if a BamAlignmentRecord has the "next fragment unmapped" flag set. | |
Return true if a BamAlignmentRecord has the "does not pass quality controls" flag set. | |
Return true if a BamAlignmentRecord has the "reverse-complemented" flag set. | |
Return true if a BamAlignmentRecord has the "reverse-complemented" flag set. | |
Return true if a BamAlignmentRecord has the "secondary alignment" flag set. | |
Return true if a BamAlignmentRecord has the "fragment unmapped" flag set. | |
Seek to orphans block in BAM BGZF stream using an index. | |
Seek in BAM BGZF stream using an index. | |
Return reference to name store from BamIOContext. | |
Return reference to name store cache from BamIOContext. | |
Load a BAM index from a given file name. | |
Set tag value of a BamHeaderRecord. | |
Set the value of a tag through a BamTagsDict. |
Basic
Reset all pointers connected to a given one. | |
Return underlying object. |
Bit Twiddling
Set all bits to 0. | |
Set the bit with the given index to 0. | |
Returns whether the bit with the given index is set to 1. | |
Returns number of set bits in an integer. | |
Set the bit with the given index to 1. | |
Set the bit with the given index to the given value. |
C++ built-in
C++ built-in cast operator. | |
C++ built-in deallocation operator. | |
C++ built-in array deallocation operator. | |
C++ built-in allocation operator. | |
C++ built-in array allocation operator operator. | |
C++ built-in logical negation operator. | |
C++ built-in inequal comparison operator. | |
C++ built-in modulo operator. | |
C++ built-in modulo assignment operator. | |
C++ built-in bitwise AND operator. | |
C++ built-in reference/address-of operator. | |
C++ built-in logical AND operator. | |
C++ built-in bitwise AND assignment operator. | |
C++ built-in greater-than comparison operator. | |
C++ built-in bitwise right shift operator. | |
C++ built-in bitwise get-from/stream extraction operator. | |
C++ built-in bitwise right shift assignment operator. | |
C++ built-in greather-than-or-equal comparison operator. | |
C++ built-in less-than comparison operator. | |
C++ built-in bitwise left shift operator. | |
C++ built-in bitwise put-to/stream insertion operator. | |
C++ built-in bitwise left shift assignment operator. | |
C++ built-in less-than-or-equal comparison operator. | |
C++ built-in function call operator. | |
C++ built-in multiplication operator. | |
C++ built-in indirection/object-pointed-to-by operator. | |
C++ built-in multiplication assignment operator. | |
C++ built-in addition operator. | |
C++ built-in unary plus (integer promotion) operator. | |
C++ built-in prefix increment operator. | |
C++ built-in suffix increment operator. | |
C++ built-in addition assignment operator. | |
C++ built-in comma operator. | |
C++ built-in subtraction operator. | |
C++ built-in unary minus (additive inverse) operator. | |
C++ built-in structure dereference operator. | |
C++ built-in member-pointed-to-by-b-of-object-pointed-to-by-a operator. | |
C++ built-in prefix decrement operator. | |
C++ built-in suffix decrement operator. | |
C++ built-in subtraction assignment operator. | |
C++ built-in division operator. | |
C++ built-in division assignment operator. | |
C++ built-in Assignment operator. | |
C++ built-in equal comparison operator. | |
C++ built-in array subscript operator. | |
C++ built-in bitwise XOR operator. | |
C++ built-in bitwise XOR assignment operator. | |
C++ built-in bitwise NOT operator. |
Class: Align
Integrates an alignment into another by copying the gaps. |
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. |
Concepts
Removes unused variable warning. | |
Tests for a boolean expression. | |
Tests for equality of types. |
Consensus
Compute consensus alignment. | |
Perform realignment similar to Anson-Myers algorithm. |
Containers
The last item in container. | |
The begin of a container. | |
Begin position of object in host. | |
The maximal length. | |
Resets an object. | |
Makes an object to owner of its content. | |
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. | |
Destoys an object at specified position. |
Dependent Object
Assign to the host of a given value. | |
Clear the host of the given object. | |
Construct the host of the given object. | |
Query dependent state of a hosted object. | |
Query emptiness state of a hosted object. | |
Assign to the host of a given value. |
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. | |
Return host iterator. | |
Sets begin of object in host. | |
Sets begin position of object in host. | |
Set container of an adaptor iterator. | |
Sets end of object in host. | |
Sets begin position of object in host. | |
Sets the host of an object. | |
Sets the position of a finder. |
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. | |
Add or update a key-value pair of the current annotation. | |
Build index for a BamTagsDict object. | |
Calculates a string with insert sizes for each pair match. | |
Calculates a string that maps the | |
Removes all contigs from a fragment store. | |
Removes all reads from a fragment store. | |
Clear all key-value pairs of the current annotation. | |
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. | |
Creates a new left-most child of the current node and returns an iterator to it. | |
Creates a new right-most child of the current node and returns an iterator to it. | |
Creates a new right sibling of the current node and returns an iterator to it. | |
Returns the current annotation. | |
Get the "clear" range of a read alignment. | |
Get the id/index of a string in a name store with a cache. | |
Returns the mate number of read for a given | |
Returns the identifier of the current annotation. | |
Returns the identifier of the parent node in the annotation tree of the current annotation. | |
Returns the read with the given | |
Returns the type name of the current annotation. | |
Returns a unique name of the current annotation. | |
Given a key, retrieve its value of the current annotation. | |
Move the iterator down to the left-most child in the annotation tree. | |
Go to the next node in preorder DFS skipping the current node's subtree. | |
Go to the next node in preorder DFS skipping the subtrees of the current node and of all its siblings. | |
Move the iterator right to the next sibling in the annotation tree. | |
Go to the root node in the annotation tree. | |
Moves the iterator to an arbitrary node given its annotationId. | |
Move the iterator up in the annotation tree. | |
Return | |
Returns a boolean value that indicates whether the current node is the last child. | |
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. | |
Returns a new iterator to the first child node of the current annotation in the annotation tree. | |
Returns a new iterator to the right sibling of the current annotation in the annotation tree. | |
Returns a new iterator to the parent node of the current annotation in the annotation tree. | |
Convert from gap-space in the global alignment to the sequence-space on the reference. | |
Convert from sequence space on the reference to gap space in the global alignment. | |
Prints a window of the visible layout of reads into a outstream. | |
Loads records from a file. | |
Recreate a name store cache. | |
Sets the identifier of the current annotation. | |
Sets the type name of the current annotation. | |
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. |
GFF I/O
Return reference to name store from GffIOContext. | |
Return reference to name store cache from GffIOContext. |
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. | |
Initializes a vertex map with values of an array. | |
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 to an existing edge. | |
Initializes a vertex map with values of an array. | |
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. | |
Builds an Alignment Graph from a set of input alignments. | |
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. | |
Computes a guide tree from a distance matrix. | |
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 or vertex. | |
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. | |
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. | |
Compute weakly connected components of a directed graph. |
Index
Appends a value to a container. | |
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 rank (number of occurrences) of a specified character up to a specified position. | |
Returns the number of occurrences of representative substring or a q-gram in the index text. | |
Returns the number of occurrences of a q-gram for every sequence of a StringSet . | |
Return the number of sequences in an index' underlying 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 | |
Search for repeats in a text. | |
Returns a specific fibre of a container. | |
Returns a specific fibre of a fm index. | |
Returns a specific fibre of a container. | |
Returns a specific fibre of a prefix-sum table. | |
Returns a specific fibre of a dictionary. | |
Returns a specific fibre of a container. | |
Returns a specific fibre of a container. | |
Returns a specific fibre of a dictionary. | |
Returns a specific fibre of a container. | |
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 occurrence of the representative substring or a q-gram in the index text. | |
Returns all occurrences of the representative substring or a q-gram in the index text. | |
Returns the characters left beside all occurrence 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. | |
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Creates a specific Fibre. | |
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On-demand creation of a specific Fibre. | |
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Returns whether a specific Fibre is present. | |
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Test whether a tree iterator points to a leaf. | |
Test whether the occurrences of an iterator's representative mutually differ in the character left of the hits. | |
Test whether the characters left of the two occurrences of representative are equal. | |
Test whether iterator points to a suffix. | |
Test whether a tree 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 | |
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Returns the position of an character at a specified position of L in F. L corresponds to the last column of the sorted cyclic rotations of the original text, while F correspond to the first column. | |
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 occurrences of representative substring or a q-gram in the index text. | |
Shortcut for | |
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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 | |
Inverse of the hash function; for ungapped shapes. | |
Number of relevant positions in a shape. |
Input/Output
Give advice about use of a memory-mapped file segment. | |
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. | |
Returns | |
Attach to already open input / output file. | |
Cancels an asynchronous request. | |
Cancel all outstanding transactions of a memory-mapped file segment. | |
Check that the EOF marker is present in a BGZF(/BAM) file. | |
Reset a FaiIndex object to the state after default construction. | |
Reset a GenomicRegion object to the same state after default construction. | |
Reset a GffRecord object. | |
Close a file and its memory mapping. | |
Closes a file. | |
Close a memory mapping and resize and close the underlying file. | |
count characters in a line not including \r and \n | |
Check whether a sequence ends with a given suffix. | |
Waits for all open requests to complete. | |
Wait for all outstanding transactions of a memory-mapped file segment. | |
Return id (numeric index in the file) of a sequence in a FAI file. | |
Advance record reader to next position. | |
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. | |
check whether the data provided by reader is (one of) the specified format(s). | |
Query a GZ File Stream for being "direct." | |
Check if character is alpha-numeric | |
Check if character is a upper or lowercase letter | |
Check if character is either ' ' or '\t' | |
Check if character is a control character | |
Check if character is a digit | |
Check if character is printable and not white space | |
Check if character is printable, i.e. not a control character | |
Check if character is a white-space character | |
Return the file size of a memory mapping. | |
The number of items/characters. | |
Cast from a String-type to a numerical type | |
Cast from a String-type to a numerical type | |
Load a score matrix from a file. | |
Map a segment of a file into memory. | |
Query whether the next record is of a given type. | |
Return number of sequences known to an FaiIndex. | |
Open a file to be mapped into memory. | |
Opens a file, stream, or persistent string. | |
Open a temporary file to be mapped into memory. | |
Opens a temporary file. | |
Parse genomic region string store results in GenomicRegion. | |
Returns the current position of the reader. | |
Read a FAI index. | |
Loads a record from file. | |
Loads records from a file. | |
reads an entire document from a StreamConcept, by the means of RecordReader | |
Read characters from stream as long as characters are letters | |
Loads records from a specific position in a file. | |
Read characters from stream as long as characters are digits | |
Read characters from stream, as long as they are DNA5 characters. Skip over whitespaces. | |
Read first sequence from a FASTA 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"). | |
Read characters from stream as long as the number is a valid floating point numbers. | |
Read characters from stream as long as characters are graph characters. | |
Read characters from stream as long as characters are identifiers (alphanumeric, | |
Read characters from stream as long as characters are letters | |
Read a line from stream and save it to buffer | |
Read a line from stream and save it to buffer, remove trailing blanks | |
Reads the information belonging to the two-character line code specified. | |
Read meta information from file. | |
Read exactly n characters from stream into buffer | |
Read n characters from stream into buffer, but skip certain Chars | |
Read one gff record. | |
reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader | |
Load the infix of a sequence from a FaiIndex. | |
Load a whole sequence from an FaiIndex. | |
Read characters from stream into buffer until Blank is encountered | |
Read characters from stream into buffer until Char is encountered | |
Read characters from stream into buffer until one of the given characters is encountered | |
Read characters from stream until a tab or line-break occurs. | |
Read characters from stream into buffer until Whitespace is encountered | |
Change the size of a memory-mapped file segment. | |
Resize the underlying file. | |
Resizes a container. If the new length exceeds the old length the new elements are filled with copies of | |
Returns | |
Sets the current file pointer to the beginning. | |
Changes the current file pointer. | |
Return length of the sequence with the given id in the FaiIndex. | |
Return the name of the sequence with the given id in the FaiIndex. | |
Sets the file end to the current pointer. | |
Returns the current position of the reader. | |
Gets the file size. | |
Skip (i.e. read without saving) characters from stream until non-Blank is encountered | |
Skip one character that must be equal to a given one for this function to succeed. | |
Skip a line in stream and go to beginning of next | |
Skip exactly n characters from stream | |
Skip n characters from stream, not counting whitespaces | |
Skip (i.e. read without saving) characters from stream until Blank is encountered | |
Skip (i.e. read without saving) characters from stream until Char is encountered | |
Skip (i.e. read without saving) characters from stream until printable, non-' ' character is encountered | |
Skip input until the first graphical(see isgraph) character of a line is equal to c | |
Skip input until a line begins with a one of the characters in str | |
Skip input until a line begins with str. | |
Skip (i.e. read without saving) characters from stream until String is encountered | |
Skip (i.e. read without saving) characters from stream until Whitespace is encountered | |
Skip (i.e. read without saving) characters from stream until non-Whitespace is encountered | |
Divides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter. | |
Split an EMBL header line. | |
Split an GenBank header field/value. | |
Start the first reading pass. | |
Start the second reading pass. | |
Check whether a sequence starts with a given prefix. | |
Check end-of-file state of a StreamConcept. | |
Return the stream's error code. | |
Flush the underlying stream. | |
Read next character from stream without advancing current position. | |
Write different types to stream | |
Read a block of bytes into a buffer. | |
Read next character from stream and advance the current position. | |
Perform a seek operation on the stream. | |
Get the position in the current stream. | |
Write a block of bytes from a buffer into a stream. | |
Write one character to the stream. | |
Gets the current file pointer. | |
Unmap a memory-mapped file segment. | |
Returns the current value of the reader. | |
Waits for an asynchronous request to complete. | |
Write out an FaiIndex object. | |
Writes to stream. | |
Write a score matrix to a stream. | |
Saves records to a file. | |
writes an entire document to a StreamConcept | |
Saves records to a specific position in a file. | |
Writes one gff record to a stream. | |
write one record (e.g. a single DNA-sequence and its meta data) to a StreamConcept |
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. |
Local Match Store
Append a new local match to a LocalMatchStore | |
Read Lastz "general" format record. | |
reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader | |
reads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader |
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. | |
An implementation of |
Miscellaneous
Adds a ArgParseArgument object to the ArgumentParser. | |
Adds/appends a new value to the list of default values. | |
Appends a description paragraph to the ArgumentParser documentation. | |
Adds an interval to an interval tree. | |
Adds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions. | |
Appends a list item to the ArgumentParser. | |
Add list item to ToolDoc object. | |
Adds a ArgParseOption object to the ArgumentParser. | |
Begins a new section of ArgParseOption the help output of the ArgumentParser. | |
Add section to ToolDoc object. | |
Add subsection to ToolDoc object. | |
Appends a text paragraph to the ArgumentParser. | |
Add text line/paragraph to ToolDoc. | |
Adds a text section to the ArgumentParser. | |
Adds a text subsection to the ArgumentParser. | |
Adds a line of text to the usage output of the ArgumentParser. | |
Adjusts the priority of the first item. | |
Append two ToolDoc objects. | |
Return average from an accumulator. | |
Clear entries from ToolDoc object. | |
Return sum from an accumulator. | |
Returns the cpu time in seconds. | |
Create an interval tree. | |
Find all intervals that contain the query point or overlap with the query interval. | |
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. | |
Return set identifier, given an element identifier. | |
Get tool name of ArgumentParser object. | |
Returns a reference to the specified argument. | |
Returns the label for the given ArgParseArgument. Either the user defined label is returned or a default label (based on the ArgumentType is used). | |
Returns the value of the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) you can specify which value you want to get. If not set the first value will be returned. | |
Retrieves the value of an argument given by its position. | |
Returns the number of values stored in the specified option. | |
Returns all values of an option given on the command line. | |
Returns all values of the ArgParseArgument object as const std::vector. | |
Get tool category of ArgumentParser object. | |
Get tool category of ToolDoc object. | |
Get date string from ToolDoc object. | |
Get method for the left boundary. | |
Get man title from ToolDoc object. | |
Get tool name of ToolDoc object. | |
A value that identifies the underlying sequence. | |
Returns a reference to the specified option. | |
Retrieves the value of an option given either the short or long name. | |
Returns the number of values stored in the specified option. | |
Returns all values of an option given on the command line. | |
Get method for the right boundary. | |
Gets short description of ArgumentParser. | |
Get short description of ToolDoc object. | |
Retrieve size of terminal. | |
Get version string from ArgumentParser object. | |
Get version string from ToolDoc object. | |
Returns true if a default value was given for that argument. | |
Returns whether an option has a default value or not. | |
Returns whether a certain option is registered in the parser. | |
Returns true if a value for the given position is available. | |
Hides the ArgParseOption from the help screen. | |
Hides the ArgParseOption defined by the parameter | |
Check whether we are printing to a terminal. | |
Returns whether option is a switch. | |
Returns whether the argument is a double. | |
Returns whether option is hidden on the help screen. Default is false. | |
Returns whether the argument is an input file. | |
Returns whether the argument is a 64 bit integer. | |
Returns whether the argument is an integer. | |
Returns whether the argument can be given multiple times. | |
Returns whether the argument is an output file. | |
Returns whether the option is mandatory. | |
Returns true if a value was assigned to the argument. | |
Returns whether an option was set on the parsed command line. | |
Returns whether the argument is a string. | |
Check whether we are printing to a terminal. | |
UNION() operation for UF data structure. | |
Access to the left boundary. | |
Computes floored logarithm of base 2 for integer types | |
Returns the number of allowed values for this ArgParseArgument. | |
Parses the command line. | |
Print ToolDoc object in a given format. | |
Prints the complete help message for the parser to a stream. | |
Prints a short help message for the parser to a stream | |
Prints the version information of the parser to a stream. | |
Adds a value to an accumulator. | |
Removes an interval from the interval tree. | |
Access to the right boundary. | |
Sets application name of ArgumentParser. | |
Set tool category for ArgumentParser object. | |
Set tool category for ToolDoc object. | |
Sets date string of ArgumentParser. | |
Set date string for ToolDoc object. | |
Sets the default value for the given option. | |
Sets the set of allowed values of a ArgParseArgument object. | |
Set version string for ToolDoc object. | |
Sets the maximum value of a ArgParseArgument object. | |
Sets the minimum value of a ArgParseArgument object. | |
Set tool name for ToolDoc object. | |
Sets whether or not the option is mandatory. | |
Sets whether or not the option defined by the parameter | |
Sets short description of the ArgumentParser object. | |
Set short description for ToolDoc object. | |
Sets the set of allowed values of a ArgParseArgument object. | |
Sets version string of ArgumentParser. | |
Set version string for ToolDoc object. | |
Determines whether two sequences share the same resource. | |
Return sum from an accumulator. | |
Returns the system time in seconds. | |
Writes the basic information about the ArgParseOption to the provided stream. | |
Exports the app's interface description to a .ctd file. | |
Replaces invalid XML characters in the given sequence with their valid XML equivalent. |
Modifier
Complement a sequence or a StringSet in-place. | |
Reverse an object/container 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. |
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. |
Parallelism
Compute splitters for a sequence of objects. |
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
Default default random number generator object of a given type. | |
Pick a random number using a random number generator object, possibly following the given distribution. | |
Reset and re-seed MersenneTwister | |
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. | |
Returns the maximal out-of-order distance of adjacent hits. | |
Score of the last found match in approximate searching. | |
Returns 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 getWindowFindHits 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 Chained Seed. | |
Returns the diagonal of the start point. | |
Returns the begin position of the seed in the database. | |
Returns the begin position of the seed in the query. | |
Returns the diagonal of the end point. | |
Returns the end position of the seed in the database. | |
Returns the end position of the seed in the query. | |
Extends a seed. | |
Returns the leftmost diagonal of the seed (minimum diagonal value). | |
Returns the threshold to distinguish between high-scoring and low-scoring seeds. | |
Returns the score of the seed. | |
Sets the begin position of the seed in the database. | |
Sets the begin position of the seed in the query. | |
Sets the end position of the seed in the database. | |
Returns the end position of the seed in the query. | |
Sets a new value for the leftmost diagonal. | |
Sets the threshold at which seeds are considered high-scoring. | |
Set the score value of a seed. | |
Sets a new value for the rightmost diagonal. | |
Removes diagonals from the given first one to the end of the seed's diagonals. | |
Returns the rightmost diagonal of the seed (maximum diagonal value). |
Sequences
Adds a new string to the StringSet and returns an id. | |
Returns true if the iterator is at the end of a sequence. | |
Returns the concatenation sequence of all sequences in a StringSet. | |
Creates the global reference of a Journaled Set. | |
Apply the journal to the underlying string, destructively on the underlying string. | |
Returns the sequence number of a position. | |
Returns the local sequence offset of a position. | |
Retrieves a string from the StringSet given an id. | |
Returns the global reference sequence of a Journaled Set. | |
Retrieves the position of a string in the StringSet given an id. | |
Returns whether journaled string has modifications. | |
Joins a Journaled String to a Journaled Set by computing and journaling differences to the global reference sequence. | |
Call advise function for memory mapped files. | |
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. | |
Prepend a value to a container. | |
Removes a string from the StringSet given an id. | |
Sets the global reference of a Journaled Set. | |
Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions. | |
Append a list of the words in the string, using sep as the delimiter string StringSet. | |
Retrieves a string from the StringSet given an id. |
Statistics
Computes the expectation 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 |
Testing & Debugging
Print the current SeqAn debug level and the compiler flags to the given stream. |
internal
Returns an alignment of the occurrences of the representative substring in the index text. |
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