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 
atEndCheck whether a BamStream object is at end when reading.
atEndCheck whether a SequenceStream is at the end of the file.
beginPositionReturn the clipping begin position as a source position.
buildCreate FaiIndex from FASTA file.
class 
clearValue 
clippedBeginPositionReturn the begin position of the clipping in the unclipped gapped sequence.
clippedEndPositionReturn the end position of the clipping in the unclipped gapped sequence.
closeClose BamStream object's underlying file.
closeClose the SequenceStream.
computeRightArrayBinaryTreeComputes the wavelet tree structure of a text.
createLfTableCreates the LF table
endPositionReturn the clipping end position as a source position.
flushFlush output when writing.
flushWrite all data from SequenceStream to disk.
getAutoSeqStreamFormatNameReturns
getBitReturns whether a specified bit is set or not.
getCharacterReturns the character of a specified position.
getDollarPositionSets the dollar position..
getDollarSubstituteReturns the character used to substitute the dollar sign.
getLeftChildPosReturns the position in RightArrayBinaryTree of the left child vertex.
getPositionReturns the position of the iterator in the host.
getRankReturns the rank (the number of bits set from the start of the bit string) of a specified position.
getRightChildPosReturns the position in RightArrayBinaryTree of the right child vertex.
getSubTreeSizeReturns the number of vertices in the subtree starting at the position an iterator points to.
goLeftChild 
goRightChild 
goToPosition 
hasValue 
hostToVirtualPositionTranslates position in host to virtual (view) position.
isGoodCheck whether the BamStream object has is in the failure state.
isGoodCheck whether a SequenceStream object is ready for reading.
openOpen a BamStream object for reading/writing.
operatorpipe 
operatorpipe= 
operatorpipepipe 
readAllRead all sequence records from a SequenceStream object.
readBatchRead a given number of sequence records from SequenceStream.
readRecordRead one BamAlignmentRecord from a BamStream.
readRecordRead the next sequence record from SequenceStream. Read the next sequence record from SequenceStream.
resetReset BamStream object to status after construction.
save 
setBeginPositionSet the begin position of the clipped gapped sequence, given a source position.
setCharacter 
setClippedBeginPositionSets the begin position of the clipping.
setClippedEndPositionSets the end position of the clipping.
setDollarPositionSets the dollar position..
setDollarSubstituteSets the character used to substitute the dollar sign.
setEndPositionSet the end position of the clipped gapped sequence, given a source position.
setLfTableSet the LfTable of the compressed suffix array..
virtualToHostPositionTranslates virtual (view) position to position in host.
writeAllWrite sequence records from to a SequenceStream object.
writeRecordWrite one BamAlignmentRecord to a BamStream.
writeRecordWrite one sequence record from to a SequenceStream object.
Alignment Free
alignmentFreeComparisonComputes the pairwise similarity scores for a set of sequences
calculateCovarianceCalculates the covariance for the number of word occurences for two words in a sequence of length n, given a background model.
calculateOverlapIndicatorCalculate word overlaps: epsilon(word1,word2)= 1 where word2[j]=word1[j+p] for all j=1...(k-p)
calculatePeriodicityCalculate word periodicity (indicator for overlaps)
calculateProbabilityCalculates the probability of a sequence given a Bernoulli model (String of background frequencies)
calculateVarianceCalculates the variance for the number of word occurences of a word in a sequence of length n given a background model.
countKmersCounts kmers in a sequence. Optionally, a background model is returned.
cutNsCut out all masked sequences from a Dna5String.
stringToStringSetTransform a String into a StringSet containing this String.
Alignments
assignSourceAssign the source of a Gaps object, copying data.
clearClippingClear clipping from Gaps object.
clearGapsClear gaps and clipping from Gaps object.
colA column in an alignment.
colsThe container of columns in an alignment.
gapValueReturn the "gap" value from an alphabet.
getProjectedPositionProjects a position of one sequence taking part in a pairwise match onto the other sequence.
getScoreCompute next suboptimal local alignment.
globalAlignmentComputes the best global pairwise alignment.
globalAlignmentScoreComputes the best global pairwise alignment score.
globalMsaAlignmentComputes a global multiple alignment.
heaviestCommonSubsequenceComputes the heaviest common subsequence between two strings using the match information given in an alignment graph.
heaviestIncreasingSubsequenceComputes the heaviest increasing subsequence.
insertGapInsert one gap into a gapped sequence.
insertGapsInsert multiple gaps into a gapped sequence.
integrateAlignIntegrates an alignment into another by copying the gaps.
isGapQuery whether a given clipped view position is a gap.
isReversedReturns true if the segment match is in reverse orientation.
lengthReturn length of the gapped sequence.
localAlignmentComputes the best pairwise local alignment using the Smith-Waterman algorithm.
longestCommonSubsequenceComputes the longest common subsequence.
longestIncreasingSubsequenceComputes the longest increasing subsequence.
matchRefinementRefines (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.
nextLocalAlignmentCompute next suboptimal local alignment.
removeGapRemove one gap from a gapped sequence.
removeGapsRemove multiple gaps from a gapped sequence.
rowA row in an alignment.
rowsThe container of rows in an alignment.
scoreGapScore for gaps.
scoreGapExtendScore for extending gaps.
scoreGapOpenScore for opening a gap.
scoreMatchMatch score.
scoreMismatchMismatch score.
setScoreGapSet gap opening and extension score.
setScoreGapExtendSet gap extension score.
setScoreGapOpenSet gap opening score.
setScoreMatchSet match score.
setScoreMismatchSet mismatch score.
setSourceSet the source of a Gaps object, do not copy if possible.
setStringsLoads the sequences of a stringset into an alignment.
toSourcePositionTransforms view to source position, if the view position is a gap, the original position of the next non-gap entry is returned.
toViewPositionTransforms source to view position.
unclippedLengthReturn length of the gapped sequence without clipping.
Alphabets
assignQualitiesAssign quality values between strings.
assignQualityValueAssigns quality to a character from an alphabet with integrated quality, e.g. to a specified element from a sequence.
convertConverts a value into another value.
convertQualityConvert an integer quality value into its ASCII representation for FASTQ (Phred scale).
gapValueReturn the "gap" value from an alphabet.
getQualityValueReturns the quality of a character from an alphabet with integrated quality, e.g. the quality associated with a specified element from a sequence.
maxValueSupremum for a given type.
minValueInfimum for a given type.
ordValueMaps an alphabet 1-to-1 to the interval [0..ValueSize).
unknownValueReturn the "unknown" value from an alphabet.
valueSizeReturns size of an alphabet.
Array Handling
arrayClearSpaceDestroys the begin of an array and keeps the rest.
arrayConstructConstruct objects in a given memory buffer.
arrayConstructCopyCopy constructs an array of objects into in a given memory buffer.
arrayConstructMoveMove constructs an array of objects into in a given memory buffer.
arrayCopyCopies a range of objects into another range of objects.
arrayCopyBackwardCopies a range of objects into another range of objects starting from the last element.
arrayCopyForwardCopies a range of objects into another range of objects starting from the first element.
arrayDestructDestroys an array of objects.
arrayFillAssigns one object to each element of a range.
arrayMoveMoves a range of objects into another range of objects.
arrayMoveBackwardMoves a range of objects into another range of objects starting from the last element.
arrayMoveForwardMoves a range of objects into another range of objects starting from the first element.
Atomic Operations
atomicAddAtomically add an integer to another integer.
atomicCasCompare-and-Swap operation.
atomicDecAtomically decrement an integer.
atomicIncAtomically increment an integer.
atomicMaxLock-free implementation of x = max(x, y).
atomicMinLock-free implementation of x = min(x, y).
atomicOrAtomically combine two integers with OR operation.
atomicXorAtomically combine wto integers with XOR operation.
BAM I/O
assignTagsBamToSamAssign tags in BAM format to tags in SAM format.
assignTagsSamToBamAssign tags in SAM format to tags in BAM format.
bamRecordToAlignmentConvert BamAlignmentRecord to an Align object.
eraseTagErase tag from BamTagsDict.
extractTagValueExtract and cast "atomic" value from tags string with index idx.
findTagKeyFind a tag's key of a BamHeaderRecord.
getAlignmentLengthInRefReturns length of BamAlignmentRecord's projection in reference.
getBamTypeCharReturn char identifying the type of the atomic argument.
getBamTypeSizeReturn size of the type identified by c.
getTagKeyReturn key of a tag by index.
getTagTypeGet key of a tag by index.
getTagValueReturn tag value from a BamHeaderRecord or BamTagsDict.
getTagValueReturn tag value from a BamHeaderRecord or BamTagsDict.
getUnalignedCountQuery index for number of unaligned reads.
hasFlagAllProperReturn true if a BamAlignmentRecord has the "all properly aligned" flag set.
hasFlagDuplicateReturn true if a BamAlignmentRecord has the "PCR or optical duplicate" flag set.
hasFlagFirstReturn true if a BamAlignmentRecord has the "first fragment of template" flag set.
hasFlagLastReturn true if a BamAlignmentRecord has the "last fragment of template" flag set.
hasFlagMultipleReturn true if a BamAlignmentRecord has the "multiple" flag set.
hasFlagNextRCReturn true if a BamAlignmentRecord has the "next fragment reverse-complemented" flag set.
hasFlagNextUnmappedReturn true if a BamAlignmentRecord has the "next fragment unmapped" flag set.
hasFlagQCNoPassReturn true if a BamAlignmentRecord has the "does not pass quality controls" flag set.
hasFlagRCReturn true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagRCReturn true if a BamAlignmentRecord has the "reverse-complemented" flag set.
hasFlagSecondaryReturn true if a BamAlignmentRecord has the "secondary alignment" flag set.
hasFlagUnmappedReturn true if a BamAlignmentRecord has the "fragment unmapped" flag set.
jumpToPosSeek in BAM BGZF stream using an index.
nameStoreReturn reference to name store from BamIOContext.
nameStoreCacheReturn reference to name store cache from BamIOContext.
readLoad a BAM index from a given file name.
setTagValueSet the value of a tag through a BamTagsDict.
Basic
nukeCopiesReset all pointers connected to a given one.
Bit Twiddling
clearAllBitsSet all bits to 0.
clearBitSet the bit with the given index to 0.
isBitSetReturns whether the bit with the given index is set to 1.
popCountReturns number of set bits in an integer.
setBitSet the bit with the given index to 1. Set a specified bit to true or false.
setBitToSet the bit with the given index to the given value.
Blast
atBeginDetermines whether an iterator is at the beginning position.
atBeginDetermines whether an iterator is at the beginning position.
atEndDetermines whether an iterator is at the end position.
atEndDetermines whether an iterator is at the end position.
atEndDetermines whether an iterator is at the end position.
databaseNameReference to the name (identifier) of the database in a Blast report.
databaseOrientationPlusOrientation of the database sequence within a Blast HSP alignment.
getAlignmentTurns a HSP from a Blast search into an Alignment object.
getAlignmentTurns a HSP from a Blast search into an Alignment object.
getBitScoreThe bit score associated with a Blast HSP.
getBlastMatchScoreThe Smith-Waterman score associated with a Blast HSP.
getDatabaseBeginThe begin position of the HSP on the database sequence.
getDatabaseEndThe end position of the HSP on the database sequence.
getDatabaseNameThe name (identifier) of the database in a Blast report.
getEValueThe e-value associated with a Blast HSP.
getEValueCutoffThe Expect-Value cutoff parsed from a Blast report.
getGappedKappaThe gapped kappa value parsed from a Blast report.
getGappedLambdaThe lambda value parsed from a Blast report.
getGetExtensionThe gap extension penalty parsed from a Blast report.
getGetOpenThe gap open penalty parsed from a Blast report.
getKappaThe kappa value parsed from a Blast report.
getLambdaThe lambda value parsed from a Blast report.
getNextGet next Blast report from a file containing multiple Blast reports.
getNumGapsThe number of gaps within a Blast HSP alignment.
getQueryBeginThe begin position of the HSP on the query sequence.
getQueryEndThe end position of the HSP on the query sequence.
getQueryNameThe name (identifier) of the query in a Blast report.
getValueAccess to the value.
getValueAccess to the value.
goBeginIterates to the first position of a container.
goBeginIterates to the first position of a container.
goEndIterates to the last position of a container.
goNextIterates to next position.
goNextIterates to next position.
goPreviousIterates to pevious position.
hostHitThe BlastHit this iterator is working on.
hostReportThe BlastReport this iterator is working on.
lengthThe number of items/characters.
numHitsThe total number of hits in a Blast report.
numHspsThe number of HSPs for an entire Blast report or for one Blast hit.
queryNameReference to the name (identifier) of the query in a Blast report.
queryOrientationPlusOrientation of the query sequence within a Blast HSP alignment.
readLoads records from a file.
valueReference to the value.
valueReference to the value.
Bsic
sourceReturn underlying object.
C++ built-in
cast operatorC++ built-in cast operator.
operator deleteC++ built-in deallocation operator.
operator delete[]C++ built-in array deallocation operator.
operator newC++ 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
globalChainingComputes the chain on a set of fragments.
Class: Align
integrateAlignIntegrates an alignment into another by copying the gaps.
Comparisons
compareCompares two objects.
hasPrefixTest whether a sequence is prefix of another sequence.
isEqualOperator "==".
isGreaterOperator ">".
isGreaterOrEqualOperator ">=".
isLessOperator "<".
isLessOrEqualOperator "<=".
isNotEqualOperator "!=".
isPrefixTest whether a sequence is prefix of another sequence.
lcpLengthLength of longest common prefix.
Concepts
ignoreUnusedVariableWarningRemoves unused variable warning.
requireBooleanExprTests for a boolean expression.
sameTypeTests for equality of types.
Consensus
consensusAligmentCompute consensus alignment.
reAlignPerform realignment similar to Anson-Myers algorithm.
Containers
backThe last item in container.
beginThe begin of a container.
beginPositionBegin position of object in host.
capacityThe maximal length.
clearResets an object.
createMakes an object to owner of its content.
emptyTest a container for being empty.
endThe end of a container.
endPositionEnd position of object in host.
eraseErases a part of a container
eraseBackDeletes the last item of a container and reduces its size by 1. The container must have a size greater than or equal to 1.
frontThe first item in container.
getValueAccess to the value.
infixCreates infix object.
infixWithLengthCreates infix object.
iterIterator to item at given position.
lengthThe number of items/characters.
prefixCreates prefix object.
reserveIncreases the capacity.
resizeResizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
resizeSpaceMakes free space in container
shrinkToFitResizes container to minimum capacity
suffixCreates suffix object.
toCStringAccess sequence as c-style string.
valueReference to the value.
Content Manipulation
appendConcatenate two containers.
appendValueAppends a value to a container.
assignAssigns one object to another object.
assignValueAssigns value to item.
getValueAccess to the value.
insertInserts a sequence into a container.
insertValueInserts a single value into a container.
moveHands over content from one container to another container.
moveValueAssigns value to item.
popDeletes item with the highest priority and adjusts the priority queue.
pushInserts a new item and adjusts the priority queue if necessary.
replaceReplaces a part of a container with another container.
setAssigns one object to another object avoiding to copy contents.
setValueMakes holder dependent.
swapSwaps the contents of two values.
topReference to the item with the highest priority.
valueConstructConstructs an object at specified position.
valueDestructDestoys an object at specified position.
Dependent Object
assignHostAssign to the host of a given value.
clearHostClear the host of the given object.
createHostConstruct the host of the given object.
dependentHostQuery dependent state of a hosted object.
emptyHostQuery emptiness state of a hosted object.
moveHostAssign to the host of a given value.
Dependent Objects
createMakes an object to owner of its content.
dependentTest whether object depends on other objects.
detachMakes an object independent from other objects.
hostThe object a given object depends on.
hostIteratorReturn host iterator.
setBeginSets begin of object in host.
setBeginPositionSets begin position of object in host.
setContainerSet container of an adaptor iterator.
setEndSets end of object in host.
setEndPositionSets begin position of object in host.
setHostSets the host of an object.
setPositionSets the position of a finder.
Fragment Store
appendAlignedReadAppends an aligned read entry to a fragment store.
appendMatePairAppends two paired-end reads to a fragment store.
appendNameAppends a name to a name store.
appendReadAppends a read to a fragment store.
assignValueByKeyAdd or update a key-value pair of the current annotation.
buildIndexBuild index for a BamTagsDict object.
calculateInsertSizesCalculates a string with insert sizes for each pair match.
calculateMateIndicesCalculates a string that maps the readId of a read to the readId of its mate.
clearReadsRemoves all reads from a fragment store.
clearValuesClear all key-value pairs of the current annotation.
compactAlignedReadsRemoves invalid aligned reads and rename alignId sequentially beginning with 0.
compactPairMatchIdsRenames pairMatchId sequentially beginning with 0.
convertMatchesToGlobalAlignmentConverts all matches to a multiple global alignment in gap-space.
convertPairWiseToGlobalAlignmentConverts pair-wise alignments to a multiple global alignment.
createLeftChildCreates a new left-most child of the current node and returns an iterator to it.
createRightChildCreates a new right-most child of the current node and returns an iterator to it.
createSiblingCreates a new right sibling of the current node and returns an iterator to it.
getAnnotationReturns the current annotation.
getClrRangeGet the "clear" range of a read alignment.
getIdByNameAppends a name to a name store.
getMateNoReturns the mate number of read for a given readId.
getNameReturns the identifier of the current annotation.
getParentNameReturns the identifier of the parent node in the annotation tree of the current annotation.
getReadReturns the read with the given readId.
getTypeReturns the type name of the current annotation.
getUniqueNameReturns a unique name of the current annotation.
getValueByKeyGiven a key, retrieve its value of the current annotation.
goDownMove the iterator down to the left-most child in the annotation tree.
goNextRightGo to the next node in preorder DFS skipping the current node's subtree.
goNextUpGo to the next node in preorder DFS skipping the subtrees of the current node and of all its siblings.
goRightMove the iterator right to the next sibling in the annotation tree.
goRootGo to the root node in the annotation tree.
goToMoves the iterator to an arbitrary node given its annotationId.
goUpMove the iterator up in the annotation tree.
hasIndexReturn true if BamTagsDict has an index.
isLastChildReturns a boolean value that indicates whether the current node is the last child.
layoutAlignmentCalculates a visible layout of aligned reads.
loadContigManually loads a contig sequence.
loadContigsLoads contigs into fragment store.
loadReadsLoads reads into fragment store.
lockContigLocks a contig sequence from being removed.
lockContigsLocks all contig sequences from being removed.
lowerBoundAlignedReadsPerforms a binary lower bound search on the aligned reads.
nodeDownReturns a new iterator to the first child node of the current annotation in the annotation tree.
nodeRightReturns a new iterator to the right sibling of the current annotation in the annotation tree.
nodeUpReturns a new iterator to the parent node of the current annotation in the annotation tree.
positionGapToSeqConvert from gap-space in the global alignment to the sequence-space on the reference.
positionSeqToGapConvert from sequence space on the reference to gap space in the global alignment.
printAlignmentPrints a window of the visible layout of reads into a outstream.
readLoads records from a file.
refreshRecreate a name store cache.
setNameSets the identifier of the current annotation.
setTypeSets the type name of the current annotation.
sortAlignedReadsStably sort aligned reads.
unlockAndFreeContigRemoves a previous contig lock and clears sequence no further lock exist.
unlockAndFreeContigsRemoves a previous lock for all contigs and clears sequences without lock.
unlockContigRemoves a previous contig lock.
unlockContigsRemoves a previous lock for all contigs.
upperBoundAlignedReadsPerforms a binary upper bound search on the aligned reads.
writeSaves records to a file. Writes the basic information about the ArgParseOption to the provided stream.
writeContigsWrite contigs from fragment store into file.
Graph
addChildAdds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge.
addEdgeAdds a new edge to the graph, either with or without cargo.
addEdgesShortcut to add multiple edges at once. Creates vertices implicitly.
addVertexAdds a new vertex to the graph.
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics.
allPairsShortestPathFinds shortest paths between all pairs of vertices in a graph.
assignBeginStateAssigns a begin state.
assignCargoAssigns a new cargo to the edge.
assignEdgeMapInitializes a vertex map with values of an array.
assignEmissionProbabilityAssigns a new emission probability.
assignEndStateAssigns an end state.
assignNextSAssigns another EdgeStump to the next source pointer.
assignNextTAssigns another EdgeStump to the next target pointer.
assignPropertyAssigns a property to an item in the property map.
assignRootAssigns a new root vertex to the graph.
assignSilentStatusAssigns a silent status to a state.
assignSourceAssigns a source vertex to an edge.
assignStringSetAssigns a new string set to an alignment graph.
assignTargetAssigns a target vertex to an edge.
assignTransitionProbabilityAssigns a new transition probability to an existing edge.
assignVertexMapInitializes a vertex map with values of an array.
atBeginDetermines whether an iterator is at the beginning position.
atEndDetermines whether an iterator is at the end position.
backwardAlgorithmImplements the backward algorithm.
beginStateReturns a reference to the begin state.
bellmanFordAlgorithmComputes shortest paths from a single source in a directed graph.
breadthFirstSearchImplements a breadth-first search on a graph.
buildAlignmentGraphBuilds an Alignment Graph from a set of input alignments.
canParseStringTest whether an automaton can parse a string completely.
cargoAccess to the cargo.
childVertexReturns the child vertex of an edge.
clearResets an object.
clearEdgesRemoves all edges in a graph.
clearVerticesRemoves all vertices in a graph.
collectLeavesReturns all leaves underneath a given vertex.
connectedComponentsDecomposes an undirected graph into its connected components.
convertAlignmentConverts an alignment graph into an alignment matrix.
createOracleCreates a factor oracle.
createOracleOnReverseCreates a factor oracle for the reversed string.
createRootCreates the root in a tree or an automaton.
createSuffixTrieCreates a trie of all suffixes of a text.
createTrieCreates a trie.
createTrieOnReverseCreates a trie for all reversed keywords.
dagShortestPathComputes shortest paths from a single source in a directed acyclic graph (DAG).
degreeNumber of incident edges for a given vertex.
depthFirstSearchImplements a depth-first search on a graph.
dijkstraComputes shortest paths from a single source in a graph.
emissionProbabilityReturns a reference to the emission probability.
emptyTest a container for being empty.
endStateReturns a reference to the end state.
findEdgeFinds an edge.
findVertexFinds a vertex given a sequence id and a position.
floydWarshallAlgorithmFinds shortest paths between all pairs of vertices in a graph.
fordFulkersonAlgorithmComputes a maximum flow in a directed graph.
forwardAlgorithmImplements the forward algorithm.
fragmentBeginGets the begin position for this fragment or this vertex descriptor in the sequence.
fragmentLengthGets the length of the label of a given vertex descriptor in the sequence.
generateSequenceGenerates random state and alphabet sequences of a given HMM.
getAdjacencyMatrixReturns an adjacency matrix representation of the graph.
getBeginStateReturns the begin state.
getCargoGet method for the edge cargo.
getDistanceMatrixComputes a pairwise distance matrix from an alignment graph.
getEmissionProbabilityReturns the emission probability.
getEndStateReturns the end state.
getFirstCoveredPositionFinds the first position in a sequence that is not assigned to a nil vertex.
getIdLowerBoundReturns the smallest distributed id. That is, the return value is guaranteed to be the smallest id obtained so far.
getIdUpperBoundReturns the largest distributed id plus 1. That is, the return value is guaranteed to be an upper bound on all distributed ids.
getLastCoveredPositionFinds the last position in a sequence that is not assigned to a nil vertex.
getNextSGet method for the next source pointer.
getNextTGet method for the next target pointer.
getNilUtility function returning a value that represents nil. Useful for various graph algorithms, e.g., missing predecessors, vertices that have not been visited, etc.
getPropertyGet method for an item's property.
getRootGet method for the root of a tree or an automaton.
getSourceGet method for the source.
getStringSetGets the string set of an alignment graph.
getSuccessorGets 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.
getTargetGet method for the target.
getTransitionProbabilityReturns the transition probability.
getValueAccess to the value.
goBeginIterates to the first position of a container.
goEndIterates to the last position of a container.
goNextIterates to next position.
goPreviousIterates to pevious position.
hostGraphThe graph this iterator is working on.
idCountDetermines the number of ids that were obtained.
idInUseChecks whether the given id is in use or not.
inDegreeNumber of incoming edges for a given vertex.
isLeafTests whether a given vertex is a leaf or not.
isRootTests whether a given vertex is the root or not.
isSilentIndicates whether a state is silent or not.
kruskalsAlgorithmComputes a minimum spanning tree on a graph.
labelReturns the label of the out-edge this iterator points to (for automatons).
labelGets the label that is associated with this vertex descriptor or the sequence that is associated with a fragment.
nextSAccesses the next source pointer.
nextTAccesses the next target pointer.
njTreeComputes a guide tree from a distance matrix.
numChildrenNumber of children of a given tree vertex.
numEdgesNumber of edges in a graph.
numTreeEdgesNumber of tree edges.
numVerticesNumber of vertices in a graph. Returns the number of vertices in a wavelet tree.
obtainIdObtains a new id from the id manager.
outDegreeNumber of outgoing edges for a given vertex.
parentVertexReturns the parent vertex of an edge or vertex.
parseStringParses a string one character at a time and moves accordingly in the automaton.
primsAlgorithmComputes a minimum spanning tree on a graph.
progressiveAlignmentPerforms a progressive alignment.
propertyAccesses the property of an item in the property map.
releaseAllReleases all ids handled by this id manager at once.
releaseIdReleases a given id so it can be redistributed later on.
removeAllChildrenRemoves all children from the tree given a parent.
removeChildRemoves a child from the tree given a parent.
removeEdgeRemoves an edge from the graph. For automatons a label is required.
removeInEdgesRemoves the incoming edges of a given vertex.
removeOutEdgesRemoves the outgoing edges of a given vertex.
removeVertexRemoves a vertex.
resizeEdgeMapInitializes an edge map
resizeVertexMapInitializes a vertex map.
rootGets a reference to the root of the tree.
sequenceIdGets the sequence id that is associated with this vertex descriptor or with a sequence of a fragment.
silentStatusReference to the silent status of a state.
sourceVertexReturns the source vertex of an edge.
stringSetGets the string set of an alignment graph.
stronglyConnectedComponentsDecomposes a directed graph into its strongly connected components.
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score.
targetAccesses the target of an EdgeStump.
targetVertexReturns the target vertex of an edge.
topologicalSortPerforms a topological sort on a directed acyclic graph (DAG).
transitionProbabilityReturns a reference to the transition probability.
transitiveClosureDetermines whether there is a path between any two given vertices or not.
transposeTransposes a graph, either in-place or from source to dest.
tripletLibraryExtensionPerforms a full or group-based consistency extension.
upgmaTreeComputes a guide tree from a distance matrix.
valueReference to the value.
viterbiAlgorithmImplements the viterbi algorithm.
weaklyConnectedComponentsCompute weakly connected components of a directed graph.
Index
bwtAtShortcut for value(indexBwt(..), ..).
childAtShortcut for value(indexChildtab(..), ..).
childrenAreLeavesTest whether iterator points to a node with only leaf-children.
countChildrenCount the number of children of a tree node.
countOccurrencesReturns the number of occurences of representative substring or a q-gram in the index text.
countOccurrencesMultipleReturns the number of occurences of a q-gram for every sequence of a StringSet .
countSequencesReturn the number of sequences in an index' underlying text.
createBWTableCreates a Burrows-Wheeler table from a given text and suffix array.
createChildtabCreates a child table from a given lcp table.
createCountArrayBuilds an index on a StringSet storing how often a q-gram occurs in each sequence.
createLcpTableCreates a lcp table from a given text and suffix array.
createQGramIndexBuilds a q-gram index on a sequence.
createQGramIndexDirOnlyBuilds the directory of a q-gram index on a sequence.
createQGramIndexSAOnlyBuilds the suffix array of a q-gram index on a sequence.
createSuffixArrayCreates a suffix array from a given text.
createWotdIndexBuilds a q-gram index on a sequence.
dirAtShortcut for value(indexDir(..), ..).
emptyParentEdgeReturns true iff the edge label from the iterator node to its parent is empty.
findRepeatsSearch for repeats in a text.
getFibreReturns a specific fibre of a container.
getFrequencyReturns the number of sequences, which contain the representative as a substring.
getKmerSimilarityMatrixCreates a matrix storing the number of common q-grams between all pairs of sequences.
getOccurrenceReturns an occurence of the representative substring or a q-gram in the index text.
getOccurrencesReturns all occurences of the representative substring or a q-gram in the index text. Returns the number of occurrences of a specified character from the start to a specified position.
getOccurrencesBwtReturns the characters left beside all occurrence of the representative substring in the index text.
getStepSizeReturn the q-gram step size used for index creation.
goDownIterates down one edge or a path in a tree.
goRightIterates to the next sibling in a tree.
goRootMove iterator to the root node.
goUpIterates up one edge to the parent in a tree.
hashComputes a (lower) hash value for a shape applied to a sequence.
hash2Computes an unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span
hash2NextComputes a unique hash value for the adjacent shape, even if it is shorter than q.
hash2UpperComputes an upper unique hash value of a shape applied to a sequence, even if the sequence is shorter than the shape span.
hashNextComputes the hash value for the adjacent shape.
hashUpperComputes an upper hash value for a shape applied to a sequence.
indexBucketMapShortcut for getFibre(.., QGramBucketMap).
indexBwtShortcut for getFibre(.., EsaBwt).
indexChildtabShortcut for getFibre(.., EsaChildtab).
indexCountsShortcut for getFibre(.., QGramCounts).
indexCountsDirShortcut for getFibre(.., QGramCountsDir).
indexCreateCreates a specific Fibre.
indexDirShortcut for getFibre(.., QGramDir).
indexLcpShortcut for getFibre(.., EsaLcp).
indexLcpeShortcut for getFibre(.., EsaLcpe).
indexRawSAShortcut for getFibre(.., EsaRawSA).
indexRawTextShortcut for getFibre(.., EsaRawText).
indexRequireOn-demand creation of a specific Fibre.
indexSAShortcut for getFibre(.., EsaSA).
indexShapeShortcut for getFibre(.., QGramShape).
indexSuppliedReturns whether a specific Fibre is present.
indexTextShortcut for getFibre(.., EsaText).
isLeafTest whether a tree iterator points to a leaf.
isLeftMaximalTest whether the occurences of an iterator's representative mutually differ in the character left of the hits.
isPartiallyLeftExtensibleTest whether the characters left of the two occurences of representative are equal.
isRightTerminalTest whether iterator points to a suffix.
isRootTest whether a tree iterator points to the root node.
isUniqueTest whether the representative occurs only once in every sequence.
lcaReturns the last common ancestor of two tree nodes.
lcpReturns the length of the longest-common-prefix of two suffix tree nodes.
lcpAtShortcut for value(indexLcp(..), ..).
lcpeAtShortcut for value(indexLcpe(..), ..).
lfMappingReturns the position of the character L[c] in F.
nodeDepthReturns the zero-based node depth of the iterator node.
nodeHullPredicateIf false this node and its subtree is concealed.
nodePredicateIf false this node will be skipped during the bottom-up traversal.
nodeUpReturns the vertex descriptor of the parent node.
orderOccurrencesSorts a string of occurrences.
parentEdgeFirstCharReturns the first character of the edge from an iterator node to its parent.
parentEdgeLabelReturns a substring representing the edge from an iterator node to its parent.
parentEdgeLengthReturns the length of the edge from the iterator node to its parent.
parentRepLengthReturns the length of the substring representing the path from root to iterator's parent node.
rangeReturns the suffix array interval borders of occurences of representative substring or a q-gram in the index text.
rawsaAtShortcut for value(indexRawSA(..), ..).
rawtextAtShortcut for value(indexRawText(..), ..).
repLengthReturns the length of the substring representing the path from root to iterator node.
representativeReturns a substring representing the path from root to iterator node.
resizeVertexMapInitializes a vertex map.
saAtShortcut for value(indexSA(..), ..).
setStepSizeChange the q-gram step size used for index creation.
shapeToStringConverts a given shape into a sequence of '1' (relevant position) and '0' (irrelevant position).
stringToShapeTakes a shape given as a string of '1' (relevant position) and '0' (irrelevant position) and converts it into a Shape object.
textAtShortcut for value(indexText(..), ..).
unhashInverse of the hash function; for ungapped shapes.
weightNumber of relevant positions in a shape.
Input / Output
attachToFileAttach to already open input / output file.
checkEofCheck that the EOF marker is present in a BGZF(/BAM) file.
clearReset a FaiIndex object to the state after default construction.
clearReset a GenomicRegion object to the same state after default construction.
getIdByNameReturn id (index in the file) of a sequence in a FAI file.
isDirectQuery a GZ File Stream for being "direct."
numSeqsReturn number of sequences known to an FaiIndex.
parseParse genomic region string store results in GenomicRegion.
readRead a FAI index.
readFastaRead first sequence from a FASTA file.
readRegionLoad the infix of a sequence from a FaiIndex.
readSequenceLoad a whole sequence from an FaiIndex.
sequenceLengthReturn length of the sequence with the given id in the FaiIndex.
sequenceNameReturn the name of the sequence with the given id in the FaiIndex.
writeWrite out an FaiIndex object.
Input/Output
appendSeqsAppends all sequences stored in files of directory to a StringSet.
assignCroppedSeqIdExtracts the sequence id up to the first whitespace of a sequence file fragment.
assignQualExtracts the quality values of a sequence file fragment.
assignQualIdExtracts the quality value id of a sequence file fragment.
assignSeqExtracts the sequence part of a sequence file fragment.
assignSeqIdExtracts the sequence id of a sequence file fragment.
asyncReadAtAsynchronously loads records from a specific position in a file.
asyncWriteAtAsynchronously saves records to a specific position in a file.
atEndDetermines whether an iterator is at the end position.
cancelCancels an asynchronous request.
checkStreamFormatcheck whether the data provided by reader is (one of) the specified format(s).
closeCloses a file.
countLinecount characters in a line not including \r and \n
endsWithCheck whether a sequence ends with a given suffix.
flushWaits for all open requests to complete.
goNextIterates to next position.
goNextIterates to next position.
guessFileFormatTries to determine the format of a file.
guessFormatGuesses a file format from the contents of a sequence file.
guessFormatFromFilenameGuesses a file format from a sequence file name.
isalnumCheck if character is alpha-numeric
isalphaCheck if character is a upper or lowercase letter
isblankCheck if character is either ' ' or '\t'
iscntrlCheck if character is a control character
isdigitCheck if character is a digit
isgraphCheck if character is printable and not white space
isprintCheck if character is printable, i.e. not a control character
isspaceCheck if character is a white-space character
lengthThe number of items/characters.
lexicalCastCast from a String-type to a numerical type
lexicalCast2Cast from a String-type to a numerical type
loadScoreMatrixLoad a score matrix from a file.
nextIsQuery whether the next record is of a given type.
openOpens a file.
openTempOpens a temporary file.
readLoads a record from file.
readLoads records from a file.
read2reads an entire document from a Stream, by the means of RecordReader
readAlphaNumsRead characters from stream as long as characters are letters
readAtLoads records from a specific position in a file.
readDigitsRead characters from stream as long as characters are digits
readDna5IgnoringWhitespacesRead characters from stream, as long as they are DNA5 characters. Skip over whitespaces.
readFeatureFinds 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").
readFloatRead characters from stream as long as the number is a valid floating point numbers.
readGraphsRead characters from stream as long as characters are graph characters.
readIdentifierRead characters from stream as long as characters are identifiers (alphanumeric, '-', and '_').
readLettersRead characters from stream as long as characters are letters
readLineRead a line from stream and save it to buffer
readLineStripTrailingBlanksRead a line from stream and save it to buffer, remove trailing blanks
readLineTypeReads the information belonging to the two-character line code specified.
readMetaRead meta information from file.
readNCharsRead exactly n characters from stream into buffer
readNCharsIgnoringWhitespaceRead n characters from stream into buffer, but skip certain Chars
readRecordreads 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.
readUntilBlankRead characters from stream into buffer until Blank is encountered
readUntilCharRead characters from stream into buffer until Char is encountered
readUntilOneOfRead characters from stream into buffer until one of the given characters is encountered
readUntilTabOrLineBreakRead characters from stream until a tab or line-break occurs.
readUntilWhitespaceRead characters from stream into buffer until Whitespace is encountered
resizeResizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
resultCodeReturns int current status code for reader (0 on success).
rewindSets the current file pointer to the beginning.
seekChanges the current file pointer.
setEofSets the file end to the current pointer.
sizeGets the file size.
skipBlanksSkip (i.e. read without saving) characters from stream until non-Blank is encountered
skipCharSkip one character that must be equal to a given one for this function to succeed.
skipLineSkip a line in stream and go to beginning of next
skipNCharsSkip exactly n characters from stream
skipNCharsIgnoringWhitespaceSkip n characters from stream, not counting whitespaces
skipUntilBlankSkip (i.e. read without saving) characters from stream until Blank is encountered
skipUntilCharSkip (i.e. read without saving) characters from stream until Char is encountered
skipUntilGraphSkip (i.e. read without saving) characters from stream until printable, non-' ' character is encountered
skipUntilLineBeginsWithCharSkip input until the first graphical(see isgraph) character of a line is equal to c
skipUntilLineBeginsWithOneCharOfStrSkip input until a line begins with a one of the characters in str
skipUntilLineBeginsWithStrSkip input until a line begins with str.
skipUntilStringSkip (i.e. read without saving) characters from stream until String is encountered
skipUntilWhitespaceSkip (i.e. read without saving) characters from stream until Whitespace is encountered
skipWhitespacesSkip (i.e. read without saving) characters from stream until non-Whitespace is encountered
splitDivides the contents of a sequence file into sequence file fragments separated by a file format specific delimiter.
splitEmblHeaderSplit an EMBL header line.
splitGenBankHeaderSplit an GenBank header field/value.
startFirstPassStart the first reading pass.
startSecondPassStart the second reading pass.
startsWithCheck whether a sequence starts with a given prefix.
streamEofCheck end-of-file state of a Stream.
streamErrorReturn the stream's error code.
streamFlushFlush the underlying stream.
streamPeekRead next character from stream without advancing current position.
streamPutWrite different types to stream
streamReadBlockRead a block of bytes into a buffer.
streamReadCharRead next character from stream and advance the current position.
streamSeekPerform a seek operation on the stream.
streamTellGet the position in the current stream.
streamWriteBlockWrite a block of bytes from a buffer into a stream.
streamWriteCharWrite one character to the stream.
tellGets the current file pointer.
valueReference to the value.
waitForWaits for an asynchronous request to complete.
writeWrites to stream.
write 
writeSaves records to a file. Writes the basic information about the ArgParseOption to the provided stream.
write2writes an entire document to a Stream
writeAtSaves records to a specific position in a file.
writeRecordwrite one record (e.g. a single DNA-sequence and its meta data) to a Stream
Iteration
assignValueAssigns value to item.
atBeginDetermines whether an iterator is at the beginning position.
atEndDetermines whether an iterator is at the end position.
atNilTests whether iterator is at nil position.
beginThe begin of a container.
containerContainer of an iterator.
differenceThe difference between two iterators.
endThe end of a container.
getValueAccess to the value.
goBeginIterates to the first position of a container.
goEndIterates to the last position of a container.
goFurtherIterates some steps further.
goNextIterates to next position.
goNilMoves iterator to nil position.
goPreviousIterates to pevious position.
moveValueAssigns value to item.
positionPosition of an iterator.
valueReference to the value.
Local Match Store
appendLocalMatchAppend a new local match to a LocalMatchStore
readRecordreads 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.
readRecordreads 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.
readRecordreads 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
addInsert another value into a multi map.
cargoReturns a cargo given a key.
eraseRemoves a value from a map.
eraseAllRemoves a value from a map.
findFind a value in a map.
hasKeyDetermines whether a map contains a value given key.
insertInsert new value into map.
keyGet the the key of the element.
mapValueSubscript operator [ ] of maps.
valueReturns a value given a key.
Memory
allocateAllocates memory from heap.
clearDeallocates all memory blocks.
deallocateDeallocates memory.
memsetAn implementation of memset with fixed number of bytes using Metaprogramming.
Miscellaneous
addArgumentAdds a ArgParseArgument object to the ArgumentParser.
addDefaultValueAdds/appends a new value to the list of default values.
addDescriptionAppends a description paragraph to the ArgumentParser documentation.
addIntervalAdds an interval to an interval tree.
addLineAdds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions.
addListItemAdd list item to ToolDoc object. Appends a list item to the ArgumentParser.
addListItemAdd list item to ToolDoc object. Appends a list item to the ArgumentParser.
addOptionAdds a ArgParseOption object to the ArgumentParser.
addSectionAdd section to ToolDoc object. Begins a new section of ArgParseOption the help output of the ArgumentParser.
addSectionAdd section to ToolDoc object. Begins a new section of ArgParseOption the help output of the ArgumentParser.
addSubSectionAdd subsection to ToolDoc object.
addTextAdd text line/paragraph to ToolDoc. Appends a text paragraph to the ArgumentParser.
addTextAdd text line/paragraph to ToolDoc. Appends a text paragraph to the ArgumentParser.
addTextSectionAdds a text section to the ArgumentParser.
addTextSubSectionAdds a text subsection to the ArgumentParser.
addUsageLineAdds a line of text to the usage output of the ArgumentParser.
adjustTopAdjusts the priority of the first item.
averageReturn average from an accumulator.
clearEntriesClear entries from ToolDoc object.
countReturn sum from an accumulator.
cpuTimeReturns the cpu time in seconds.
createIntervalTreeCreate an interval tree.
findIntervalsFind all intervals that contain the query point or overlap with the query interval.
findIntervalsExcludeTouchingFind 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.
findSetReturn set identifier, given an element identifier.
getAppNameGet tool name of ArgumentParser object.
getArgumentReturns a reference to the specified argument.
getArgumentLabelReturns the label for the given ArgParseArgument. Either the user defined label is returned or a default label (based on the ArgumentType is used).
getArgumentValueReturns the value of the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) you can specify which value you want to get. If not set the first value will be returned. Retrieves the value of an argument given by its position.
getArgumentValueReturns the value of the ArgParseArgument object. If the ArgParseArgument is a list or can hold multiple values (numberOfArguments) you can specify which value you want to get. If not set the first value will be returned. Retrieves the value of an argument given by its position.
getArgumentValueCountReturns the number of values stored in the specified option.
getArgumentValuesReturns all values of the ArgParseArgument object as const std::vector. Returns all values of an option given on the command line.
getArgumentValuesReturns all values of the ArgParseArgument object as const std::vector. Returns all values of an option given on the command line.
getCategoryGet tool category of ToolDoc object. Get tool category of ArgumentParser object.
getCategoryGet tool category of ToolDoc object. Get tool category of ArgumentParser object.
getDateGet date string from ToolDoc object.
getLeftBoundaryGet method for the left boundary.
getManTitleGet man title from ToolDoc object.
getNameGet tool name of ToolDoc object.
getObjectIdA value that identifies the underlying sequence.
getOptionReturns a reference to the specified option.
getOptionValueRetrieves the value of an option given either the short or long name.
getOptionValueCountReturns the number of values stored in the specified option.
getOptionValuesReturns all values of an option given on the command line.
getRightBoundaryGet method for the right boundary.
getShortDescriptionGet short description of ToolDoc object. Gets short description of ArgumentParser.
getShortDescriptionGet short description of ToolDoc object. Gets short description of ArgumentParser.
getTerminalSizeRetrieve size of terminal.
getVersionGet version string from ToolDoc object. Get version string from ArgumentParser object.
getVersionGet version string from ToolDoc object. Get version string from ArgumentParser object.
hasArgumentValueReturns true if a value for the given position is available.
hasDefaultReturns true if a default value was given for that argument. Returns whether an option has a default value or not.
hasDefaultReturns true if a default value was given for that argument. Returns whether an option has a default value or not.
hasOptionReturns whether a certain option is registered in the parser.
hideOptionHides the ArgParseOption from the help screen. Hides the ArgParseOption defined by the parameter name (which can be either the short or the long name) from the help screen.
hideOptionHides the ArgParseOption from the help screen. Hides the ArgParseOption defined by the parameter name (which can be either the short or the long name) from the help screen.
isAnsiColorTerminalCheck whether we are printing to a terminal.
isBooleanOptionReturns whether option is a switch.
isDoubleArgumentReturns whether the argument is a double.
isInputFileArgumentReturns whether the argument is an input file.
isIntegerArgumentReturns whether the argument is an integer.
isListArgumentReturns whether the argument can be given multiple times.
isOutputFileArgumentReturns whether the argument is an output file.
isRequiredReturns whether the option is mandatory.
isSetReturns true if a value was assigned to the argument. Returns whether an option was set on the parsed command line.
isSetReturns true if a value was assigned to the argument. Returns whether an option was set on the parsed command line.
isStringArgumentReturns whether the argument is a string.
isTerminal()Check whether we are printing to a terminal.
isVisibleReturns whether option is visible on the help screen. Default is true.
joinSetsUNION() operation for UF data structure.
leftBoundaryAccess to the left boundary.
log2Computes floored logarithm of base 2 for integer types
numberOfAllowedValuesReturns the number of allowed values for this ArgParseArgument.
parseParses the command line.
printPrint ToolDoc object in a given format.
printHelpPrints the complete help message for the parser to a stream.
printShortHelpPrints a short help message for the parser to a stream
printVersionPrints the version information of the parser to a stream.
pushAdds a value to an accumulator.
removeIntervalRemoves an interval from the interval tree.
rightBoundaryAccess to the right boundary.
setAppNameSets application name of ArgumentParser.
setCategorySet tool category for ToolDoc object. Set tool category for ArgumentParser object.
setCategorySet tool category for ToolDoc object. Set tool category for ArgumentParser object.
setDateSet date string for ToolDoc object. Sets date string of ArgumentParser.
setDateSet date string for ToolDoc object. Sets date string of ArgumentParser.
setDefaultValueSets the default value for the given option.
setManTitleSet version string for ToolDoc object.
setMaxValueSets the maximum value of a ArgParseArgument object.
setMinValueSets the minimum value of a ArgParseArgument object.
setNameSet tool name for ToolDoc object.
setRequiredSets whether or not the option is mandatory. Sets whether or not the option defined by the parameter name (which can be either the short or the long name) is mandatory.
setRequiredSets whether or not the option is mandatory. Sets whether or not the option defined by the parameter name (which can be either the short or the long name) is mandatory.
setShortDescriptionSet short description for ToolDoc object. Sets short description of the ArgumentParser object.
setShortDescriptionSet short description for ToolDoc object. Sets short description of the ArgumentParser object.
setValidValuesSets the set of allowed values of a ArgParseArgument object.
setVersionSet version string for ToolDoc object. Sets version string of ArgumentParser.
setVersionSet version string for ToolDoc object. Sets version string of ArgumentParser.
shareResourcesDetermines whether two sequences share the same resource.
sumReturn sum from an accumulator.
sysTimeReturns the system time in seconds.
writeSaves records to a file. Writes the basic information about the ArgParseOption to the provided stream.
writeCTDExports the app's interface description to a .ctd file.
xmlEscapeReplaces invalid XML characters in the given sequence with their valid XML equivalent.
Modifier
complementComplement a sequence or a StringSet in-place.
reverseReverse an object/container in-place.
reverseComplementReverse and complement a sequence or a StringSet in-place.
toLowerConvert characters in sequence or StringSet to lower case in-place.
toUpperConvert characters in sequence or StringSet to lower case in-place.
Motif Search
absFreqOfLettersInSeqCounts the number of times each residue of a fixed sequence alphabet occurs in a given sequence.
absFreqOfLettersInSetOfSeqsCounts the number of times each residue of a fixed sequence alphabet occurs in a given set of sequences.
addValueAdds a value of a specific type to each element of a given FrequencyDistribution object.
backgroundFrequencyDetermines the background letter frequencies in a given dataset
binomialCoefficientCalculates the binomial coefficient C(n,k).
completeProfileConcatenates the background frequency with the profile for the motif component.
convertPatternToProfileConverts a pattern into a profile which consists of a set of frequency distributions.
convertResidueToFrequencyDistCoverts a residue to a frequency distribution (profile).
convertSetOfPatternsToProfileConverts a set of sequence patterns into a profile.
determineConsensusSeqDetermines the consensus pattern of a given profile.
displayDisplays a given set of strings.
displayResultDisplays all found motif candidates. In the case of the Projection Motif Finder the function displays the consensus pattern of the found motif candidate.
emRepresents the EM algorithm as used by MEME.
factorialCalculates the factorial value of any integer number.
findMotifRepresents the main function which is used to start the search for noticeable motif patterns.
getMotifGets the motif out of a MotifFinder. If pos is given, the pos-th motif is returned, otherwise the first motif is returned.
hammingDistanceDetermines the Hamming distance between two sequences.
inverseHashDetermines the corresponding sequence pattern given the hash value.
logarithmizeLogarithmizes each element of a given FrequencyDistribution object.
motifCountGets number of motifs in the MotifFinder.
normalizeDetermines the normalized frequencies.
posOfMaxDetermines the residue position in a given FrequencyDistribution object with the maximum frequency.
sumDetermines the sum of all frequencies in a given FrequencyDistribution object.
Parallelism
computeSplittersCompute splitters for a sequence of objects.
Pipelining
beginReadInitiates a read process.
beginWriteInitiates a write process.
bundle2Returns a bundle of two objects.
bundle3Returns a bundle of three objects.
bundle5Returns a bundle of five objects.
endReadTerminates a read process.
endWriteTerminates a write process.
frontGets the first element of the remaining stream.
popPops the first element of the remaining stream.
pushAppends an item at the end of an input stream.
Random
defaultRngDefault default random number generator object of a given type.
mtRandReturn a Mersenne-Twister random number.
mtRandDoubleReturn a random number between 0 and 1 using mtRand.
mtRandInitInitialize the Mersenne-Twister random number generator.
pickRandomNumberPick a random number using a random number generator object, possibly following the given distribution.
reSeedReset and re-seed MersenneTwister
shuffleShuffle the given container.
Scoring
scoreReturns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.
scoreReturns the score for aligning the characters seq1[pos1] and seq2[pos2]. This function allows to define a position-dependent scoring scheme.
scoreGapExtendHorizontalReturns the score for extending a horizontal gap after pos1 in seq1.
scoreGapExtendVerticalReturns the score for extending a vertical gap after pos2 in seq2.
scoreGapHorizontalReturns the score for a horizontal gap after pos1 in seq1.
scoreGapOpenHorizontalReturns the score for opening a horizontal gap after pos1 in seq1.
scoreGapOpenVerticalReturns the score for opening a vertical gap after pos2 in seq2.
scoreGapVerticalReturns the score for a vertical gap after pos2 in seq2.
setDefaultScoreMatrixSet the value of the given matrix to the default value.
setScoreSet the substitution score between two values.
Searching
findSearch for a Pattern in a Finder object.
findBeginSearch the begin of an approximate match.
getBeginScoreScore of the last match found by findBegin during approximate searching.
getMaxDeviationOfOrderReturns the maximal out-of-order distance of adjacent hits.
getScoreScore of the last found match in approximate searching.
getWindowFindHitsReturns the string of hits from the finder.
haystackReturns the haystack of a Finder object.
needleReturns the needle of a Pattern object (not implemented for some online-algorithms).
positionRangeReturns a pair of the begin and end position in the haystack or needle for the last hit found.
positionRangeNoClipReturns a pair of the begin and end position in or beyond the haystack or needle for the last hit found.
scoreLimitThe minimal score a match must reach in approximate searching.
scoringSchemeThe scoring scheme used for finding or aligning.
setHaystackSets the haystack of a Finder object.
setNeedleSets the needle of a Pattern object and optionally induces preprocessing.
setPositionSets the position of a finder.
setScoreLimitSets the minimal score a match must reach in approximate searching.
setScoringSchemeSets the scoring scheme used for finding or aligning.
windowFindBeginInitializes 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.
windowFindEndFlushes the pattern. Used together with windowFindBegin and windowFindNext.
windowFindNextSearches over the next window with the finder. The found hits can be retrieved with getWindowFindHits Used together with windowFindBegin and windowFindEnd.
Seed Handling
addSeedAdds a seed to an existing set.
addSeedsAdds 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.
bandedAlignmentCalculates a banded alignment around a Seed.
bandedChainAlignment Calculates a banded alignment around a chain of seeds.
dimensionDimension of a seed.
endDiagonal Returns the diagonal of the end point.
extendSeedExtends a seed.
extendSeedScoreExtends 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.
leftPositionThe begin position of segment in a seed.
maximumDistanceSets the maximal distance between two seed during a chaining process.
obtainID btains a new id from the id manager.
qualityValueSets 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.
rightPositionThe end position of segment in a seed.
scoreSeed Calculates the score of a seed.
seedScoreReturns 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.
setLeftPositionSets begin position of segment in a seed.
setMaximumDistanceSets the maximal distance between two seed during a chaining process.
setQualityValueSets 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.
setRightPositionSets end position of segment in a seed.
startDiagonal Returns the diagonal of the start point.
Sequences
assignValueByIdAdds a new string to the StringSet and returns an id.
atEndOfSequenceReturns true if the iterator is at the end of a sequence.
concatReturns the concatenation sequence of all sequences in a StringSet.
createGlobalReferenceCreates the global reference of a Journaled Set.
flattenApply the journal to the underlying string, destructively on the underlying string.
getSeqNoReturns the sequence number of a position.
getSeqOffsetReturns the local sequence offset of a position.
getValueByIdRetrieves a string from the StringSet given an id.
globalReferenceReturns the global reference sequence of a Journaled Set.
idToPositionRetrieves the position of a string in the StringSet given an id.
isFlatReturns whether journaled string has modifications.
joinJoins a Journaled String to a Journaled Set by computing and journaling differences to the global reference sequence.
mmapAdviseCall advise function for memory mapped files.
posGlobalizeConverts a local/global to a global position.
posLocalToXConverts a local to a local/global position.
posLocalizeConverts a local/global to a local position.
positionToIdRetrieves the id of a string in the StringSet given a position.
prependValuePrepend a value to a container.
removeValueByIdRemoves a string from the StringSet given an id.
setGlobalReferenceSets the global reference of a Journaled Set.
stringSetLimitsRetrieves a string of delimiter positions of a StringSet which is needed for local<->global position conversions.
stringSplitAppend a list of the words in the string, using sep as the delimiter string StringSet.
valueByIdRetrieves a string from the StringSet given an id.
Statistics
expectationComputes the expectation for a set of patterns w.r.t. a set of text strings and a MarkovModel
varianceComputes the variance for a set of patterns w.r.t. a set of text strings and a MarkovModel
zscoreComputes the z-score index for a set of patterns w.r.t. a set of text strings and a MarkovModel
Synopsis Data Structures
getItemsGet the frequent items.
registerItemRegister an item as seen with a HotList.
removeItemManually remove an item from a HotList.
Testing & Debugging
printDebugLevelPrint the current SeqAn debug level and the compiler flags to the given stream.
internal
alignmentReturns an alignment of the occurences of the representative substring in the index text.
SeqAn - Sequence Analysis Library - www.seqan.de
 

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