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addChild
addEdge
addEdges
addVertex
alignmentEvaluation
all_pairs_shortest_path
assignBeginState
assignCargo
assignEmissionProbability
assignEndState
assignNextS
assignNextT
assignProperty
assignRoot
assignSilentStatus
assignSource
assignStringSet
assignTarget
assignTransitionProbability
atBegin
atEnd
backwardAlgorithm
beginState
bellman_ford_algorithm
breadth_first_search
canParseString
cargo
childVertex
clear
clearEdges
clearVertices
collectLeaves
connected_components
convertAlignment
createOracle
createOracleOnReverse
createRoot
createSuffixTrie
createTrie
createTrieOnReverse
dag_shortest_path
degree
depth_first_search
dijkstra
emissionProbability
empty
endState
findEdge
findVertex
floyd_warshall
ford_fulkerson
forwardAlgorithm
fragmentBegin
fragmentLength
generateSequence
getAdjacencyMatrix
getBeginState
getCargo
getDistanceMatrix
getEmissionProbability
getEndState
getFirstCoveredPosition
getIdLowerBound
getIdUpperBound
getLastCoveredPosition
getNextS
getNextT
getNil
getProperty
getRoot
getSource
getStringSet
getSuccessor
getTarget
getTransitionProbability
getValue
goBegin
goEnd
goNext
goPrevious
hostGraph
idCount
idInUse
inDegree
isLeaf
isRoot
isSilent
kruskals_algorithm
label
label
nextS
nextT
numChildren
numEdges
numTreeEdges
numVertices
obtainId
outDegree
parentVertex
parseString
prims_algorithm
progressiveAlignment
property
releaseAll
releaseId
removeAllChildren
removeChild
removeEdge
removeInEdges
removeOutEdges
removeVertex
resizeEdgeMap
resizeVertexMap
root
sequenceId
silentStatus
slowNjTree
sourceVertex
stringSet
strongly_connected_components
sumOfPairsScore
target
targetVertex
topological_sort
transitionProbability
transitive_closure
transpose
tripletLibraryExtension
upgmaTree
value
viterbiAlgorithm
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