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.

Hmm |

Include Headers

seqan/graph_types.h

Parameters

The alphabet type that is used for the emission profile in each vertex. Metafunctions: Alphabet Default: Remarks: Use Alphabet to get the alphabet type. | |

The cargo type that can be attached to the edges (the tranisition probabilities). Metafunctions: Cargo Default: Remarks: Use Cargo to get the cargo type. | |

The specializing type for the graph. Metafunctions: Spec Remarks: Use WithoutEdgeId here to omit edge ids.
Note: If edges do not store ids external property maps do not work. |

Specialization of

Metafunctions

Access to the Alphabet type. (Graph) | |

Type of additional data stored in an object. (Graph) | |

Type of an object that represents an edge descriptor. (Graph) | |

Type of an object that represents an Id Manager. (Graph) | |

Edge type of a graph object. (Graph) | |

Type of the object a given object depends on. (Graph) | |

Type of iterator objects that are used to traverse the container. (Graph) | |

The spec of a class. (Graph) | |

Type of an object that represents a vertex descriptor. (Graph) |

Functions

Adds a new edge to the graph, either with or without cargo. (Graph) | |

Shortcut to add multiple edges at once. Creates vertices implicitly. (Graph) | |

Adds a new vertex to the graph. (Graph) | |

Assigns a begin state. | |

Initializes a vertex map with values of an array. (Graph) | |

Assigns a new emission probability. | |

Assigns an end state. | |

Assigns a silent status to a state. | |

Assigns a new transition probability to an existing edge. | |

Initializes a vertex map with values of an array. (Graph) | |

Implements the backward algorithm. | |

Returns a reference to the begin state. | |

Resets an object. (Graph) | |

Removes all edges in a graph. (Graph) | |

Removes all vertices in a graph. (Graph) | |

Create an interval tree. (Graph) | |

Number of incident edges for a given vertex. (Graph) | |

Returns a reference to the emission probability. | |

Test a container for being empty. (Graph) | |

Returns a reference to the end state. | |

Finds an edge. (Graph) | |

Implements the forward algorithm. | |

Generates random state and alphabet sequences of a given HMM. | |

Returns an adjacency matrix representation of the graph. (Graph) | |

Returns the begin state. | |

Returns the emission probability. | |

Returns the end state. | |

Returns the transition probability. | |

Number of incoming edges for a given vertex. (Graph) | |

Indicates whether a state is silent or not. | |

Number of edges in a graph. (Graph) | |

Number of vertices in a graph. (Graph) | |

Number of outgoing edges for a given vertex. (Graph) | |

Removes an edge from the graph. For automatons a label is required. (Graph) | |

Removes the incoming edges of a given vertex. (Graph) | |

Removes the outgoing edges of a given vertex. (Graph) | |

Removes a vertex. (Graph) | |

Initializes an edge map (Graph) | |

Initializes a vertex map. (Graph) | |

Reference to the silent status of a state. | |

Returns the source vertex of an edge. (Graph) | |

Returns the target vertex of an edge. (Graph) | |

Returns a reference to the transition probability. | |

Transposes a graph, either in-place or from source to dest. (Graph) | |

Implements the viterbi algorithm. | |

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

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