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

Class
getAutoSeqStreamFormatName	Returns
hasValue
operatorpipe
operatorpipe=
operatorpipepipe

Alignment Free

alignmentFreeComparison	Computes the pairwise similarity scores for a set of sequences
calculateCovariance	Calculates the covariance for the number of word occurences for two words in a sequence of length n, given a background model.
calculateOverlapIndicator	Calculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p)
calculatePeriodicity	Calculate word periodicity (indicator for overlaps)
calculateProbability	Calculates the probability of a sequence given a Bernoulli model (String of background frequencies)
calculateVariance	Calculates the variance for the number of word occurences of a word in a sequence of length n given a background model.
countKmers	Counts kmers in a sequence. Optionally, a background model is returned.
cutNs	Cut out all masked sequences from a Dna5String.
stringToStringSet	Transform a String into a StringSet containing this String.

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	Return the "gap" value from an alphabet.
getProjectedPosition	Projects a position of one sequence taking part in a pairwise match onto the other sequence.
globalAlignment	Computes the best global alignment of the two sequences.
globalMsaAlignment	Computes a global multiple alignment.
heaviestCommonSubsequence	Computes the heaviest common subsequence between two strings using the match information given in an alignment graph.
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.
isReversed	Returns true if the segment match is in reverse orientation.
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 values between strings.
assignQualityValue	Assign quality to a character from an alphabet with integrated quality.
convert	Converts a value into another value.
convertQuality	Convert an integer quality value into its ASCII representation for FASTQ (Phred scale).
gapValue	Return the "gap" value from an alphabet.
getQualityValue	Returns the quality of a character from an alphabet with integrated quality.
maxValue	Supremum for a given type.
minValue	Infimum for a given type.
ordValue	Maps an alphabet 1-to-1 to the interval [0..ValueSize).
unknownValue	Return the "unknown" value from an alphabet.
valueSize	Returns size of an alphabet.

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.

BAM I/O

assignTagsBamToSam	Assign tags in BAM format to tags in SAM format.
assignTagsSamToBam	Assign tags in SAM format to tags in BAM format.
bamRecordToAlignment	Convert BamAlignmentRecord to an Align object.
eraseTag	Erase tag from BamTagsDict.
extractTagValue	Extract and cast "atomic" value from tags string with index idx.
findTagKey	Find a tag's key of a BamHeaderRecord.
getAlignmentLengthInRef	Returns length of BamAlignmentRecord's projection in reference.
getBamTypeChar	Return char identifying the type of the atomic argument.
getBamTypeSize	Return size of the type identified by c.
getTagKey	Return key of a tag by index.
getTagType	Get key of a tag by index.
getTagValue	Return tag value from a BamHeaderRecord or BamTagsDict.
getTagValue	Return tag value from a BamHeaderRecord or BamTagsDict.
getUnalignedCount	Query index for number of unaligned reads.
hasFlagAllProper	Return true if a BamAlignmentRecord has the "all properly aligned" flag set.
hasFlagDuplicate	Return true if a BamAlignmentRecord has the "PCR or optical duplicate" flag set.
hasFlagFirst	Return true if a BamAlignmentRecord has the "first fragment of template" flag set.
hasFlagLast	Return true if a BamAlignmentRecord has the "last fragment of template" flag set.
hasFlagMultiple	Return true if a BamAlignmentRecord has the "multiple" flag set.
hasFlagNextRC	Return true if a BamAlignmentRecord has the "next fragment reverse-complemented" flag set.
hasFlagNextUnmapped	Return true if a BamAlignmentRecord has the "next fragment unmapped" flag set.
hasFlagQCNoPass	Return true if a BamAlignmentRecord has the "does not pass quality controls" flag set.
hasFlagRC	Return true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagRC	Return true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagSecondary	Return true if a BamAlignmentRecord has the "secondary alignment" flag set.
hasFlagUnmapped	Return true if a BamAlignmentRecord has the "fragment unmapped" flag set.
jumpToPos	Seek in BAM BGZF stream using an index.
load	Load a BAM index from a given file name.
nameStore	Return reference to name store from BamIOContext.
nameStoreCache	Return reference to name store cache from BamIOContext.
setTagValue	Set the value of a tag through a BamTagsDict.

Basic

nukeCopies

Reset all pointers connected to a given one.

Bit Twiddling

clearAllBits	Set all bits to 0.
clearBit	Set the bit with the given index to 0.
isBitSet	Returns whether the bit with the given index is set to 1.
setBit	Set the bit with the given index to 1.
setBitTo	Set the bit with the given index to the given value.

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.

C++ built-in

cast operator	C++ built-in cast operator.
operator delete	C++ built-in deallocation operator.
operator delete[]	C++ built-in array deallocation operator.
operator new	C++ built-in allocation operator.
operator new[]	C++ built-in array allocation operator operator.
operator!	C++ built-in logical negation operator.
operator!=	C++ built-in inequal comparison operator.
operator%	C++ built-in modulo operator.
operator%=	C++ built-in modulo assignment operator.
operator&	C++ built-in bitwise AND operator.
operator& (reference)	C++ built-in reference/address-of operator.
operator&&	C++ built-in logical AND operator.
operator&=	C++ built-in bitwise AND assignment operator.
operator>	C++ built-in greater-than comparison operator.
operator>>	C++ built-in bitwise right shift operator.
operator>> (Stream)	C++ built-in bitwise get-from/stream extraction operator.
operator>>=	C++ built-in bitwise right shift assignment operator.
operator>=	C++ built-in greather-than-or-equal comparison operator.
operator<	C++ built-in less-than comparison operator.
operator<<	C++ built-in bitwise left shift operator.
operator<< (Stream)	C++ built-in bitwise put-to/stream insertion operator.
operator<<=	C++ built-in bitwise left shift assignment operator.
operator<=	C++ built-in less-than-or-equal comparison operator.
operator()	C++ built-in function call operator.
operator*	C++ built-in multiplication operator.
operator* (indirection)	C++ built-in indirection/object-pointed-to-by operator.
operator*=	C++ built-in multiplication assignment operator.
operator+	C++ built-in addition operator.
operator+ (unary)	C++ built-in unary plus (integer promotion) operator.
operator++ (prefix)	C++ built-in prefix increment operator.
operator++ (suffix)	C++ built-in suffix increment operator.
operator+=	C++ built-in addition assignment operator.
operator,	C++ built-in comma operator.
operator-	C++ built-in subtraction operator.
operator- (unary)	C++ built-in unary minus (additive inverse) operator.
operator->	C++ built-in structure dereference operator.
operator->*	C++ built-in member-pointed-to-by-b-of-object-pointed-to-by-a operator.
operator-- (prefix)	C++ built-in prefix decrement operator.
operator-- (suffix)	C++ built-in suffix decrement operator.
operator-=	C++ built-in subtraction assignment operator.
operator/	C++ built-in division operator.
operator/=	C++ built-in division assignment operator.
operator=	C++ built-in Assignment operator.
operator==	C++ built-in equal comparison operator.
operator[]	C++ built-in array subscript operator.
operator^	C++ built-in bitwise XOR operator.
operator^=	C++ built-in bitwise XOR assignment operator.
operator~	C++ built-in bitwise NOT operator.

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.

Concepts

ignoreUnusedVariableWarning	Removes unused variable warning.
requireBooleanExpr	Tests for a boolean expression.
sameType	Tests for equality of types.

Consensus

consensusAligment	Compute consensus alignment.
reAlign	Perform realignment similar to Anson-Myers algorithm.

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.
valueDestruct	Destoys an object at specified position.

Dependent Object

assignHost	Assign to the host of a given value.
clearHost	Clear the host of the given object.
createHost	Construct the host of the given object.
dependentHost	Query dependent state of a hosted object.
emptyHost	Query emptiness state of a hosted object.
moveHost	Assign to the host of a given value.

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.
hostIterator	Return host iterator.
setBegin	Sets begin of object in host.
setBeginPosition	Sets begin position of object in host.
setContainer	Set container of an adaptor iterator.
setEnd	Sets end of object in host.
setEndPosition	Sets begin position of object in host.
setHost	Sets the host of an object.
setPosition	Sets the position of a finder.

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.
buildIndex	Build index for a BamTagsDict object.
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.
getClrRange	Get the "clear" range of a read 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.
hasIndex	Return true if BamTagsDict has an index.
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.
positionGapToSeq	Convert from gap-space in the global alignment to the sequence-space on the reference.
positionSeqToGap	Convert from sequence space on the reference to gap space in the global alignment.
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	Writes the basic information about the ArgParseOption to the provided stream. Writes the basic information about the CommandLineOption to the provided stream. 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.
assignEdgeMap	Initializes a vertex map with values of an array.
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 to an existing edge.
assignVertexMap	Initializes a vertex map with values of an array.
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.
buildAlignmentGraph	Builds an Alignment Graph from a set of input alignments.
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.
njTree	Computes a guide tree from a distance matrix.
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 or vertex.
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.
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.
weaklyConnectedComponents	Compute weakly connected components of a directed graph.

Index

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.
countOccurrencesMultiple	Returns the number of occurences of a q-gram for every sequence of a StringSet .
countSequences	Return the number of sequences in an index' underlying 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.
findRepeats	Search for repeats in a text.
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(..), ..).
unhash	Inverse of the hash function; for ungapped shapes.
weight	Number of relevant positions in a shape.

Input / Output

attachToFile	Attach to already open input / output file.
checkEof	Check that the EOF marker is present in a BGZF(/BAM) file.
isDirect	Query a GZ File Stream for being "direct."

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.
atEnd	Determines whether an iterator is at the end position.
cancel	Cancels an asynchronous request.
checkStreamFormat	check whether the data provided by reader is (one of) the specified format(s).
close	Closes a file.
countLine	count characters in a line not including \r and \n
flush	Waits for all open requests to complete.
goNext	Iterates to next position.
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.
isalnum	Check if character is alpha-numeric
isalpha	Check if character is a upper or lowercase letter
isblank	Check if character is either ' ' or '\t'
iscntrl	Check if character is a control character
isdigit	Check if character is a digit
isgraph	Check if character is printable and not white space
isprint	Check if character is printable, i.e. not a control character
isspace	Check if character is a white-space character
length	The number of items/characters.
lexicalCast	Cast from a String-type to a numerical type
lexicalCast2	Cast from a String-type to a numerical type
loadScoreMatrix	Load a score matrix from a file.
nextIs	Query whether the next record is of a given type.
open	Opens a file.
openTemp	Opens a temporary file.
read	Loads a record from file.
read	Loads records from a file.
read2	reads an entire document from a Stream, by the means of RecordReader
readAlphaNums	Read characters from stream as long as characters are letters
readAt	Loads records from a specific position in a file.
readDigits	Read characters from stream as long as characters are digits
readDna5IgnoringWhitespaces	Read characters from stream, as long as they are DNA5 characters. Skip over whitespaces.
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").
readLetters	Read characters from stream as long as characters are letters
readLine	Read a line from stream and save it to buffer
readLineStripTrailingBlanks	Read a line from stream and save it to buffer, remove trailing blanks
readLineType	Reads the information belonging to the two-character line code specified.
readMeta	Read meta information from file.
readNChars	Read exactly n characters from stream into buffer
readNCharsIgnoringWhitespace	Read n characters from stream into buffer, but skip certain Chars
readRecord	reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record.
readUntilBlank	Read characters from stream into buffer until Blank is encountered
readUntilChar	Read characters from stream into buffer until Char is encountered
readUntilOneOf	Read characters from stream into buffer until one of the given characters is encountered
readUntilTabOrLineBreak	Read characters from stream until a tab or line-break occurs.
readUntilWhitespace	Read characters from stream into buffer until Whitespace is encountered
resize	Resizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
resultCode	Returns true if there is more data to read.
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.
skipBlanks	Skip (i.e. read without saving) characters from stream until non-Blank is encountered
skipChar	Skip one character that must be equal to a given one for this function to succeed.
skipLine	Skip a line in stream and go to beginning of next
skipNChars	Skip exactly n characters from stream
skipNCharsIgnoringWhitespace	Skip n characters from stream, not counting whitespaces
skipUntilBlank	Skip (i.e. read without saving) characters from stream until Blank is encountered
skipUntilChar	Skip (i.e. read without saving) characters from stream until Char is encountered
skipUntilGraph	Skip (i.e. read without saving) characters from stream until printable, non-' ' character is encountered
skipUntilLineBeginsWithChar	Skip input until the first graphical(see isgraph) character of a line is equal to c
skipUntilLineBeginsWithOneCharOfStr	Skip input until a line begins with a one of the characters in str
skipUntilLineBeginsWithStr	Skip input until a line begins with str.
skipUntilString	Skip (i.e. read without saving) characters from stream until String is encountered
skipUntilWhitespace	Skip (i.e. read without saving) characters from stream until Whitespace is encountered
skipWhitespaces	Skip (i.e. read without saving) characters from stream until non-Whitespace is encountered
split	Divides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter.
splitEmblHeader	Split an EMBL header line.
splitGenBankHeader	Split an GenBank header field/value.
startFirstPass	Start the first reading pass.
startSecondPass	Start the second reading pass.
startsWith	Check whether a sequence starts with a given prefix.
streamEof	Check end-of-file state of a Stream.
streamError	Return the stream's error code.
streamFlush	Flush the underlying stream.
streamPeek	Read next character from stream without advancing current position.
streamPut	Write different types to stream
streamReadBlock	Read a block of bytes into a buffer.
streamReadChar	Read next character from stream and advance the current position.
streamSeek	Perform a seek operation on the stream.
streamTell	Get the position in the current stream.
streamWriteBlock	Write one character to the stream.
streamWriteChar	Write one character to the stream.
tell	Gets the current file pointer.
value	Reference to the value.
waitFor	Waits for an asynchronous request to complete.
write	Writes to stream.
write	Writes the basic information about the ArgParseOption to the provided stream. Writes the basic information about the CommandLineOption to the provided stream. Saves records to a file.
write	Writes the basic information about the ArgParseOption to the provided stream. Writes the basic information about the CommandLineOption to the provided stream. Saves records to a file.
write	Writes the basic information about the ArgParseOption to the provided stream. Writes the basic information about the CommandLineOption to the provided stream. Saves records to a file.
write2	writes an entire document to a Stream
writeAt	Saves records to a specific position in a file.
writeRecord	write one record (e.g. a single DNA-sequence and its meta data) to a Stream

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.

Local Match Store

appendLocalMatch	Append a new local match to a LocalMatchStore
readRecord	reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record.
readRecord	reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record.
readRecord	reads one record (e.g. a single DNA-sequence and its meta data) from a Stream, by the means of RecordReader Read Lastz "general" format record.

Map

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.
memset	An implementation of memset with fixed number of bytes using Metaprogramming.

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.

Miscalleneous

addListItem	Appends a list item to the ArgumentParser. Add list item to ToolDoc object.
addSection	Begins a new section of ArgParseOption the help output of the ArgumentParser. Add section to ToolDoc object. Adds a new section the help output of the CommandLineParser.
addSubSection	Add subsection to ToolDoc object.
addText	Appends a text paragraph to the ArgumentParser. Add text line/paragraph to ToolDoc.
clearEntries	Clear entries from ToolDoc object.
getAppName	Get tool name of ArgumentParser object.
getDate	Get date string from ToolDoc object.
getManTitle	Get man title from ToolDoc object.
getName	Get tool name of ToolDoc object.
getShortDescription	Get short description of ToolDoc object.
getTerminalSize	Retrieve size of terminal.
getVersion	Get version string from ArgumentParser object. Get version string from ToolDoc object.
getVersion	Get version string from ArgumentParser object. Get version string from ToolDoc object.
isAnsiColorTerminal	Check whether we are printing to a terminal.
isTerminal()	Check whether we are printing to a terminal.
print	Print ToolDoc object in a given format.
setDate	Sets date string of ArgumentParser. Set date string for ToolDoc object.
setManTitle	Set version string for ToolDoc object.
setName	Set tool name for ToolDoc object.
setShortDescription	Sets short description test of ArgumentParser. Set short description for ToolDoc object.
setVersion	Sets version string of ArgumentParser. Set version string for ToolDoc object.

Miscellaneous

addArgument	Adds a ArgParseArgument object to the ArgumentParser.
addArgumentText	Return a CommandLineOption object extended by an argument text.
addDescription	Appends a description paragraph to the ArgumentParser documentation.
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 ArgumentParser in the block of ArgParseOptions. Adds a line of text to the help output of the CommandLineParser.
addLine	Adds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions. Adds a line of text to the help output of the CommandLineParser.
addListItem	Appends a list item to the ArgumentParser. Add list item to ToolDoc object.
addOption	Adds a ArgParseOption object to the ArgumentParser. Adds a CommandLineOption object to the CommandLineParser.
addOption	Adds a ArgParseOption object to the ArgumentParser. Adds a CommandLineOption object to the CommandLineParser.
addSection	Begins a new section of ArgParseOption the help output of the ArgumentParser. Add section to ToolDoc object. Adds a new section the help output of the CommandLineParser.
addSection	Begins a new section of ArgParseOption the help output of the ArgumentParser. Add section to ToolDoc object. Adds a new section the help output of the CommandLineParser.
addText	Appends a text paragraph to the ArgumentParser. Add text line/paragraph to ToolDoc.
addTextSection	Adds a text section to the ArgumentParser.
addTextSubSection	Adds a text subsection to the ArgumentParser.
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 ArgumentParser. Adds a line of text to the usage output of the CommandLineParser.
addUsageLine	Adds a line of text to the usage output of the ArgumentParser. 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.
average	Return average from an accumulator.
count	Return sum from an accumulator.
createIntervalTree	Create an interval tree.
findIntervals	Find all intervals that contain the query point or overlap with the query interval.
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.
findSet	Return set identifier, given an element identifier.
getArgument	Returns a reference to the specified argument.
getArgumentLabel	Returns the label for the given ArgParseArgument. Either the user defined label is returned or a default label (based on the ArgumentType is used).
getArgumentValue	Retrieves the value of an argument given by its position. Returns the value of the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) you can specify which value you want to get. If not set the first value will be returned. Returns an argument set on the command line.
getArgumentValue	Retrieves the value of an argument given by its position. Returns the value of the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) you can specify which value you want to get. If not set the first value will be returned. Returns an argument set on the command line.
getArgumentValue	Retrieves the value of an argument given by its position. Returns the value of the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) you can specify which value you want to get. If not set the first value will be returned. Returns an argument set on the command line.
getArgumentValueCount	Retunrs the number of values stored in the specified option.
getArgumentValues	Returns all values of an option given on the command line. Returns all values of the ArgParseArgument object as const std::vector. Returns all _arguments set on the command line.
getArgumentValues	Returns all values of an option given on the command line. Returns all values of the ArgParseArgument object as const std::vector. Returns all _arguments set on the command line.
getArgumentValues	Returns all values of an option given on the command line. Returns all values of the ArgParseArgument object as const std::vector. Returns all _arguments set on the command line.
getLeftBoundary	Get method for the left boundary.
getObjectId	A value that identifies the underlying sequence.
getOption	Returns a reference to the specified option.
getOptionValue	Retrieves the value of an option given either the short or long name. Retrieves the value of an option given either the short or long name.
getOptionValue	Retrieves the value of an option given either the short or long name. Retrieves the value of an option given either the short or long name.
getOptionValueCount	Returns the number of values stored in the specified option.
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.
getOptionValues	Returns all values of an option given on the command line. Returns all values of an option given on the command line.
getOptionValues	Returns all values of an option given on the command line. Returns all values of an 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.
hasArgumentValue	Returns true if a value for the given position is available.
hasOption	Returns whether a certain option is registered in the parser. Returns whether a certain option is registered in the parser.
hasOption	Returns whether a certain option is registered in the parser. Returns whether a certain option is registered in the parser.
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.
hideOption	Hides the ArgParseOption defined by the parameter name (which can be either the short or the long name) from the help screen. Hides the ArgParseOption from the help screen.
hideOption	Hides the ArgParseOption defined by the parameter name (which can be either the short or the long name) from the help screen. Hides the ArgParseOption from the help screen.
isBooleanOption	Returns whether option is a switch. Returns whether option is a switch.
isBooleanOption	Returns whether option is a switch. Returns whether option is a switch.
isDoubleArgument	Returns whether the argument is a double.
isDoubleOption	Returns whether option argument can be a double.
isHiddenOption	Returns whether option is hidden on the help screen.
isInputFile	Returns whether the argument of the given option is an input file.
isInputFileArgument	Returns whether the argument is an input file.
isIntOption	Returns whether option argument can be an integer.
isIntegerArgument	Returns whether the argument is an integer.
isLabelOption	Returns whether an option label should be printed on the help screen.
isListArgument	Returns whether the argument can be given multiple times.
isOptionList	Returns whether the option can be given multiple times.
isOptionMandatory	Returns whether option is mandatory.
isOutputFile	Returns whether the argument of the given option is an output file.
isOutputFileArgument	Returns whether the argument is an output file.
isRequired	Returns whether the option is mandatory.
isSet	Returns whether an option was set on the parsed command line. Returns true if a value was assigned to the argument. Returns whether an option was set on the parsed command line.
isSet	Returns whether an option was set on the parsed command line. Returns true if a value was assigned to the argument. Returns whether an option was set on the parsed command line.
isSet	Returns whether an option was set on the parsed command line. Returns true if a value was assigned to the argument. Returns whether an option was set on the parsed command line.
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.
isStringArgument	Returns whether the argument is a string.
isStringOption	Returns whether option argument can be a string.
isVisible	Returns whether option is visible on the help screen. Default is true.
joinSets	UNION() operation for UF data structure.
leftBoundary	Access to the right boundary.
log2	Computes floored logarithm of base 2 for integer types
mtRandDouble	Return a random number between 0 and 1 using mtRand.
numberOfAllowedValues	Returns the number of allowed values for this ArgParseArgument.
parse	Parses the command line.
printHelp	Prints the complete help message for the parser to a stream. Prints the complete help message for the parser to a stream.
printHelp	Prints the complete help message for the parser to a stream. Prints the complete help message for the parser to a stream.
printShortHelp	Prints a short help message for the parser to a stream Prints a short help message for the parser to a stream
printShortHelp	Prints a short help message for the parser to a stream Prints a short help message for the parser to a stream
printVersion	Prints the version information of the parser to a stream. Prints a version text to a stream.
printVersion	Prints the version information of the parser to a stream. Prints a version text to a stream.
push	Adds a value to an accumulator.
requiredArguments	Sets the number of _arguments (non-parameterized options) are required by the program.
rightBoundary	Access to the right boundary.
setAppName	Sets application name of ArgumentParser.
setDate	Sets date string of ArgumentParser. Set date string for ToolDoc object.
setMaxValue	Sets the maximum value of a ArgParseArgument object. Sets the maximum value of a CommandLineOption object. Sets the maximum value of a CommandLineOption object.
setMaxValue	Sets the maximum value of a ArgParseArgument object. Sets the maximum value of a CommandLineOption object. Sets the maximum value of a CommandLineOption object.
setMaxValue	Sets the maximum value of a ArgParseArgument object. Sets the maximum value of a CommandLineOption object. Sets the maximum value of a CommandLineOption object.
setMinValue	Sets the minimum value of a ArgParseArgument object. Sets the minimum value of a CommandLineOption object. Sets the minimum value of a CommandLineOption object identified by .
setMinValue	Sets the minimum value of a ArgParseArgument object. Sets the minimum value of a CommandLineOption object. Sets the minimum value of a CommandLineOption object identified by .
setMinValue	Sets the minimum value of a ArgParseArgument object. Sets the minimum value of a CommandLineOption object. Sets the minimum value of a CommandLineOption object identified by .
setOptionType	Set the option type.
setRequired	Sets whether or not the option defined by the parameter name (which can be either the short or the long name) is mandatory. Sets whether or not the option is mandatory.
setRequired	Sets whether or not the option defined by the parameter name (which can be either the short or the long name) is mandatory. Sets whether or not the option is mandatory.
setRequiredArguments	Sets the number of _arguments (non-parameterized options) are required by the program.
setShortDescription	Sets short description test of ArgumentParser. Set short description for ToolDoc object.
setValidValues	Sets the set of allowed values of a ArgParseArgument object. Sets the set of allowed values of a CommandLineOption object. Sets the set of allowed values of a CommandLineOption object.
setValidValues	Sets the set of allowed values of a ArgParseArgument object. Sets the set of allowed values of a CommandLineOption object. Sets the set of allowed values of a CommandLineOption object.
setValidValues	Sets the set of allowed values of a ArgParseArgument object. Sets the set of allowed values of a CommandLineOption object. Sets the set of allowed values of a CommandLineOption object.
setVersion	Sets version string of ArgumentParser. Set version string for ToolDoc object.
shareResources	Determines whether two sequences share the same resource.
shortHelp	Prints a short help message for the parser to a stream
sum	Return sum from an accumulator.
version	Prints a version text to a stream.
write	Writes the basic information about the ArgParseOption to the provided stream. Writes the basic information about the CommandLineOption to the provided stream. Saves records to a file.
write	Writes the basic information about the ArgParseOption to the provided stream. Writes the basic information about the CommandLineOption to the provided stream. Saves records to a file.
writeCTD	Exports the app's interface description to a .ctd file. Exports the app's interface description to a .ctd file.
writeCTD	Exports the app's interface description to a .ctd file. Exports the app's interface description to a .ctd file.

Modifier

complement	Complement a sequence or a StringSet in-place.
reverse	Reverse an object/container 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.

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.

Parallelism

computeSplitters

Compute splitters for a sequence of objects.

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

defaultRng	Default default random number generator object of a given type.
pickRandomNumber	Pick a random number using a random number generator object, possibly following the given distribution.
reSeed	Reset and re-seed MersenneTwister
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.
getMaxDeviationOfOrder	Returns the maximal out-of-order distance of adjacent hits.
getScore	Score of the last found match in approximate searching.
getWindowFindHits	Returns 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 getWindowFindHits 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.
atEndOfSequence	Returns true if the iterator is at the end of a sequence.
concat	Returns the concatenation sequence of all sequences in a StringSet.
flatten	Apply the journal to the underlying string, destructively on the underlying string.
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.
mmapAdvise	Call advise function for memory mapped files.
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.
prependValue	Prepend a value to a container.
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.
stringSplit	Append a list of the words in the string, using sep as the delimiter string StringSet.
valueById	Retrieves a string from the StringSet given an id.

Statistics

expectation	Computes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel
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

Synopsis Data Structures

getItems	Get the frequent items.
registerItem	Register an item as seen with a HotList.
removeItem	Manually remove an item from a HotList.

Testing & Debugging

printDebugLevel

Print the current SeqAn debug level and the compiler flags to the given stream.

internal

_assignArgumentValue	Assigns the given value (if applicable) to the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) the value will be appended. Otherwise the value will be overwritten.
alignment	Returns an alignment of the occurences of the representative substring in the index text.

SeqAn - Sequence Analysis Library - www.seqan.de