Class Specialization
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> >
Include Headers
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.
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.
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
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)
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)
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)
assignBeginStateAssigns a begin state.
assignEmissionProbabilityAssigns a new emission probability.
assignEndStateAssigns an end state.
assignSilentStatusAssigns a silent status to a state.
assignTransitionProbabilityAssigns a new transition probability.
backwardAlgorithmImplements the backward algorithm.
beginStateReturns a reference to the begin state.
clearResets an object. (Graph)
clearEdgesRemoves all edges in a graph. (Graph)
clearVerticesRemoves all vertices in a graph. (Graph)
createIntervalTreeCreate an interval tree. (Graph)
degreeNumber of incident edges for a given vertex. (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)
forwardAlgorithmImplements the forward algorithm.
generateSequenceGenerates random state and alphabet sequences of a given HMM.
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)
isSilentIndicates whether a state is silent or not.
numEdgesNumber of edges in a graph. (Graph)
numVerticesNumber of vertices in a graph. (Graph)
outDegreeNumber of outgoing edges for a given vertex. (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)
silentStatusReference to the silent status of a state.
sourceVertexReturns the source vertex of an edge. (Graph)
targetVertexReturns the target vertex of an edge. (Graph)
transitionProbabilityReturns a reference to the transition probability.
transposeTransposes a graph, either in-place or from source to dest. (Graph)
transposeTransposes a graph, either in-place or from source to dest. (Graph)
viterbiAlgorithmImplements the viterbi algorithm.
writeSaves records to a file. (Graph)
SeqAn - Sequence Analysis Library -

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