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

buildPam	Coordinates computation by invokating extrapolation, alphabet extension, rounding, scaling, type conversion and symmetrization.
getDist	returns the distance on which PAM matrix computation is based.
getEntropy	returns entropy of the PAM matrix.
getScale	Access function returning the distance dependent scaling factor used for PAM matrix computation
score	The score for aligning two values according to a scoring scheme.

Alignment

matchRefinement

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.

Alignments

assignSource	Assigns the source to a new value.
clearGaps	Remove blanks from a gapped sequence.
col	A column in an alignment.
cols	The container of columns in an alignment.
countGaps	Count blanks at a specific position in a gapped sequence.
createSource	Creates a new source.
dependentSource	Test if object depends from it's source.
detach	Makes an object independent from other objects.
emptySource	Test if there is a source.
gapValue	Returns reference to a value that is used as gap character.
globalAlignment	Computes the best global alignment of the two sequences.
heaviestIncreasingSubsequence	Computes the heaviest increasing subsequence.
insertGap	Insert one blank into a gapped sequence.
insertGaps	Insert blanks into a gapped sequence.
isGap	Test a gapped sequence for gaps at a specific position.
localAlignment	Computes the best local alignment of two sequences.
longestCommonSubsequence	Computes the longest common subsequence.
longestIncreasingSubsequence	Computes the longest increasing subsequence.
moveSource	Moves the source to a new value.
removeGap	Removes one blank from a gapped sequence.
removeGaps	Removes blanks from a gapped sequence.
row	A row in an alignment.
rows	The container of rows in an alignment.
scoreGap	Score for gaps.
scoreGapExtend	Score for extending gaps.
scoreGapOpen	Score for opening a gap.
scoreMatch	Match score.
scoreMismatch	Mismatch score.
setSource	Let an external object be the source.
smithWaterman	Computes the best local alignment of the (two) sequences given in align.
smithWatermanGetNext	Computes next best local alignment.
source	The source of an object.
sourceBegin	Begin of the source segment.
sourceEnd	End of the source segment.
sourceSegment	The used part of the source.

Alphabets

convert	Converts a value into another value.
gapValue	Returns reference to a value that is used as gap character.
infimumValue	Infimum for a given type.
ordValue	Maps an alphabet 1-to-1 to the interval [0..ValueSize).
supremumValue	Supremum for a given type.

Array Handling

arrayClearSpace	Destroys the begin of an array and keeps the rest.
arrayConstruct	Construct objects in a given memory buffer.
arrayConstructCopy	Copy constructs an array of objects into in a given memory buffer.
arrayConstructMove	Move constructs an array of objects into in a given memory buffer.
arrayCopy	Copies a range of objects into another range of objects.
arrayCopyBackward	Copies a range of objects into another range of objects starting from the last element.
arrayCopyForward	Copies a range of objects into another range of objects starting from the first element.
arrayDestruct	Destroys an array of objects.
arrayFill	Assigns one object to each element of a range.
arrayMove	Moves a range of objects into another range of objects.
arrayMoveBackward	Moves a range of objects into another range of objects starting from the last element.
arrayMoveForward	Moves a range of objects into another range of objects starting from the first element.

Chaining

chain

Computes the chain on a set of fragments.

Comparisons

compare	Compares two objects.
hasPrefix	Test whether a sequence is prefix of another sequence.
isEqual	Operator "==".
isGreater	Operator ">".
isGreaterOrEqual	Operator ">=".
isLess	Operator "<".
isLessOrEqual	Operator "<=".
isNotEqual	Operator "!=".
isPrefix	Test whether a sequence is prefix of another sequence.
lcpLength	Length of longest common prefix.

Container

clear

Resets an object.

Containers

back	The last item in container.
begin	The begin of a container.
beginPosition	Begin position of object in host.
capacity	The maximal length.
empty	Test a container for being empty.
end	The end of a container.
endPosition	End position of object in host.
erase	Erases a part of a container
fill	Resizes and fills a container.
front	The first item in container.
getValue	Access to the value.
infix	Creates infix object.
iter	Iterator to item at given position.
length	The number of items/characters.
prefix	Creates prefix object.
reserve	Increases the capacity.
resize	Changes the length.
resizeSpace	Makes free space in container
shrinkToFit	Resizes container to minimum capacity
suffix	Creates suffix object.
toCString	Access sequence as c-style string.
value	Reference to the value.

Content Manipulation

append	Concatenate two containers.
appendValue	Appends a value to a container.
assign	Assigns one object to another object.
assignValue	Assigns value to item.
getValue	Access to the value.
insertValue	Inserts a single value into a container.
move	Hands over content from one container to another container.
moveValue	Assigns value to item.
pop	Deletes item with the highest priority and adjusts the priority queue.
push	Inserts a new item and adjusts the priority queue if necessary.
replace	Replaces a part of a container with another container.
setValue	Makes holder dependent.
top	Reference to the item with the highest priority.
valueConstruct	Constructs an object at specified position.
valueDestruct	Destoys an object at specified position.

Dependent Objects

addRef	Called when dependency is added.
create	Makes an object to owner of its content.
dependent	Test whether object depends on other objects.
detach	Makes an object independent from other objects.
host	The object a given object depends on.
releaseRef	Called when dependency is released.
setBegin	Sets begin of object in host.
setBeginPosition	Sets begin position of object in host.
setEnd	Sets end of object in host.
setEndPosition	Sets begin position of object in host.
setHost	Sets the host of an object.

File

readFeature	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").
readLineType	Reads the information belonging to the two-character line code specified.

Graph

addEdge	Adds a new edge to the graph, either with or without cargo.
addEdges	Shortcut to add multiple edges at once. Creates vertices implicitly.
addVertex	Adds a new vertex to the graph.
all_pairs_shortest_path	Finds shortest paths between all pairs of vertices in a graph.
assignCargo	Assigns a new cargo to the edge.
assignNextS	Assigns another EdgeStump to the next source pointer.
assignNextT	Assigns another EdgeStump to the next target pointer.
assignProperty	Assigns a property to an item in the property map.
assignSource	Assigns a source vertex to an edge.
assignTarget	Assigns a target vertex to an edge.
atBegin	Determines whether an iterator is at the beginning position.
atEnd	Determines whether an iterator is at the end position.
bellman_ford_algorithm	Computes shortest paths from a single source in a graph.
breadth_first_search	Implements a breadth-first search on a graph.
cargo	Access to the cargo.
clear	Resets an object.
clearEdges	Removes all edges in a graph.
clearVertices	Removes all vertices in a graph.
dag_shortest_path	Computes shortest paths from a single source in a directed acyclic graph (DAG).
degree	Number of incident edges for a given vertex.
depth_first_search	Implements a depth-first search on a graph.
dijkstra	Computes shortest paths from a single source in a graph.
empty	Test a container for being empty.
findEdge	Finds an edge.
floyd_warshall	Finds shortest paths between all pairs of vertices in a graph.
ford_fulkerson	Computes a maximum flow in a directed graph.
getAdjacencyMatrix	Returns an adjacency matrix representation of the graph.
getCargo	Get method for the edge cargo.
getIdLowerBound	Returns the smallest distributed id. That is, the return value is guaranteed to be the smallest id obtained so far.
getIdUpperBound	Returns the largest distributed id plus 1. That is, the return value is guaranteed to be an upper bound on all distributed ids.
getInfinity	Utility function returning a value that represents infinity. Useful for various graph algorithms, e.g., Dijkstra.
getInfinityDistance	Utility function for various graph algorithms. The infinity distance can be used to indicate not reachable, e.g., in shortest path problem.
getNextS	Get method for the next source pointer.
getNextT	Get method for the next target pointer.
getNil	Utility function returning a value that represents nil. Useful for various graph algorithms, e.g., missing predecessors, vertices that have not been visited, etc.
getNilPredecessor	Utility function for various graph algorithms.
getProperty	Get method for an item's property.
getSource	Get method for the source.
getTarget	Get method for the target.
getValue	Access to the value.
goBegin	Iterates to the first position of a container.
goEnd	Iterates to the first position of a container.
goNext	Iterates to next position.
goPrevious	Iterates to pevious position.
hostGraph	The graph this iterator is working on.
idCount	Determines the number of ids that were obtained.
idInUse	Checks whether the given id is in use or not.
inDegree	Number of incoming edges for a given vertex.
kruskals_algorithm	Computes a minimum spanning tree on a graph.
nextS	Accesses the next source pointer.
nextT	Accesses the next target pointer.
numEdges	Number of edges in a graph.
numVertices	Number of vertices in a graph.
obtainId	Obtains a new id from the id manager.
outDegree	Number of outgoing edges for a given vertex.
prims_algorithm	Computes a minimum spanning tree on a graph.
property	Accesses the property of an item in the property map.
releaseAll	Releases all ids handled by this id manager at once.
releaseId	Releases a given id so it can be redistributed later on.
removeEdge	Removes an edge from the graph. For automatons a label is required.
removeInEdges	Removes the incoming edges of a given vertex.
removeOutEdges	Removes the outgoing edges of a given vertex.
removeVertex	Removes a vertex.
resizeEdgeMap	Initializes an edge map
resizeVertexMap	Initializes a vertex map.
sourceVertex	Returns the source vertex of an edge.
strongly_connected_components	Decomposes a directed graph into its strongly connected components.
target	Accesses the target of an EdgeStump.
targetVertex	Returns the target vertex of an edge.
topological_sort	Performs a topological sort on a directed acyclic graph (DAG).
transitive_closure	Determines whether there is a path between any two given vertices or not.
transpose	Transposes a graph, either in-place or from source to dest.
value	Reference to the value.

Graph: Alignment Graph

assignStringSet	Assigns a new string set to an alignment graph.
convertAlignment	Converts an alignment graph into an alignment matrix.
findVertex	Finds a vertex given a sequence id and a position.
fragmentBegin	Gets the begin position for this vertex descriptor in the sequence.
fragmentLength	Gets the length of the label of a given vertex descriptor in the sequence.
getFirstCoveredPosition	Finds the first position in a sequence that is not assigned to a nil vertex.
getLastCoveredPosition	Finds the last position in a sequence that is not assigned to a nil vertex.
getProjectedPosition	Finds the projected position given a sequence id and a position. Works only on alignment graphs of two sequences (Pairwise alignment).
getStringSet	Gets the string set of an alignment graph.
label	Gets the label that is associated with this vertex descriptor.
sequenceId	Gets the sequence id that is associated with this vertex descriptor.
stringSet	Gets the string set of an alignment graph.

Graph: Automaton

assignRoot	Assigns a new root vertex to the automaton.
createRoot	Creates the root in a tree or an automaton.
getRoot	Get method for the root of a tree or an automaton.
getSuccessor	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.
isRoot	Tests whether a given vertex is the root or not.
label	Returns the label of the out-edge this iterator points to.
parseString	Parses a string one character at a time and moves accordingly in the automaton.
root	Gets a reference to the root of the tree.

Graph: Oracle

createOracle	Creates a factor oracle.
createOracleOnReverse	Creates a factor oracle for the reversed string.

Graph: Tree

addChild	Adds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge.
assignRoot	Assigns a new root vertex to the automaton.
childVertex	Returns the child vertex of an edge.
collectLeaves	Returns all leaves underneath a given vertex.
createRoot	Creates the root in a tree or an automaton.
getRoot	Get method for the root of a tree or an automaton.
isLeaf	Tests whether a given vertex is a leaf or not.
isRoot	Tests whether a given vertex is the root or not.
numChildren	Number of children of a given tree vertex.
numTreeEdges	Number of tree edges.
parentVertex	Returns the parent vertex of an edge.
removeAllChildren	Removes all children from the tree given a parent.
removeChild	Removes a child from the tree given a parent.
root	Gets a reference to the root of the tree.

Graph: Trie

createTrie	Creates a trie.
createTrieOnReverse	Creates a trie for all reversed keywords.

Graph: Word Graph

getSuccessor	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.
parseString	Parses a string one character at a time and moves accordingly in the automaton.

Index

alignment	Returns an alignment of the occurences of the representative substring in the index text.
bwtAt	Shortcut for value(indexBWT(..), ..).
childAt	Shortcut for value(indexChildTab(..), ..).
childrenAreLeaves	Test whether iterator points to a node with only leaf-children.
countChildren	Count the number of children of a tree node.
countOccurrences	Returns the number of occurences of representative in the index text.
createBWTable	Creates a Burrows-Wheeler table from a given text and suffix array.
createChildTable	Creates a child table from a given lcp table.
createCountArray	Builds an index on a StringSet storing how often a q-gram occurs in each sequence.
createLCPTable	Creates a lcp table from a given text and suffix array.
createQGramIndex	Builds a q-gram index on a sequence.
createQGramIndexDirOnly	Builds the directory of a q-gram index on a sequence.
createQGramIndexSAOnly	Builds the suffix array of a q-gram index on a sequence.
createSuffixArray	Creates a suffix array from a given text.
dirAt	Shortcut for value(indexDir(..), ..).
getFibre	Returns a specific Fibre of an Index object.
getFrequency	Returns the number of sequences, which contain the representative as a substring.
getOccurrence	Returns an occurence of the representative substring in the index text.
getOccurrences	Returns all occurences of the representative substring in the index text.
getOccurrencesBWT	Returns the characters left beside all occurence of the representative substring in the index text.
goDown	Iterates down one edge or a path in a tree.
goRight	Iterates to the next sibling in a tree.
goUp	Iterates up one edge to the parent in a tree.
hash	Computes a (lower) hash value for a shape applied to a sequence.
hash2	Computes a unique hash value of a shape, even if it is shorter than its span.
hash2Next	Computes a unique hash value for the adjacent shape, even if it is shorter than q.
hashNext	Computes the hash value for the adjacent shape.
hashUpper	Computes an upper hash value for a shape applied to a sequence.
indexBWT	Shortcut for getFibre(.., ESA_BWT).
indexChildTab	Shortcut for getFibre(.., ESA_ChildTab).
indexCreate	Creates a specific Fibre.
indexDir	Shortcut for getFibre(.., QGram_Dir).
indexLCP	Shortcut for getFibre(.., ESA_LCP).
indexLCPE	Shortcut for getFibre(.., ESA_LCPE).
indexRawSA	Shortcut for getFibre(.., ESA_RawSA).
indexRawText	Shortcut for getFibre(.., ESA_RawText).
indexRequire	On-demand creation of a specific Fibre.
indexSA	Shortcut for getFibre(.., ESA_SA).
indexShape	Shortcut for getFibre(.., QGram_Shape).
indexSupplied	Returns whether a specific Fibre is present.
indexText	Shortcut for getFibre(.., ESA_Text).
isLeaf	Test whether iterator points to a leaf.
isLeftMaximal	Test whether the occurences of an iterator's representative mutually differ in the character left of the hits.
isPartiallyLeftExtensible	Test whether the characters left of the two occurences of representative are equal.
isRightTerminal	Test whether iterator points to a suffix.
isRoot	Test whether iterator points to the root node.
isUnique	Test whether the representative occurs only once in every sequence.
lca	Returns the last common ancestor of two tree nodes.
lcp	Returns the length of the longest-common-prefix of two Suffix Tree nodes.
lcpAt	Shortcut for value(indexLCP(..), ..).
lcpeAt	Shortcut for value(indexLCPE(..), ..).
orderOccurrences	Sorts a string of occurrences.
parentEdgeLabel	Returns a substring representing the edge from an iterator node to its parent.
rawtextAt	Shortcut for value(indexRawText(..), ..).
repLength	Returns the length of the substring representing the path from root to iterator node.
representative	Returns a substring representing the path from root to iterator node.
saAt	Shortcut for value(indexSA(..), ..).
stringToShape	Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object.
weight	Number of relevant positions in a shape.

Input/Output

areadAt	Asynchronously loads records from a specific position in a file.
awriteAt	Asynchronously saves records to a specific position in a file.
cancel	Cancels an asynchronous request.
close	Closes a file.
flush	Waits for all open requests to complete.
goNext	Iterates to next position.
guessFileFormat	Tries to determine the format of a file.
length	The number of items/characters.
open	Opens a file.
openTemp	Opens a temporary file.
read	Loads a record from file.
read	Loads records from a file.
readAt	Loads records from a specific position in a file.
readMeta	Read meta information from file.
resize	Changes the length.
rewind	Sets the current file pointer to the beginning.
seek	Changes the current file pointer.
setEOF	Sets the file end to the current pointer.
size	Gets the file size.
tell	Gets the current file pointer.
waitFor	Waits for an asynchronous request to complete.
write	Writes to stream.
write	Saves records to a file.
writeAt	Saves records to a specific position in a file.

Iteration

assignValue	Assigns value to item.
atBegin	Determines whether an iterator is at the beginning position.
atEnd	Determines whether an iterator is at the end position.
atNil	Tests whether iterator is at nil position.
begin	The begin of a container.
container	Container of an iterator.
difference	The difference between two iterators.
end	The end of a container.
getValue	Access to the value.
goBegin	Iterates to the first position of a container.
goEnd	Iterates to the first position of a container.
goFurther	Iterates some steps further.
goNext	Iterates to next position.
goNil	Moves iterator to nil position.
goPrevious	Iterates to pevious position.
moveValue	Assigns value to item.
position	Position of an iterator.
value	Reference to the value.

Memory

allocate	Allocates memory from heap.
clear	Deallocates all memory blocks.
deallocate	Deallocates memory.

Miscellaneous

adjustTop	Adjusts the priority of the first item.
id	A value that identifies the underlying sequence.
log2	Computes logarithm of base 2 for integer types
shareResources	Determines whether two sequences share the same resource.

Motif Search

absFreqOfLettersInSeq	Counts the number of times each residue of a fixed sequence alphabet occurs in a given sequence.
absFreqOfLettersInSetOfSeqs	Counts the number of times each residue of a fixed sequence alphabet occurs in a given set of sequences.
addValue	Adds a value of a specific type to each element of a given FrequencyDistribution object.
backgroundFrequency	Determines the background letter frequencies in a given dataset
binomialCoefficient	Calculates the binomial coefficient C(n,k).
completeProfile	Concatenates the background frequency with the profile for the motif component.
convertPatternToProfile	Converts a pattern into a profile which consists of a set of frequency distributions.
convertResidueToFrequencyDist	Coverts a residue to a frequency distribution (profile).
convertSetOfPatternsToProfile	Converts a set of sequence patterns into a profile.
determineConsensusSeq	Determines the consensus pattern of a given profile.
display	Displays a given set of strings.
displayResult	Displays all found motif candidates. In the case of the Projection Motif Finder the function displays the consensus pattern of the found motif candidate.
em	Represents the EM algorithm as used by MEME.
factorial	Calculates the factorial value of any integer number.
findMotif	Represents the main function which is used to start the search for noticeable motif patterns.
hammingDistance	Determines the Hamming distance between two sequences.
inverseHash	Determines the corresponding sequence pattern given the hash value.
logarithmize	Logarithmizes each element of a given FrequencyDistribution object.
normalize	Determines the normalized frequencies.
posOfMax	Determines the residue position in a given FrequencyDistribution object with the maximum frequency.
sum	Determines the sum of all frequencies in a given FrequencyDistribution object.

Pipelining

beginRead	Initiates a read process.
beginWrite	Initiates a write process.
bundle2	Returns a bundle of two objects.
bundle3	Returns a bundle of three objects.
bundle5	Returns a bundle of five objects.
endRead	Terminates a read process.
endWrite	Terminates a write process.
front	Gets the first element of the remaining stream.
pop	Pops the first element of the remaining stream.
push	Appends an item at the end of an input stream.

Searching

find	Search for a Pattern in a Finder object.
getScore	Score of the last found match in approximate searching.
haystack	Returns the haystack of a Finder object.
needle	Returns the needle of a Pattern object (not implemented for some online-algorithms).
scoreLimit	The minimal score a match must reach in approximate searching.
scoringScheme	The scoring scheme used for finding or aligning.
setHaystack	Sets the haystack of a Finder object.
setNeedle	Sets the needle of a Pattern object and optionally induces preprocessing.
setPosition	Sets the position of a finder.
setScoreLimit	Sets the minimal score a match must reach in approximate searching.
setScoringScheme	Sets the scoring scheme used for finding or aligning.

Sequences

assignValueById	Adds a new string to the StringSet and returns an id.
getSeqNo	Returns the sequence number of a position.
getSeqOffset	Returns the local sequence offset of a position.
getValueById	Retrieves a string from the StringSet given an id.
idToPosition	Retrieves the position of a string in the StringSet given an id.
posGlobalize	Converts a local/global to a global position.
posLocalize	Converts a local/global to a local position.
positionToId	Retrieves the id of a string in the StringSet given a position.
removeValueById	Removes a string from the StringSet given an id.
stringSetLimits	Retrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
subset	Creates a subset of a given StringSet.
valueById	Retrieves a string from the StringSet given an id.

SeqAn - Sequence Analysis Library - www.seqan.de