| Class Graph Generic graph.
Graph
Alignment Graph | Automaton | Directed graph | Hmm | Oracle | Tree
Word Graph
Trie | Undirected graph
Graph<TSpec> Parameters
TSpec | The specializing type determines the kind of graph, e.g., directed, undirected, tree, or automaton. Default: Directed<> Remarks: The default Graph<> corresponds to a directed graph.
Specializations
Alignment Graph | An alignment graph.
Automaton | An Automaton has directed edges, labeled with input symbols, and a distinct start state, called root. The input symbols require the use of a third parameter: The alphabet of the input symbols.
Directed graph | A directed graph that stores the edges in an adjacency list.
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.
Oracle | A factor oracle.
Tree | A Tree has a distinct root and directed edges. The source vertex of each edge is the parent vertex, the target vertex of each edge is the child. Trees provide fast access to child vertices and the parent.
Trie | A keyword trie.
Undirected graph | An undirected graph that stores the edges in an adjacency list.
Metafunctions
Alphabet | Access to the Alphabet type.
Cargo | Type of additional data stored in an object.
EdgeDescriptor | Type of an object that represents an edge descriptor.
EdgeIdHandler | Type of an object that represents an Id Manager.
EdgeType | Edge type of a graph object.
Host | Type of the object a given object depends on.
Iterator | Type of iterator objects that are used to traverse the container.
Spec | The spec of a class.
VertexDescriptor | Type of an object that represents a vertex descriptor.
Functions
addEdge | Adds a new edge to the graph, either with or without cargo.
addEdges | Shortcut to add multiple edges at once. Creates vertices implicitly.
addVertex | Adds a new vertex to the graph.
clear | Resets an object.
clearEdges | Removes all edges in a graph.
clearVertices | Removes all vertices in a graph.
degree | Number of incident edges for a given vertex.
empty | Test a container for being empty.
findEdge | Finds an edge.
getAdjacencyMatrix | Returns an adjacency matrix representation of the graph.
inDegree | Number of incoming edges for a given vertex.
numEdges | Number of edges in a graph.
numVertices | Number of vertices in a graph.
outDegree | Number of outgoing edges for a given vertex.
removeEdge | Removes an edge from the graph. For automatons a label is required.
removeInEdges | Removes the incoming edges of a given vertex.
removeOutEdges | Removes the outgoing edges of a given vertex.
removeVertex | Removes a vertex.
resizeEdgeMap | Initializes an edge map
resizeVertexMap | Initializes a vertex map.
sourceVertex | Returns the source vertex of an edge.
targetVertex | Returns the target vertex of an edge.
transpose | Transposes a graph, either in-place or from source to dest.
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