| 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
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 Graph Metafunctions
Alphabet | Access to the Alphabet type. (Graph)
Cargo | Type of additional data stored in an object. (Graph)
EdgeDescriptor | Type of an object that represents an edge descriptor. (Graph)
EdgeIdHandler | Type of an object that represents an Id Manager. (Graph)
EdgeType | Edge type of a graph object. (Graph)
Host | Type of the object a given object depends on. (Graph)
Iterator | Type of iterator objects that are used to traverse the container. (Graph)
Spec | The spec of a class. (Graph)
VertexDescriptor | Type of an object that represents a vertex descriptor. (Graph)
Functions
addEdge | Adds a new edge to the graph, either with or without cargo. (Graph)
addEdges | Shortcut to add multiple edges at once. Creates vertices implicitly. (Graph)
addVertex | Adds a new vertex to the graph. (Graph)
assignBeginState | Assigns a begin state.
assignEmissionProbability | Assigns a new emission probability.
assignEndState | Assigns an end state.
assignSilentStatus | Assigns a silent status to a state.
assignTransitionProbability | Assigns a new transition probability.
backwardAlgorithm | Implements the backward algorithm.
beginState | Returns a reference to the begin state.
clear | Resets an object. (Graph)
clearEdges | Removes all edges in a graph. (Graph)
clearVertices | Removes all vertices in a graph. (Graph)
degree | Number of incident edges for a given vertex. (Graph)
emissionProbability | Returns a reference to the emission probability.
empty | Test a container for being empty. (Graph)
endState | Returns a reference to the end state.
findEdge | Finds an edge. (Graph)
forwardAlgorithm | Implements the forward algorithm.
generateSequence | Generates random state and alphabet sequences of a given HMM.
getAdjacencyMatrix | Returns an adjacency matrix representation of the graph. (Graph)
getBeginState | Returns the begin state.
getEmissionProbability | Returns the emission probability.
getEndState | Returns the end state.
getTransitionProbability | Returns the transition probability.
inDegree | Number of incoming edges for a given vertex. (Graph)
isSilent | Indicates whether a state is silent or not.
numEdges | Number of edges in a graph. (Graph)
numVertices | Number of vertices in a graph. (Graph)
outDegree | Number of outgoing edges for a given vertex. (Graph)
removeEdge | Removes an edge from the graph. For automatons a label is required. (Graph)
removeInEdges | Removes the incoming edges of a given vertex. (Graph)
removeOutEdges | Removes the outgoing edges of a given vertex. (Graph)
removeVertex | Removes a vertex. (Graph)
resizeEdgeMap | Initializes an edge map (Graph)
resizeVertexMap | Initializes a vertex map. (Graph)
silentStatus | Reference to the silent status of a state.
sourceVertex | Returns the source vertex of an edge. (Graph)
targetVertex | Returns the target vertex of an edge. (Graph)
transitionProbability | Returns a reference to the transition probability.
transpose | Transposes a graph, either in-place or from source to dest. (Graph)
viterbiAlgorithm | Implements the viterbi algorithm.
Example Programs All Pairs Shortest Path, Bellman-Ford Algorithm, Breadth-First Search, Depth-First Search, Dijkstras Algorithm, Floyd-Warshall Algorithm, Heaviest Increasing Subsequence, HMM, HMM Silent States, Kruskals Algorithm, Longest Common Subsequence, Longest Increasing Subsequence, Maximum Flow, Prims Algorithm, Shortest Path in DAGs, Strongly Connected Components, Topological Sort, Transitive Closure SeqAn - Sequence Analysis Library - www.seqan.de