Class Specialization
Hmm
An Hmm is a directed graph with edges labeled with transition probabilities and emission profiles for each vertex. Vertices correspond to states in an HMM.
Graph<Hmm<TAlphabet, TCargo, TSpec> >
Parameters
TAlphabet
The alphabet type that is used for the emission profile in each vertex.
Metafunctions: Alphabet
Default: Dna
Remarks: Use Alphabet to get the alphabet type.
TCargo
The cargo type that can be attached to the edges (the tranisition probabilities).
Metafunctions: Cargo
Default: double
Remarks: Use Cargo to get the cargo type.
TSpec
The specializing type for the graph.
Metafunctions: Spec
Default: Default, see Default.
Remarks: Use WithoutEdgeId here to omit edge ids. Note: If edges do not store ids external property maps do not work.
Specialization of
Metafunctions
AlphabetAccess to the Alphabet type. (Graph)
CargoType of additional data stored in an object. (Graph)
EdgeDescriptorType of an object that represents an edge descriptor. (Graph)
EdgeIdHandlerType of an object that represents an Id Manager. (Graph)
EdgeTypeEdge type of a graph object. (Graph)
HostType of the object a given object depends on. (Graph)
IteratorType of iterator objects that are used to traverse the container. (Graph)
SpecThe spec of a class. (Graph)
VertexDescriptorType of an object that represents a vertex descriptor. (Graph)
Functions
addEdgeAdds a new edge to the graph, either with or without cargo. (Graph)
addEdgesShortcut to add multiple edges at once. Creates vertices implicitly. (Graph)
addVertexAdds a new vertex to the graph. (Graph)
all_pairs_shortest_pathFinds shortest paths between all pairs of vertices in a graph. (Graph)
assignBeginStateAssigns a begin state.
assignEmissionProbabilityAssigns a new emission probability.
assignEndStateAssigns an end state.
assignTransitionProbabilityAssigns a new transition probability.
backwardAlgorithmImplements the backward algorithm.
beginStateReturns a reference to the begin state.
bellman_ford_algorithmComputes shortest paths from a single source in a graph. (Graph)
breadth_first_searchImplements a breadth-first search on a graph. (Graph)
clearResets an object. (Graph)
clearEdgesRemoves all edges in a graph. (Graph)
clearVerticesRemoves all vertices in a graph. (Graph)
degreeNumber of incident edges for a given vertex. (Graph)
depth_first_searchImplements a depth-first search on a graph. (Graph)
dijkstraComputes shortest paths from a single source in a graph. (Graph)
emissionProbabilityReturns a reference to the emission probability.
emptyTest a container for being empty. (Graph)
endStateReturns a reference to the end state.
findEdgeFinds an edge. (Graph)
floyd_warshallFinds shortest paths between all pairs of vertices in a graph. (Graph)
forwardAlgorithmImplements the forward algorithm.
getAdjacencyMatrixReturns an adjacency matrix representation of the graph. (Graph)
getBeginStateReturns the begin state.
getEmissionProbabilityReturns the emission probability.
getEndStateReturns the end state.
getTransitionProbabilityReturns the transition probability.
inDegreeNumber of incoming edges for a given vertex. (Graph)
kruskals_algorithmComputes a minimum spanning tree on a graph. (Graph)
numEdgesNumber of edges in a graph. (Graph)
numVerticesNumber of vertices in a graph. (Graph)
outDegreeNumber of outgoing edges for a given vertex. (Graph)
prims_algorithmComputes a minimum spanning tree on a graph. (Graph)
removeEdgeRemoves an edge from the graph. For automatons a label is required. (Graph)
removeInEdgesRemoves the incoming edges of a given vertex. (Graph)
removeOutEdgesRemoves the outgoing edges of a given vertex. (Graph)
removeVertexRemoves a vertex. (Graph)
resizeEdgeMapInitializes an edge map (Graph)
resizeVertexMapInitializes a vertex map. (Graph)
sourceVertexReturns the source vertex of an edge. (Graph)
targetVertexReturns the target vertex of an edge. (Graph)
transitionProbabilityReturns a reference to the transition probability.
transitive_closureDetermines whether there is a path between any two given vertices or not. (Graph)
transposeTransposes a graph, either in-place or from source to dest. (Graph)
viterbiAlgorithmImplements the viterbi algorithm.
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