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addChild
addEdge
addEdges
addVertex
alignmentEvaluation
allPairsShortestPath
assignBeginState
assignCargo
assignEmissionProbability
assignEndState
assignNextS
assignNextT
assignProperty
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assignSilentStatus
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atBegin
atEnd
backwardAlgorithm
beginState
bellmanFordAlgorithm
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canParseString
cargo
childVertex
clear
clearEdges
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collectLeaves
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convertAlignment
createOracle
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createRoot
createSuffixTrie
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createTrieOnReverse
dagShortestPath
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endState
findEdge
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floydWarshallAlgorithm
fordFulkersonAlgorithm
forwardAlgorithm
fragmentBegin
fragmentLength
generateSequence
getAdjacencyMatrix
getBeginState
getCargo
getDistanceMatrix
getEmissionProbability
getEndState
getFirstCoveredPosition
getIdLowerBound
getIdUpperBound
getLastCoveredPosition
getNextS
getNextT
getNil
getProperty
getRoot
getSource
getStringSet
getSuccessor
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getTransitionProbability
getValue
goBegin
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hostGraph
idCount
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inDegree
isLeaf
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kruskalsAlgorithm
label
label
nextS
nextT
numChildren
numEdges
numTreeEdges
numVertices
obtainId
outDegree
parentVertex
parseString
primsAlgorithm
progressiveAlignment
property
releaseAll
releaseId
removeAllChildren
removeChild
removeEdge
removeInEdges
removeOutEdges
removeVertex
resizeEdgeMap
resizeVertexMap
root
sequenceId
silentStatus
slowNjTree
sourceVertex
stringSet
stronglyConnectedComponents
sumOfPairsScore
target
targetVertex
topologicalSort
transitionProbability
transitiveClosure
transpose
tripletLibraryExtension
upgmaTree
value
viterbiAlgorithm
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Miscellaneous
Miscellaneous:
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