Hmm

| 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> > Include Headers seqan/graph_types.h 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)
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)
createIntervalTree | Create an interval tree. (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)
transpose | Transposes a graph, either in-place or from source to dest. (Graph)
viterbiAlgorithm | Implements the viterbi algorithm.
write | Saves records to a file. (Graph)
Example Programs Bellman-Ford Algorithm, Longest Increasing Subsequence, Topological Sort, Breadth-First Search, Strongly Connected Components, Transitive Closure, HMM Silent States, Kruskals Algorithm, Heaviest Increasing Subsequence, Floyd-Warshall Algorithm, Maximum Flow, Shortest Path in DAGs, HMM, Prims Algorithm, All Pairs Shortest Path, Depth-First Search, Dijkstras Algorithm, Longest Common Subsequence SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2012/03/14 16:34:51