| 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