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sampleAllNodes - if (totallyRandom) is false, reads presampled conformations and add in 1 nodes at -50,-50.
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createRandomNodes-
sampleGivenCoord-
sampleGivenCoords - creates given nodes
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kNNLinkNode - connects node # nodeIndex to k nearest neighbors, unless it is already connected to at least k nearest neighbors
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linkNodes - links all nodes, each to kNN other nodes
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makeLinkBetweenNodes - connects 2 nodes (if they are not already connected), and updates the tree structure arising from the merge.
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addNode2Forest - node # count is not connected to the rest of the roadmap, creating a tree for itself alone
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findTransitionProbability - assigns tr.
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computeTransitionProbabilities - returns maxNumNeighbors of any node
Alphabetic index
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