Functions

| 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
countOccurrencesMultiple | Returns the number of occurences of a q-gram for every sequence of a StringSet .
expectation | Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel
findIntervals | Find all intervals that contain the query point or overlap with the query interval.
flatten | Apply the journal to the underlying string, destructively on the underlying string.
getProjectedPosition | Projects a position of one sequence taking part in a pairwise match onto the other sequence.
isReversed | Returns true if the segment match is in reverse orientation.
mtRandDouble | Return a random number between 0 and 1 using mtRand.
prependValue | Prepend a value to a container.
reAlign | Perform realignment similar to Anson-Myers algorithm.
variance | Computes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel
zscore | Computes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel
Alignments
assignSource | Assigns the source to a new value.
clearGaps | Remove blanks from a gapped sequence.
clippedBeginPosition | Begin position of the source segment.
clippedEndPosition | Position of the end of the source segment.
col | A column in an alignment.
cols | The container of columns in an alignment.
countCharacters | Count characters at a specific position in a gapped sequence.
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.
globalMsaAlignment | Computes a global multiple alignment.
heaviestIncreasingSubsequence | Computes the heaviest increasing subsequence.
insertGap | Insert one blank into a gapped sequence.
insertGaps | Insert blanks into a gapped sequence.
integrateAlign | Integrates an alignment into another by copying the gaps.
isGap | Test a gapped sequence for gaps at a specific position.
localAlignment | Computes the best local alignment of two sequences.
localAlignment | Computes the best local alignment of two sequences.
longestCommonSubsequence | Computes the longest common subsequence.
longestIncreasingSubsequence | Computes the longest increasing subsequence.
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.
moveSource | Moves the source to a new value.
multiLocalAlignment | Computes multiple local alignments of two sequences.
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.
setScoreGap | Set gap opening and extension score.
setScoreGapExtend | Set gap extension score.
setScoreGapOpen | Set gap opening score.
setScoreMatch | Set match score.
setScoreMismatch | Set mismatch score.
setSource | Let an external object be the source.
setStrings | Loads the sequences of a stringset into an alignment.
source | The source of an object.
sourceBegin | Begin of the source segment.
sourceEnd | End of the source segment.
sourceLength | Length of the source.
sourceSegment | The used part of the source.
toSourcePosition | Transforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned.
toViewPosition | Transforms source to view position.
Alphabets
assignQualities | Assign quality value between strings.
assignQualityValue | Assign quality to a character from an alphabet with integrated quality.
convert | Converts a value into another value.
gapValue | Returns reference to a value that is used as gap character.
maxValue | Supremum for a given type.
minValue | Infimum for a given type.
ordValue | Maps an alphabet 1-to-1 to the interval [0..ValueSize).
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.
Atomic Operations
atomicAdd | Atomically add an integer to another integer.
atomicCas | Compare-and-Swap operation.
atomicDec | Atomically decrement an integer.
atomicInc | Atomically increment an integer.
atomicMax | Lock-free implementation of x = max(x, y).
atomicMin | Lock-free implementation of x = min(x, y).
atomicOr | Atomically combine two integers with OR operation.
atomicXor | Atomically combine wto integers with XOR operation.
Blast
atBegin | Determines whether an iterator is at the beginning position.
atBegin | Determines whether an iterator is at the beginning position.
atEnd | Determines whether an iterator is at the end position.
atEnd | Determines whether an iterator is at the end position.
atEnd | Determines whether an iterator is at the end position.
databaseName | Reference to the name (identifier) of the database in a Blast report.
databaseOrientationPlus | Orientation of the database sequence within a Blast HSP alignment.
getAlignment | Turns a HSP from a Blast search into an Alignment object.
getAlignment | Turns a HSP from a Blast search into an Alignment object.
getBitScore | The bit score associated with a Blast HSP.
getBlastMatchScore | The Smith-Waterman score associated with a Blast HSP.
getDatabaseBegin | The begin position of the HSP on the database sequence.
getDatabaseEnd | The end position of the HSP on the database sequence.
getDatabaseName | The name (identifier) of the database in a Blast report.
getEValue | The e-value associated with a Blast HSP.
getEValueCutoff | The Expect-Value cutoff parsed from a Blast report.
getGappedKappa | The gapped kappa value parsed from a Blast report.
getGappedLambda | The lambda value parsed from a Blast report.
getGetExtension | The gap extension penalty parsed from a Blast report.
getGetOpen | The gap open penalty parsed from a Blast report.
getKappa | The kappa value parsed from a Blast report.
getLambda | The lambda value parsed from a Blast report.
getNext | Get next Blast report from a file containing multiple Blast reports.
getNumGaps | The number of gaps within a Blast HSP alignment.
getQueryBegin | The begin position of the HSP on the query sequence.
getQueryEnd | The end position of the HSP on the query sequence.
getQueryName | The name (identifier) of the query in a Blast report.
getValue | Access to the value.
getValue | Access to the value.
goBegin | Iterates to the first position of a container.
goBegin | Iterates to the first position of a container.
goEnd | Iterates to the last position of a container.
goNext | Iterates to next position.
goNext | Iterates to next position.
goPrevious | Iterates to pevious position.
hostHit | The BlastHit this iterator is working on.
hostReport | The BlastReport this iterator is working on.
length | The number of items/characters.
numHits | The total number of hits in a Blast report.
numHsps | The number of HSPs for an entire Blast report or for one Blast hit.
queryName | Reference to the name (identifier) of the query in a Blast report.
queryOrientationPlus | Orientation of the query sequence within a Blast HSP alignment.
read | Loads records from a file.
value | Reference to the value.
value | Reference to the value.
Chaining
globalChaining | Computes the chain on a set of fragments.
Class: Align
integrateAlign | Integrates an alignment into another by copying the gaps.
localAlignment | Computes the best local alignment of two sequences.
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.
Containers
back | The last item in container.
begin | The begin of a container.
beginPosition | Begin position of object in host.
capacity | The maximal length.
clear | Resets an object.
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
eraseBack | 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.
front | The first item in container.
getValue | Access to the value.
infix | Creates infix object.
infixWithLength | 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 | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
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.
insert | Inserts a sequence into a container.
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.
set | Assigns one object to another object avoiding to copy contents.
setValue | Makes holder dependent.
swap | Swaps the contents of two values.
top | Reference to the item with the highest priority.
valueConstruct | Constructs an object at specified position.
valueConstructMove | Move constructs an object at specified position.
valueDestruct | Destoys an object at specified position.
Dependent Objects
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.
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.
Fragment Store
appendAlignedRead | Appends an aligned read entry to a fragment store.
appendMatePair | Appends two paired-end reads to a fragment store.
appendName | Appends a name to a name store.
appendRead | Appends a read to a fragment store.
calculateInsertSizes | Calculates a string with insert sizes for each pair match.
calculateMateIndices | Calculates a string that maps the readId of a read to the readId of its mate.
clearReads | Removes all reads from a fragment store.
compactAlignedReads | Removes invalid aligned reads and rename alignId sequentially beginning with 0.
compactPairMatchIds | Renames pairMatchId sequentially beginning with 0.
convertMatchesToGlobalAlignment | Converts all matches to a multiple global alignment in gap-space.
convertPairWiseToGlobalAlignment | Converts pair-wise alignments to a multiple global alignment.
getIdByName | Appends a name to a name store.
getMateNo | Returns the mate number of read for a given readId.
getRead | Returns the read with the given readId.
layoutAlignment | Calculates a visible layout of aligned reads.
loadContig | Manually loads a contig sequence.
loadContigs | Loads contigs into fragment store.
loadReads | Loads reads into fragment store.
lockContig | Locks a contig sequence from being removed.
lockContigs | Locks all contig sequences from being removed.
lowerBoundAlignedReads | Performs a binary lower bound search on the aligned reads.
printAlignment | Prints a window of the visible layout of reads into a outstream.
read | Loads records from a file.
refresh | Recreate a name store cache.
sortAlignedReads | Stably sort aligned reads.
unlockAndFreeContig | Removes a previous contig lock and clears sequence no further lock exist.
unlockAndFreeContigs | Removes a previous lock for all contigs and clears sequences without lock.
unlockContig | Removes a previous contig lock.
unlockContigs | Removes a previous lock for all contigs.
upperBoundAlignedReads | Performs a binary upper bound search on the aligned reads.
write | Saves records to a file.
writeContigs | Write contigs from fragment store into file.
Graph
addChild | Adds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge.
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.
alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics.
allPairsShortestPath | Finds shortest paths between all pairs of vertices in a graph.
assignBeginState | Assigns a begin state.
assignCargo | Assigns a new cargo to the edge.
assignEmissionProbability | Assigns a new emission probability.
assignEndState | Assigns an end state.
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.
assignRoot | Assigns a new root vertex to the graph.
assignSilentStatus | Assigns a silent status to a state.
assignSource | Assigns a source vertex to an edge.
assignStringSet | Assigns a new string set to an alignment graph.
assignTarget | Assigns a target vertex to an edge.
assignTransitionProbability | Assigns a new transition probability.
atBegin | Determines whether an iterator is at the beginning position.
atEnd | Determines whether an iterator is at the end position.
backwardAlgorithm | Implements the backward algorithm.
beginState | Returns a reference to the begin state.
bellmanFordAlgorithm | Computes shortest paths from a single source in a directed graph.
breadthFirstSearch | Implements a breadth-first search on a graph.
canParseString | Test whether an automaton can parse a string completely.
cargo | Access to the cargo.
childVertex | Returns the child vertex of an edge.
clear | Resets an object.
clearEdges | Removes all edges in a graph.
clearVertices | Removes all vertices in a graph.
collectLeaves | Returns all leaves underneath a given vertex.
connectedComponents | Decomposes an undirected graph into its connected components.
convertAlignment | Converts an alignment graph into an alignment matrix.
createOracle | Creates a factor oracle.
createOracleOnReverse | Creates a factor oracle for the reversed string.
createRoot | Creates the root in a tree or an automaton.
createSuffixTrie | Creates a trie of all suffixes of a text.
createTrie | Creates a trie.
createTrieOnReverse | Creates a trie for all reversed keywords.
dagShortestPath | Computes shortest paths from a single source in a directed acyclic graph (DAG).
degree | Number of incident edges for a given vertex.
depthFirstSearch | Implements a depth-first search on a graph.
dijkstra | Computes shortest paths from a single source in a graph.
emissionProbability | Returns a reference to the emission probability.
empty | Test a container for being empty.
endState | Returns a reference to the end state.
findEdge | Finds an edge.
findVertex | Finds a vertex given a sequence id and a position.
floydWarshallAlgorithm | Finds shortest paths between all pairs of vertices in a graph.
fordFulkersonAlgorithm | Computes a maximum flow in a directed graph.
forwardAlgorithm | Implements the forward algorithm.
fragmentBegin | Gets the begin position for this fragment or this vertex descriptor in the sequence.
fragmentLength | Gets the length of the label of a given vertex descriptor in the sequence.
generateSequence | Generates random state and alphabet sequences of a given HMM.
getAdjacencyMatrix | Returns an adjacency matrix representation of the graph.
getBeginState | Returns the begin state.
getCargo | Get method for the edge cargo.
getDistanceMatrix | Computes a pairwise distance matrix from an alignment graph.
getEmissionProbability | Returns the emission probability.
getEndState | Returns the end state.
getFirstCoveredPosition | Finds the first position in a sequence that is not assigned to a nil vertex.
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.
getLastCoveredPosition | Finds the last position in a sequence that is not assigned to a nil vertex.
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.
getProperty | Get method for an item's property.
getRoot | Get method for the root of a tree or an automaton.
getSource | Get method for the source.
getStringSet | Gets the string set of an alignment 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.
getTarget | Get method for the target.
getTransitionProbability | Returns the transition probability.
getValue | Access to the value.
goBegin | Iterates to the first position of a container.
goEnd | Iterates to the last 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.
isLeaf | Tests whether a given vertex is a leaf or not.
isRoot | Tests whether a given vertex is the root or not.
isSilent | Indicates whether a state is silent or not.
kruskalsAlgorithm | Computes a minimum spanning tree on a graph.
label | Returns the label of the out-edge this iterator points to (for automatons).
label | Gets the label that is associated with this vertex descriptor or the sequence that is associated with a fragment.
nextS | Accesses the next source pointer.
nextT | Accesses the next target pointer.
numChildren | Number of children of a given tree vertex.
numEdges | Number of edges in a graph.
numTreeEdges | Number of tree edges.
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.
parentVertex | Returns the parent vertex of an edge.
parseString | Parses a string one character at a time and moves accordingly in the automaton.
primsAlgorithm | Computes a minimum spanning tree on a graph.
progressiveAlignment | Performs a progressive alignment.
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.
removeAllChildren | Removes all children from the tree given a parent.
removeChild | Removes a child from the tree given a parent.
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.
root | Gets a reference to the root of the tree.
sequenceId | Gets the sequence id that is associated with this vertex descriptor or with a sequence of a fragment.
silentStatus | Reference to the silent status of a state.
slowNjTree | Computes a guide tree from a distance matrix.
sourceVertex | Returns the source vertex of an edge.
stringSet | Gets the string set of an alignment graph.
stronglyConnectedComponents | Decomposes a directed graph into its strongly connected components.
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score.
target | Accesses the target of an EdgeStump.
targetVertex | Returns the target vertex of an edge.
topologicalSort | Performs a topological sort on a directed acyclic graph (DAG).
transitionProbability | Returns a reference to the transition probability.
transitiveClosure | 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.
tripletLibraryExtension | Performs a full or group-based consistency extension.
upgmaTree | Computes a guide tree from a distance matrix.
value | Reference to the value.
viterbiAlgorithm | Implements the viterbi algorithm.
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 substring or a q-gram in the index text.
createBWTable | Creates a Burrows-Wheeler table from a given text and suffix array.
createChildtab | 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.
createWotdIndex | Builds a q-gram index on a sequence.
dirAt | Shortcut for value(indexDir(..), ..).
emptyParentEdge | Returns true iff the edge label from the iterator node to its parent is empty.
getFibre | Returns a specific Fibre of an Index object.
getFrequency | Returns the number of sequences, which contain the representative as a substring.
getKmerSimilarityMatrix | Creates a matrix storing the number of common q-grams between all pairs of sequences.
getOccurrence | Returns an occurence of the representative substring or a q-gram in the index text.
getOccurrences | Returns all occurences of the representative substring or a q-gram in the index text.
getOccurrencesBwt | Returns the characters left beside all occurence of the representative substring in the index text.
getStepSize | Return the q-gram step size used for index creation.
goDown | Iterates down one edge or a path in a tree.
goRight | Iterates to the next sibling in a tree.
goRoot | Move iterator to the root node.
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 an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span
hash2Next | Computes a unique hash value for the adjacent shape, even if it is shorter than q.
hash2Upper | Computes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span.
hashNext | Computes the hash value for the adjacent shape.
hashUpper | Computes an upper hash value for a shape applied to a sequence.
indexBucketMap | Shortcut for getFibre(.., QGramBucketMap).
indexBwt | Shortcut for getFibre(.., EsaBwt).
indexChildtab | Shortcut for getFibre(.., EsaChildtab).
indexCounts | Shortcut for getFibre(.., QGramCounts).
indexCountsDir | Shortcut for getFibre(.., QGramCountsDir).
indexCreate | Creates a specific Fibre.
indexDir | Shortcut for getFibre(.., QGramDir).
indexLcp | Shortcut for getFibre(.., EsaLcp).
indexLcpe | Shortcut for getFibre(.., EsaLcpe).
indexRawSA | Shortcut for getFibre(.., EsaRawSA).
indexRawText | Shortcut for getFibre(.., EsaRawText).
indexRequire | On-demand creation of a specific Fibre.
indexSA | Shortcut for getFibre(.., EsaSA).
indexShape | Shortcut for getFibre(.., QGramShape).
indexSupplied | Returns whether a specific Fibre is present.
indexText | Shortcut for getFibre(.., EsaText).
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(..), ..).
nodeDepth | Returns the zero-based node depth of the iterator node.
nodeHullPredicate | If false this node and its subtree is concealed.
nodePredicate | If false this node will be skipped during the bottom-up traversal.
nodeUp | Returns the vertex descriptor of the parent node.
orderOccurrences | Sorts a string of occurrences.
parentEdgeFirstChar | Returns the first character of the edge from an iterator node to its parent.
parentEdgeLabel | Returns a substring representing the edge from an iterator node to its parent.
parentEdgeLength | Returns the length of the edge from the iterator node to its parent.
parentRepLength | Returns the length of the substring representing the path from root to iterator's parent node.
range | Returns the suffix array interval borders of occurences of representative substring or a q-gram in the index text.
rawsaAt | Shortcut for value(indexRawSA(..), ..).
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.
resizeVertexMap | Initializes a vertex map.
saAt | Shortcut for value(indexSA(..), ..).
setStepSize | Change the q-gram step size used for index creation.
shapeToString | Converts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position).
stringToShape | Takes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object.
textAt | Shortcut for value(indexText(..), ..).
weight | Number of relevant positions in a shape.
Input/Output
appendSeqs | Appends all sequences stored in files of directory to a StringSet.
assignCroppedSeqId | Extracts the sequence id up to the first whitespace of a sequence file fragment.
assignQual | Extracts the quality values of a sequence file fragment.
assignQualId | Extracts the quality value id of a sequence file fragment.
assignSeq | Extracts the sequence part of a sequence file fragment.
assignSeqId | Extracts the sequence id of a sequence file fragment.
asyncReadAt | Asynchronously loads records from a specific position in a file.
asyncWriteAt | 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.
guessFormat | Guesses a file format from the contents of a sequence file.
guessFormatFromFilename | Guesses a file format from a sequence file name.
length | The number of items/characters.
loadScoreMatrix | Load a score matrix from a file.
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.
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.
readMeta | Read meta information from file.
resize | Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
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.
split | Divides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter.
tell | Gets the current file pointer.
waitFor | Waits for an asynchronous request to complete.
write | Writes to stream.
write | Saves records to a file.
write | Saves records to a file.
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 last 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.
Map
add | Insert another value into a multi map.
cargo | Returns a cargo given a key.
erase | Removes a value from a map.
eraseAll | Removes a value from a map.
find | Find a value in a map.
hasKey | Determines whether a map contains a value given key.
insert | Insert new value into map.
key | Get the the key of the element.
mapValue | Subscript operator [ ] of maps.
value | Returns a value given a key.
Memory
allocate | Allocates memory from heap.
clear | Deallocates all memory blocks.
deallocate | Deallocates memory.
Misc
cpuTime | Returns the cpu time in seconds.
mtRand | Return a Mersenne-Twister random number.
mtRandInit | Initialize the Mersenne-Twister random number generator.
sysTime | Returns the system time in seconds.
Miscellaneous
addArgumentText | Return a CommandLineOption object extended by an argument text.
addHelpLine | Adds an extra line of text below the help text of an option.
addInterval | Adds an interval to an interval tree.
addLine | Adds a line of text to the help output of the CommandLineParser.
addOption | Adds a CommandLineOption object to the CommandLineParser.
addSection | Adds a new section the help output of the CommandLineParser.
addTitleLine | Adds a line of text to the title output of the CommandLineParser.
addUsageLine | Adds a line of text to the usage output of the CommandLineParser.
addVersionLine | Adds a line of text to the version output of the CommandLineParser.
adjustTop | Adjusts the priority of the first item.
argumentCount | Returns the count of passed arguments.
argumentText | Returns the argument text of a CommandLineOption object.
createIntervalTree | Create an interval tree.
findIntervalsExcludeTouching | :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.
getArgumentValue | Returns an argument set on the command line.
getArgumentValues | Returns all arguments set on the command line.
getLeftBoundary | Get method for the left boundary.
getOptionValueLong | Retrieves the value of a long-name option given on the command line.
getOptionValueShort | Retrieves the value of a short-name option given on the command line.
getOptionValuesLong | Returns all values of a long-name option given on the command line.
getOptionValuesShort | Returns all values of a short-name option given on the command line.
getRightBoundary | Get method for the right boundary.
hasOptionLong | Returns whether a certain long-name option is registered in the parser.
hasOptionShort | Returns whether a certain short-name option is registered in the parser.
help | Prints the complete help message for the parser to a stream.
helpText | Returns the help text associated with the CommandLineOption object.
id | A value that identifies the underlying sequence.
isBooleanOption | Returns whether option is a switch.
isDoubleOption | Returns whether option argument can be a double.
isHiddenOption | Returns whether option is hidden on the help screen.
isIntOption | Returns whether option argument can be an integer.
isLabelOption | Returns whether an option label should be printed on the help screen.
isOptionList | Returns whether the option can be given multiple times.
isOptionMandatory | Returns whether option is mandatory.
isSetLong | Returns whether a long-name option was set on the parsed command line.
isSetShort | Returns whether a short-name option was set on the parsed command line.
isStringOption | Returns whether option argument can be a string.
leftBoundary | Access to the right boundary.
log2 | Computes logarithm of base 2 for integer types
longName | Returns the long-name of a CommandLineOption object.
parse | Parses the command line.
requiredArguments | Sets the number of arguments (non-parameterized options) are required by the program.
rightBoundary | Access to the right boundary.
setHelpText | Sets the help text associated with the CommandLineOption object.
setLongName | Sets the long-name of a CommandLineOption object.
setOptionType | Set the option type.
setShortName | Sets the short-name of a CommandLineOption object.
shareResources | Determines whether two sequences share the same resource.
shortHelp | Prints a short help message for the parser to a stream
shortName | Returns the short-name of a CommandLineOption object.
version | Prints a version text to a stream.
Miscellaneous:
printDebugLevel | Print the current SeqAn debug level and the compiler flags to the given stream.
Modifier
complement | Complement a sequence or a StringSet in-place.
reverseComplement | Reverse and complement a sequence or a StringSet in-place.
toLower | Convert characters in sequence or StringSet to lower case in-place.
toUpper | Convert characters in sequence or StringSet to lower case in-place.
Modifiers
reverse | Reverse an object/container in-place.
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.
getMotif | Gets the motif out of a MotifFinder. If pos is given, the pos-th motif is returned, otherwise the first motif is returned.
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.
motifCount | Gets number of motifs in the MotifFinder.
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.
Random
pickRandomNumber | Pick a random number using a random number generator object, possibly following the given distribution.
shuffle | Shuffle the given container.
Scoring
score | Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.
score | Returns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.
scoreGapExtendHorizontal | Returns the score for extending a horizontal gap after pos1 in seq1.
scoreGapExtendVertical | Returns the score for extending a vertical gap after pos2 in seq2.
scoreGapHorizontal | Returns the score for a horizontal gap after pos1 in seq1.
scoreGapOpenHorizontal | Returns the score for opening a horizontal gap after pos1 in seq1.
scoreGapOpenVertical | Returns the score for opening a vertical gap after pos2 in seq2.
scoreGapVertical | Returns the score for a vertical gap after pos2 in seq2.
setDefaultScoreMatrix | Set the value of the given matrix to the default value.
setScore | Set the substitution score between two values.
Searching
find | Search for a Pattern in a Finder object.
findBegin | Search the begin of an approximate match.
getBeginScore | Score of the last match found by findBegin during approximate searching.
getScore | Score of the last found match in approximate searching.
getSwiftHits | Gets the string of hits from the finder
haystack | Returns the haystack of a Finder object.
needle | Returns the needle of a Pattern object (not implemented for some online-algorithms).
positionRange | Returns a pair of the begin and end position in the haystack or needle for the last hit found.
positionRangeNoClip | Returns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
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.
windowFindBegin | 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.
windowFindEnd | Flushes the pattern. Used together with windowFindBegin and windowFindNext.
windowFindNext | Searches over the next window with the finder. The found hits can be retrieved with getSwiftHits Used together with windowFindBegin and windowFindEnd.
Seed Handling
addSeed | Adds a seed to an existing set.
addSeeds | Adds several seeds to an existing set. If a merging or chaining algorithm is used seeds are added if the merging or chaining fails.
appendDiag | Adds diagonal to the seed.
bandedAlignment | Calculates a banded alignment around a Seed.
bandedChainAlignment | Calculates a banded alignment around a chain of seeds.
dimension | Dimension of a seed.
endDiagonal | Returns the diagonal of the end point.
extendSeed | Extends a seed.
extendSeedScore | Extends a seed and increases the score.
extendSeeds | Extension of seeds.
extendSeedsScore | Extension of seeds with score calculation.
getAlignment | Constructs a alignment from a ChainedSeed.
leftDiagonal | Returns the most left diagonal of the seed (maximum diagonal value).
leftDim0 | Returns the first position of the seed in the query.
leftDim1 | Returns the first position of the seed in the database.
leftPosition | The begin position of segment in a seed.
maximumDistance | Sets the maximal distance between two seed during a chaining process.
obtainID | btains a new id from the id manager.
qualityValue | Sets the minimum length for a seed to be saved permanently.
releaseID | Releases a given id so it can be redistributed later on.
rightDiagonal | Returns the most right diagonal of the seed (minimum diagonal value).
rightDim0 | Returns the last position of the seed in the query.
rightDim1 | Returns the last position of the seed in the database.
rightPosition | The end position of segment in a seed.
scoreSeed | Calculates the score of a seed.
seedScore | Returns the score of a seed.
setLeftDiagonal | Sets a new value for the most left diagonal.
setLeftDim0 | Updates the start point of the seed.
setLeftDim1 | Updates the start point of the seed.
setLeftPosition | Sets begin position of segment in a seed.
setMaximumDistance | Sets the maximal distance between two seed during a chaining process.
setQualityValue | Sets the minimum length for a seed to be saved permanently.
setRightDiagonal | Sets a new value for the most right diagonal.
setRightDim0 | Updates the end point of the seed.
setRightDim1 | Updates the end point of the seed.
setRightPosition | Sets end position of segment in a seed.
startDiagonal | Returns the diagonal of the start point.
Sequences
assignValueById | Adds a new string to the StringSet and returns an id.
concat | Returns the concatenation sequence of all sequences in a StringSet.
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.
posLocalToX | Converts a local to a local/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.
valueById | Retrieves a string from the StringSet given an id.
sequences
atEndOfSequence | Returns true if the iterator is at the end of a sequence.
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