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
addDefaultValue (ArgumentParser)Add to the default values of an option of an ArgumentParser.
atEnd (BamStream)Check whether a BamStream object is at end when reading.
atEnd (SequenceStream)Check whether a SequenceStream is at the end of the file.
back (Chained Seed)Returns a reference to the last seed diagonal.
begin (Chained Seed)Returns an iterator to the beginning of the seed digonals.
beginPosition (Gaps)Return the clipping begin position as a source position.
build (FaiIndex)Create FaiIndex from FASTA file.
chainSeedsGloballyGlobal chaining of seeds.
clear (LfTable)Clears the LF table.
clear (PrefixSumTable)Clears the prefix sum table.
clear (RankDictionary)Clears the rank dictionary.
clear (SentinelRankDictionary)Clears the dictionary.
clippedBeginPosition (Gaps)Return the begin position of the clipping in the unclipped gapped sequence.
clippedEndPosition (Gaps)Return the end position of the clipping in the unclipped gapped sequence.
close (BamStream)Close BamStream object's underlying file.
close (SequenceStream)Close the SequenceStream.
countOccurrences (SentinelRankDictionary)Returns the number of occurrences of a specified character from the start to a specified position.
createCompressedSa (CompressedSA)This functions creates a compressed suffix array with a specified compression factor.
createLfTableCreates the LF table
createPrefixSumTable (PrefixSumTable)Creates the prefix sum table
createRankDictionary (RankDictionary)This functions creates the dictionary.
createRightArrayBinaryTreeComputes the wavelet tree structure of a text.
createSentinelRankDictionary (SentinelRankDictionary)This functions creates the dictionary structure.
empty (LfTable)Clears the LF table.
empty (RankDictionary)Returns whether or not the rank dictionary is empty.
empty (SentinelRankDictionary)Returns whether or not the dictionary is empty.
end (Chained Seed)Returns an iterator to the end of the seed diagonals.
endPosition (Gaps)Return the clipping end position as a source position.
findTagKey (BamTagsDict)Find a tag by its key for a BamTagsDict object.
flush (BamStream)Flush output when writing.
flush (SequenceStream)Write all data from SequenceStream to disk.
front (Chained Seed)Returns a reference to the first seed diagonal.
getAlphabetSize (PrefixSumTable)Returns the number of different characters in the prefix sum table.
getAutoSeqStreamFormatNameReturns
getCharacter (PrefixSumTable)Returns the character of a given position within the prefix sum table.
getCharacterThis function returns the pivot character of the node the iterator currently points to.
getCharacterPosition (PrefixSumTable)Returns the position of a given character within the prefix sum table.
getFileFormatExtensions (ArgumentParser)Returns file format extensions given a format tag.
getLeftChildPosReturns the position in RightArrayBinaryTree of the left child vertex.
getPositionReturns the position of the iterator in the host.
getPrefixSum (PrefixSumTable)Returns the prefix sum of a given position.
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.
getSentinelSubstitute (SentinelRankDictionary)Returns the character used to substitute the sentinel sign.
getSubTreeSizeReturns the number of vertices in the subtree starting at the position an iterator points to.
getValue (RankDictionary)Returns the character of a specified position.
getValue (SentinelRankDictionary)Returns the character of a specified position.
getvalue (PrefixSumTable)Returns the prefix sum of a given position.
goLeftChildSets the iterator to the left child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
goRightChildSets the iterator to the right child of the current node if it exists and returns true, otherwise the iterator does not change position and the function returns false.
hostToVirtualPosition (Journaled String)Translates position in host to virtual (view) position.
indexCreate (FMIndex)Creates a specific Fibre.
indexSupplied (FMIndex)Returns whether a specific Fibre is present.
infix (Finder)Returns the segment of the last found match in haystack.
isGood (BamStream)Check whether the BamStream object has is in the failure state.
isGood (SequenceStream)Check whether a SequenceStream object is ready for reading.
isSetBitReturns whether the bit with the given index is set to 1.
length (Chained Seed)Returns the number of diagonals in the chained seed.
length (PrefixSumTable)Returns the number of different characters in the prefix-sum table.
open (BamStream)Open a BamStream object for reading/writing.
open (Index)This functions loads a dictionary from disk.
open (LfTable)This functions loads a LF table from disk.
open (PrefixSumTable)This functions loads a prefix-sum table from disk.
open (RankDictionary)This functions loads a dictionary from disk.
open (RightArrayBinaryTree)This functions loads a RightArrayBinaryTree from disk.
open (SentinelRankDictionary)This functions loads a dictionary from disk.
open (SequenceStream)Open or re-open a file using a SequenceStream.
prefixSum (PrefixSumTable)Returns a reference to the entry of the prefix sum table of a given position.
readAll (SequenceStream)Read all sequence records from a SequenceStream object.
readBatch (SequenceStream)Read a given number of sequence records from SequenceStream.
readRecord (BamStream)Read one BamAlignmentRecord from a BamStream.
readRecord (SequenceStream)Read the next sequence record from SequenceStream.
reset (BamStream)Reset BamStream object to status after construction.
resize (PrefixSumTable)Resize the prefix sum table to be able to store more or less characters.
save (CompressedSA)This functions saves a compressed suffix array to disk.
save (Index)This functions saves an index to disk.
save (LfTable)This functions saves a LF table to disk.
save (PrefixSumTable)This functions saves a prefix-sum table to disk.
save (RankDictionary)This functions saves a dictionary to disk.
save (RankSupportBitString)This functions saves a RankSupportBitString to disk.
save (RightArrayBinaryTree)This functions saves a RightArrayBinaryTree to disk.
save (SentinelRankDictionary)This functions saves a dictionary to disk.
save (SparseString)This functions saves a sparse string to disk.
seedSize (Seed)Returns the number of matches and mismatches of the seed. This is the longest true diagonal fitting into its dimensions.
sentinelPosition (SentinelRankDictionary)Returns whether a specified position is a sentinel position.
setBeginPosition (Gaps)Set the begin position of the clipped gapped sequence, given a source position.
setCharactersetCharacter(iterator, character) sets the character of the node the iterator points to to character.
setClippedBeginPosition (Gaps)Sets the begin position of the clipping.
setClippedEndPosition (Gaps)Sets the end position of the clipping.
setDefaultValue (ArgumentParser)Set default value of an option of an ArgumentParser.
setEndPosition (Gaps)Set the end position of the clipped gapped sequence, given a source position.
setHelpText (ArgumentParser)Set help text of argument parser.
setLfTableSet the LfTable of the compressed suffix array.
setMaxValue (ArgumentParser)Set largest allowed value for an option or argument of an ArgumentParser.
setMinValue (ArgumentParser)Set smallest allowed value for an option or argument of an ArgumentParser.
setPrefixSumReturns a reference to the entry of the prefix-sum table of a given position.
setSentinelPosition (SentinelRankDictionary)Sets the sentinel position..
setSentinelSubstitute (SentinelRankDictionary)Sets the character used to substitute the sentinel sign.
setValidValues (ArgumentParser)Set valid values for an argument or option of an ArgumentParser.
splitAlignmentCompute split alignments.
toSuffixPosition (FMIndex)This function computes the position of a specified position in the suffix array (additionally containing entries for the sentinels. The returned position correspond to the suffix array of the original text without sentinels.
transpose (Matrix)Transposes matrix
value (CompressedSA)Returns the value stored at a specified position in the compressed suffix-array.
virtualToHostPosition (Journaled String)Translates virtual (view) position to position in host.
write2 (FASTA/FASTQ I/O)Write FASTA or FASTQ records.
writeAll (SequenceStream)Write sequence records from to a SequenceStream object.
writeRecord (BamStream)Write one BamAlignmentRecord to a BamStream.
writeRecord (FASTA/FASTQ I/O)Write one FASTA or FASTQ record.
writeRecord (SequenceStream)Write 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 occurrences 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 occurrences 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
assignSource (Gaps)Assign the source of a Gaps object, copying data.
bandedChainAlignmentComputes the best global pairwise alignment between two sequences given a non-empty seed chain.
clearClipping (Gaps)Clear clipping from Gaps object.
clearGaps (Gaps)Clear gaps and clipping from Gaps object.
colA column in an alignment.
colsThe container of columns in an alignment.
countGaps (Gaps)Reports number of continues gaps right of current iterator position.
gapValueReturn the "gap" value from an alphabet.
getProjectedPositionProjects a position of one sequence taking part in a pairwise match onto the other sequence.
getScore (LocalAlignmentEnumerator)Compute 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.
host (ConsensusScoreSequenceEntry)Returns reference to sequence from entry.
insertGapInsert one gap into a gapped sequence.
insertGapsInsert multiple gaps into a gapped sequence.
integrateAlignIntegrates an alignment into another by copying the gaps.
isGap (Gaps)Query whether a given clipped view position is a gap.
isReversedReturns true if the segment match is in reverse orientation.
length (Gaps)Return 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.
position (ConsensusScoreSequenceEntry)Returns position stored in entry.
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.
sequenceEntryForScore (Score)Helper function for element access, depending on score type.
setScoreGapSet gap opening and extension score.
setScoreGapExtendSet gap extension score.
setScoreGapOpenSet gap opening score.
setScoreMatchSet match score.
setScoreMismatchSet mismatch score.
setSource (Gaps)Set 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.
unclippedLength (Gaps)Return length of the gapped sequence without clipping.
value (ConsensusScoreSequenceEntry)Returns value of character referenced by entry.
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.
eraseTag (BamTagsDict)Erase tag from BamTagsDict.
extractTagValue (BamTagsDict)Extract and cast "atomic" value from tags string with index idx.
findTagKey (BamHeaderRecord)Find 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.
getTagKey (BamTagsDict)Return key of a tag by index.
getTagType (BamTagsDict)Get key of a tag by index.
getTagValue (BamHeaderRecord)Return tag value from a BamHeaderRecord or BamTagsDict.
getTagValue (BamTagsDict)Return the value of a tag by its index in the BamTagsDict.
getUnalignedCount (BamIndex)Query 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.
jumpToOrphans (BamIndex)Seek to orphans block in BAM BGZF stream using an index.
jumpToRegion (BamIndex)Seek in BAM BGZF stream using an index.
nameStore (BamIOContext)Return reference to name store from BamIOContext.
nameStoreCache (BamIOContext)Return reference to name store cache from BamIOContext.
read (BamIndex)Load a BAM index from a given file name.
setTagValue (BamHeaderRecord)Set tag value of a BamHeaderRecord.
setTagValue (BamTagsDict)Set the value of a tag through a BamTagsDict.
Basic
nukeCopiesReset all pointers connected to a given one.
sourceReturn underlying object.
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.
setBitToSet the bit with the given index to the given value.
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.
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.
pop (PriorityType)Deletes item with the highest priority and adjusts the priority queue.
push (PriorityType)Inserts 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.
top (PriorityType)Reference 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.
buildIndex (BamTagsDict)Build 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.
clearContigsRemoves all contigs from a fragment store.
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.
getIdByNameGet the id/index of a string in a name store with a cache.
getMateNoReturns the mate number of read for a given readId.
getName (AnnotationTree Iterator)Returns 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.
goDown (AnnotationTree Iterator)Move the iterator down to the left-most child in the annotation tree.
goNextRight (AnnotationTree Iterator)Go to the next node in preorder DFS skipping the current node's subtree.
goNextUp (AnnotationTree Iterator)Go to the next node in preorder DFS skipping the subtrees of the current node and of all its siblings.
goRight (AnnotationTree Iterator)Move the iterator right to the next sibling in the annotation tree.
goRoot (AnnotationTree Iterator)Go to the root node in the annotation tree.
goToMoves the iterator to an arbitrary node given its annotationId.
goUp (AnnotationTree Iterator)Move the iterator up in the annotation tree.
hasIndex (BamTagsDict)Return 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.
nodeDown (AnnotationTree Iterator)Returns a new iterator to the first child node of the current annotation in the annotation tree.
nodeRight (AnnotationTree Iterator)Returns a new iterator to the right sibling of the current annotation in the annotation tree.
nodeUp (AnnotationTree Iterator)Returns 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.
setName (AnnotationTree Iterator)Sets 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.
writeContigsWrite contigs from fragment store into file.
GFF I/O
nameStore (GffIOContext)Return reference to name store from GffIOContext.
nameStoreCache (GffIOContext)Return reference to name store cache from GffIOContext.
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.
assignSource (Graph)Assigns 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.
isLeaf (Graph)Tests whether a given vertex is a leaf or not.
isRoot (Graph)Tests 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.
label (Automaton)Returns 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.
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
appendValue (RankSupportBitString)Appends a value to a container.
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.
countOccurrences (RankDictionary)Returns the rank (number of occurrences) of a specified character up to a specified position.
countOccurrencesReturns the number of occurrences of representative substring or a q-gram in the index text.
countOccurrencesMultipleReturns the number of occurrences 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.
getFibre (CompressedSA)Returns a specific fibre of a container.
getFibre (FMIndex)Returns a specific fibre of a fm index.
getFibre (LfTable)Returns a specific fibre of a container.
getFibre (PrefixSumTable)Returns a specific fibre of a prefix-sum table.
getFibre (RankDictionary)Returns a specific fibre of a dictionary.
getFibre (RankSupportBitString)Returns a specific fibre of a container.
getFibre (RightArrayBinaryTree)Returns a specific fibre of a container.
getFibre (SentinelRankDictionary)Returns a specific fibre of a dictionary.
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 occurrence of the representative substring or a q-gram in the index text.
getOccurrencesReturns all occurrences of the representative substring or a q-gram in the index text.
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 occurrences of an iterator's representative mutually differ in the character left of the hits.
isPartiallyLeftExtensibleTest whether the characters left of the two occurrences 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(..), ..).
lfMapping (LfTable)Returns the position of an character at a specified position of L in F. L corresponds to the last column of the sorted cyclic rotations of the original text, while F correspond to the first column.
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 occurrences 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
adviseFileSegmentGive advice about use of a memory-mapped file segment.
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.
atEnd (RecordReader)Returns true if there is no more data to be read.
attachToFileAttach to already open input / output file.
cancelCancels an asynchronous request.
cancelFileSegmentCancel all outstanding transactions of a memory-mapped file segment.
checkEofCheck that the EOF marker is present in a BGZF(/BAM) file.
clear (FaiIndex)Reset a FaiIndex object to the state after default construction.
clear (GenomicRegion)Reset a GenomicRegion object to the same state after default construction.
clear (GffRecord)Reset a GffRecord object.
close (FileMapping)Close a file and its memory mapping.
closeCloses a file.
closeAndResize (FileMapping)Close a memory mapping and resize and close the underlying 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.
flushFileSegmentWait for all outstanding transactions of a memory-mapped file segment.
getIdByName (FaiIndex)Return id (numeric index in the file) of a sequence in a FAI file.
goNext (RecordReader)Advance record reader 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.
guessStreamFormatcheck whether the data provided by reader is (one of) the specified format(s).
isDirectQuery a GZ File Stream for being "direct."
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
length (FileMapping)Return the file size of a memory mapping.
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.
mapFileSegmentMap a segment of a file into memory.
nextIs (RecordReader)Query whether the next record is of a given type.
numSeqs (FaiIndex)Return number of sequences known to an FaiIndex.
open (FileMapping)Open a file to be mapped into memory.
openOpens a file, stream, or persistent string.
openTemp (FileMapping)Open a temporary file to be mapped into memory.
openTempOpens a temporary file.
parse (GenomicRegion)Parse genomic region string store results in GenomicRegion.
position (RecordReader)Returns the current position of the reader.
read (FaiIndex)Read a FAI index.
read (FileFormat)Loads a record from file.
readLoads records from a file.
read2reads an entire document from a StreamConcept, 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.
readFastaRead first sequence from a FASTA file.
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
readRecord (GffRecord)Read one gff record.
readRecordreads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader
readRegion (FaiIndex)Load the infix of a sequence from a FaiIndex.
readSequence (FaiIndex)Load a whole sequence from an FaiIndex.
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
remapFileSegmentChange the size of a memory-mapped file segment.
resize (FileMapping)Resize the underlying file.
resizeResizes a container. If the new length exceeds the old length the new elements are filled with copies of value.
resultCode (RecordReader)Returns int current status code for reader (0 on success).
rewindSets the current file pointer to the beginning.
seekChanges the current file pointer.
sequenceLength (FaiIndex)Return length of the sequence with the given id in the FaiIndex.
sequenceName (FaiIndex)Return the name of the sequence with the given id in the FaiIndex.
setEofSets the file end to the current pointer.
setPosition (RecordReader)Returns the current position of the reader.
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 StreamConcept.
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.
unmapFileSegmentUnmap a memory-mapped file segment.
value (RecordReader)Returns the current value of the reader.
waitForWaits for an asynchronous request to complete.
write (FaiIndex)Write out an FaiIndex object.
write (FileFormat)Writes to stream.
write (Score Matrix)Write a score matrix to a stream.
writeSaves records to a file.
write2writes an entire document to a StreamConcept
writeAtSaves records to a specific position in a file.
writeRecord (GffRecord)Writes one gff record to a stream.
writeRecordwrite one record (e.g. a single DNA-sequence and its meta data) to a StreamConcept
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
readRecord (LocalMatchStore)Read Lastz "general" format record.
readRecordreads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader
readRecordreads one record (e.g. a single DNA-sequence and its meta data) from a StreamConcept, by the means of RecordReader
Map
add (Map)Insert another value into a multi map.
cargo (Map)Returns a cargo given a key.
erase (Map)Removes a value from a map.
eraseAll (Map)Removes a value from a map.
find (Map)Find a value in a map.
hasKey (Map)Determines whether a map contains a value given key.
insert (Map)Insert new value into map.
mapValueSubscript operator [ ] of maps.
value (Map)Returns a value given a key.
Memory
allocateAllocates memory from heap.
clear (Allocator)Deallocates all memory blocks.
deallocateDeallocates memory.
memsetAn implementation of memset with fixed number of bytes using Metaprogramming.
Miscellaneous
addArgument (ArgumentParser)Adds a ArgParseArgument object to the ArgumentParser.
addDefaultValue (ArgParseOption)Adds/appends a new value to the list of default values.
addDescription (ArgumentParser)Appends a description paragraph to the ArgumentParser documentation.
addIntervalAdds an interval to an interval tree.
addLine (ArgumentParser)Adds a line of text to the help output of the ArgumentParser in the block of ArgParseOptions.
addListItem (ArgumentParser)Appends a list item to the ArgumentParser.
addListItem (ToolDoc)Add list item to ToolDoc object.
addOption (ArgumentParser)Adds a ArgParseOption object to the ArgumentParser.
addSection (ArgumentParser)Begins a new section of ArgParseOption the help output of the ArgumentParser.
addSection (ToolDoc)Add section to ToolDoc object.
addSubSection (ToolDoc)Add subsection to ToolDoc object.
addText (ArgumentParser)Appends a text paragraph to the ArgumentParser.
addText (ToolDoc)Add text line/paragraph to ToolDoc.
addTextSection (ArgumentParser)Adds a text section to the ArgumentParser.
addTextSubSection (ArgumentParser)Adds a text subsection to the ArgumentParser.
addUsageLine (ArgumentParser)Adds a line of text to the usage output of the ArgumentParser.
adjustTopAdjusts the priority of the first item.
append (ToolDoc)Append two ToolDoc objects.
average (Accumulator)Return average from an accumulator.
clearEntries (ToolDoc)Clear entries from ToolDoc object.
count (Accumulator)Return 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.
getAppName (ArgumentParser)Get tool name of ArgumentParser object.
getArgument (ArgumentParser)Returns 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).
getArgumentValue (ArgParseArgument)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.
getArgumentValue (ArgumentParser)Retrieves the value of an argument given by its position.
getArgumentValueCount (ArgumentParser)Returns the number of values stored in the specified option.
getArgumentValues (ArgumentParser)Returns all values of an option given on the command line.
getArgumentValuesReturns all values of the ArgParseArgument object as const std::vector.
getCategory (ArgumentParser)Get tool category of ArgumentParser object.
getCategory (ToolDoc)Get tool category of ToolDoc object.
getDate (ToolDoc)Get date string from ToolDoc object.
getLeftBoundaryGet method for the left boundary.
getManTitle (ToolDoc)Get man title from ToolDoc object.
getName (ToolDoc)Get tool name of ToolDoc object.
getObjectIdA value that identifies the underlying sequence.
getOption (ArgumentParser)Returns a reference to the specified option.
getOptionValue (ArgumentParser)Retrieves the value of an option given either the short or long name.
getOptionValueCount (ArgumentParser)Returns the number of values stored in the specified option.
getOptionValues (ArgumentParser)Returns all values of an option given on the command line.
getRightBoundaryGet method for the right boundary.
getShortDescription (ArgumentParser)Gets short description of ArgumentParser.
getShortDescription (ToolDoc)Get short description of ToolDoc object.
getTerminalSizeRetrieve size of terminal.
getVersion (ArgumentParser)Get version string from ArgumentParser object.
getVersion (ToolDoc)Get version string from ToolDoc object.
hasDefault (ArgParseArgument)Returns true if a default value was given for that argument.
hasDefault (ArgumentParser)Returns whether an option has a default value or not.
hasOption (ArgumentParser)Returns whether a certain option is registered in the parser.
hasValue (ArgParseArgument)Returns true if a value for the given position is available.
hideOption (ArgParseOption)Hides the ArgParseOption from the help screen.
hideOption (ArgumentParser)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.
isBooleanOption (ArgParseOption)Returns whether option is a switch.
isDoubleArgumentReturns whether the argument is a double.
isHidden (ArgParseOption)Returns whether option is hidden on the help screen. Default is false.
isInputFileArgumentReturns whether the argument is an input file.
isInt64ArgumentReturns whether the argument is a 64 bit integer.
isIntegerArgumentReturns whether the argument is an integer.
isListArgumentReturns whether the argument can be given multiple times.
isOutputFileArgumentReturns whether the argument is an output file.
isRequired (ArgParseOption)Returns whether the option is mandatory.
isSet (ArgParseArgument)Returns true if a value was assigned to the argument.
isSet (ArgumentParser)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.
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.
parse (ArgumentParser)Parses the command line.
print (ToolDoc)Print ToolDoc object in a given format.
printHelp (ArgumentParser)Prints the complete help message for the parser to a stream.
printShortHelp (ArgumentParser)Prints a short help message for the parser to a stream
printVersion (ArgumentParser)Prints the version information of the parser to a stream.
push (Accumulator)Adds a value to an accumulator.
removeIntervalRemoves an interval from the interval tree.
rightBoundaryAccess to the right boundary.
setAppName (ArgumentParser)Sets application name of ArgumentParser.
setCategory (ArgumentParser)Set tool category for ArgumentParser object.
setCategory (ToolDoc)Set tool category for ToolDoc object.
setDate (ArgumentParser)Sets date string of ArgumentParser.
setDate (ToolDoc)Set date string for ToolDoc object.
setDefaultValue (ArgParseOption)Sets the default value for the given option.
setHelpTextSets the set of allowed values of a ArgParseArgument object.
setManTitle (ToolDoc)Set version string for ToolDoc object.
setMaxValueSets the maximum value of a ArgParseArgument object.
setMinValueSets the minimum value of a ArgParseArgument object.
setName (ToolDoc)Set tool name for ToolDoc object.
setRequired (ArgParseOption)Sets whether or not the option is mandatory.
setRequired (ArgumentParser)Sets whether or not the option defined by the parameter name (which can be either the short or the long name) is mandatory.
setShortDescription (ArgumentParser)Sets short description of the ArgumentParser object.
setShortDescription (ToolDoc)Set short description for ToolDoc object.
setValidValuesSets the set of allowed values of a ArgParseArgument object.
setVersion (ArgumentParser)Sets version string of ArgumentParser.
setVersion (ToolDoc)Set version string for ToolDoc object.
shareResourcesDetermines whether two sequences share the same resource.
sum (Accumulator)Return sum from an accumulator.
sysTimeReturns the system time in seconds.
write (ArgParseOption)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.
front (Pipe)Gets 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.
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 valH and valV.
scoreReturns the score for aligning the characters valH and valV.
scoreGapExtendHorizontalReturns the score for extending a horizontal gap after entry1.
scoreGapExtendVerticalReturns the score for extending a vertical gap after entry2.
scoreGapHorizontalReturns the score for a horizontal gap after entry1.
scoreGapOpenHorizontalReturns the score for opening a horizontal gap after entry1.
scoreGapOpenVerticalReturns the score for opening a vertical gap after entry2.
scoreGapVerticalReturns the score for a vertical gap after entry2.
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
addSeed (SeedSet)Adds a seed to an existing set.
addSeeds (SeedSet)Adds several seeds to an existing set. If a merging or chaining algorithm is used seeds are added if the merging or chaining fails.
appendDiagonal Adds diagonal to the Chained Seed.
beginDiagonal (Seed)Returns the diagonal of the start point.
beginPositionH (Seed) Returns the begin position of the seed in the database.
beginPositionV (Seed) Returns the begin position of the seed in the query.
endDiagonal (Seed)Returns the diagonal of the end point.
endPositionH (Seed) Returns the end position of the seed in the database.
endPositionV (Seed) Returns the end position of the seed in the query.
extendSeedExtends a seed.
lowerDiagonal (Seed)Returns the leftmost diagonal of the seed (minimum diagonal value).
minScore (SeedSet)Returns the threshold to distinguish between high-scoring and low-scoring seeds.
score (Seed)Returns the score of the seed.
setBeginPositionH (Seed) Sets the begin position of the seed in the database.
setBeginPositionV (Seed) Sets the begin position of the seed in the query.
setEndPositionH (Seed) Sets the end position of the seed in the database.
setEndPositionV (Seed) Returns the end position of the seed in the query.
setLowerDiagonal (Seed) Sets a new value for the leftmost diagonal.
setMinScore (SeedSet)Sets the threshold at which seeds are considered high-scoring.
setScore (Seed)Set the score value of a seed.
setUpperDiagonal (Seed) Sets a new value for the rightmost diagonal.
truncateDiagonalsRemoves diagonals from the given first one to the end of the seed's diagonals.
upperDiagonal (Seed)Returns the rightmost diagonal of the seed (maximum diagonal value).
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.
isFlat (Journaled String)Returns 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
Testing & Debugging
printDebugLevelPrint the current SeqAn debug level and the compiler flags to the given stream.
internal
alignmentReturns an alignment of the occurrences of the representative substring in the index text.
SeqAn - Sequence Analysis Library - www.seqan.de
 

Page built @2013/07/11 09:12:15