Class Specialization
Oracle
A factor oracle.

Graph

Oracle

Graph<Automaton<TAlphabet, TCargo, TSpec> >
Include Headers
seqan/graph_types.h
Parameters

TAlphabet | The alphabet type that is used for the transition labels. Metafunctions: Alphabet Default: char Remarks: Use Alphabet to get the type of the labels in an automaton.
TCargo | The cargo type that can be attached to the edges. Metafunctions: Cargo Default: void Remarks: Use Cargo to get the cargo type of an undirected graph.
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.

Remarks
A factor oracle is a special automaton and thus, it is not implemented in its own class. It solely provides create functions where based upon a string an oracle is created.
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)
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)
createOracle | Creates a factor oracle.
createOracleOnReverse | Creates a factor oracle for the reversed string.
degree | Number of incident edges for a given vertex. (Graph)
empty | Test a container for being empty. (Graph)
findEdge | Finds an edge. (Graph)
getAdjacencyMatrix | Returns an adjacency matrix representation of the graph. (Graph)
inDegree | Number of incoming edges for a given vertex. (Graph)
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)
sourceVertex | Returns the source vertex of an edge. (Graph)
targetVertex | Returns the target vertex of an edge. (Graph)
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)
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

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