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
Check whether a BamStream object is at end when reading. | |
Check whether a SequenceStream is at the end of the file. | |
Return the clipping begin position as a source position. | |
Create FaiIndex from FASTA file. | |
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. | |
Computes the wavelet tree structure of a text. | |
Creates the LF table | |
Return the clipping end position as a source position. | |
Flush output when writing. | |
Write all data from SequenceStream to disk. | |
Returns | |
Returns whether a specified bit is set or not. | |
Returns the character of a specified position. | |
Sets the dollar position.. | |
Returns the character used to substitute the dollar sign. | |
Returns the position in RightArrayBinaryTree of the left child vertex. | |
Returns the position of the iterator in the host. | |
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 number of vertices in the subtree starting at the position an iterator points to. | |
Translates position in host to virtual (view) position. | |
Check whether the BamStream object has is in the failure state. | |
Check whether a SequenceStream object is ready for reading. | |
Open a BamStream object for reading/writing. | |
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. Read the next sequence record from SequenceStream. | |
Reset BamStream object to status after construction. | |
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. | |
Sets the dollar position.. | |
Sets the character used to substitute the dollar sign. | |
Set the end position of the clipped gapped sequence, given a source position. | |
Set the LfTable of the compressed suffix array.. | |
Translates virtual (view) position to position in host. | |
Write sequence records from to a SequenceStream object. | |
Write one BamAlignmentRecord to a BamStream. | |
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 occurences 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 occurences 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. | |
Clear clipping from Gaps object. | |
Clear gaps and clipping from Gaps object. | |
A column in an alignment. | |
The container of columns in an alignment. | |
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. | |
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. | |
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. | |
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. |
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 tag value from a BamHeaderRecord or 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 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 the value of a tag through a BamTagsDict. |
Basic
Reset all pointers connected to a given one. |
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 a specified bit to true or false. | |
Set the bit with the given index to the given value. |
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. |
Bsic
Return underlying object. |
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. |
Chaining
Computes the chain on a set of fragments. |
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 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. | |
Appends a name to a name store. | |
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. Writes the basic information about the ArgParseOption to the provided stream. | |
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. | |
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. Returns the number of vertices in a wavelet tree. | |
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
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. | |
Returns the number of occurences 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 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 number of occurrences of a specified character from the start to a specified position. | |
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. | |
Shortcut for | |
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Returns whether a specific Fibre is present. | |
Shortcut for | |
Test whether a tree 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 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 | |
Shortcut for | |
Returns the position of the character L[c] in F. | |
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 | |
Inverse of the hash function; for ungapped shapes. | |
Number of relevant positions in a shape. |
Input / Output
Attach to already open input / output file. | |
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. | |
Return id (index in the file) of a sequence in a FAI file. | |
Query a GZ File Stream for being "direct." | |
Return number of sequences known to an FaiIndex. | |
Parse genomic region string store results in GenomicRegion. | |
Read a FAI index. | |
Read first sequence from a FASTA file. | |
Load the infix of a sequence from a FaiIndex. | |
Load a whole sequence from an FaiIndex. | |
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. | |
Write out an FaiIndex object. |
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. | |
Determines whether an iterator is at the end position. | |
Cancels an asynchronous request. | |
check whether the data provided by reader is (one of) the specified format(s). | |
Closes a 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. | |
Iterates 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 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 | |
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. | |
Query whether the next record is of a given type. | |
Opens a file. | |
Opens a temporary file. | |
Loads a record from file. | |
Loads records from a file. | |
reads an entire document from a Stream, 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. | |
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 | |
reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record. | |
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 | |
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. | |
Sets the file end to the current pointer. | |
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 Stream. | |
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. | |
Reference to the value. | |
Waits for an asynchronous request to complete. | |
Writes to stream. | |
Saves records to a file. Writes the basic information about the ArgParseOption to the provided stream. | |
writes an entire document to a Stream | |
Saves records to a specific position in a file. | |
write one record (e.g. a single DNA-sequence and its meta data) to a Stream |
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 | |
reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record. | |
reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record. | |
reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record. |
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. | |
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. | |
Add list item to ToolDoc object. Appends a list item to the ArgumentParser. | |
Add list item to ToolDoc object. Appends a list item to the ArgumentParser. | |
Adds a ArgParseOption object to the ArgumentParser. | |
Add section to ToolDoc object. Begins a new section of ArgParseOption the help output of the ArgumentParser. | |
Add section to ToolDoc object. Begins a new section of ArgParseOption the help output of the ArgumentParser. | |
Add subsection to ToolDoc object. | |
Add text line/paragraph to ToolDoc. Appends a text paragraph to the ArgumentParser. | |
Add text line/paragraph to ToolDoc. Appends a text paragraph to the ArgumentParser. | |
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. | |
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 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 the ArgParseArgument object as const std::vector. Returns all values of an option given on the command line. | |
Returns all values of the ArgParseArgument object as const std::vector. Returns all values of an option given on the command line. | |
Get tool category of ToolDoc object. Get tool category of ArgumentParser object. | |
Get tool category of ToolDoc object. Get tool category of ArgumentParser 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. | |
Get short description of ToolDoc object. Gets short description of ArgumentParser. | |
Get short description of ToolDoc object. Gets short description of ArgumentParser. | |
Retrieve size of terminal. | |
Get version string from ToolDoc object. Get version string from ArgumentParser object. | |
Get version string from ToolDoc object. Get version string from ArgumentParser object. | |
Returns true if a value for the given position is available. | |
Returns true if a default value was given for that argument. Returns whether an option has a default value or not. | |
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. | |
Hides the ArgParseOption from the help screen.
Hides the ArgParseOption defined by the parameter | |
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 the argument is an input file. | |
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 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. | |
Returns whether option is visible on the help screen. Default is true. | |
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 ToolDoc object. Set tool category for ArgumentParser object. | |
Set tool category for ToolDoc object. Set tool category for ArgumentParser object. | |
Set date string for ToolDoc object. Sets date string of ArgumentParser. | |
Set date string for ToolDoc object. Sets date string of ArgumentParser. | |
Sets the default value for the given option. | |
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 whether or not the option is mandatory.
Sets whether or not the option defined by the parameter | |
Set short description for ToolDoc object. Sets short description of the ArgumentParser object. | |
Set short description for ToolDoc object. Sets short description of the ArgumentParser object. | |
Sets the set of allowed values of a ArgParseArgument object. | |
Set version string for ToolDoc object. Sets version string of ArgumentParser. | |
Set version string for ToolDoc object. Sets version string of ArgumentParser. | |
Determines whether two sequences share the same resource. | |
Return sum from an accumulator. | |
Returns the system time in seconds. | |
Saves records to a file. 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. | |
Return a Mersenne-Twister random number. | |
Return a random number between 0 and 1 using mtRand. | |
Initialize the Mersenne-Twister random number generator. | |
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 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 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 |
Synopsis Data Structures
Get the frequent items. | |
Register an item as seen with a HotList. | |
Manually remove an item from a HotList. |
Testing & Debugging
Print the current SeqAn debug level and the compiler flags to the given stream. |
internal
Returns an alignment of the occurences of the representative substring in the index text. |
SeqAn - Sequence Analysis Library - www.seqan.de