Class Specialization
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.

A tree, where 0 is the root vertex.

Graph

Tree

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

TCargo | The cargo type that can be attached to the edges. Metafunctions: Cargo Default: void Remarks: Use Cargo to get the cargo type of the tree.
TSpec | The specializing type for the graph. Metafunctions: Spec Default: Default, see Default.

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

addChild | Adds a new child vertex to a parent vertex. Optionally a cargo can be attached to the parent-child edge.
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)
assignRoot | Assigns a new root vertex to the graph.
childVertex | Returns the child vertex of an edge.
clear | Resets an object. (Graph)
clearEdges | Removes all edges in a graph. (Graph)
clearVertices | Removes all vertices in a graph. (Graph)
collectLeaves | Returns all leaves underneath a given vertex.
createIntervalTree | Create an interval tree. (Graph)
createRoot | Creates the root in a tree or an automaton.
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)
getRoot | Get method for the root of a tree or an automaton.
inDegree | Number of incoming edges for a given vertex. (Graph)
isLeaf | Tests whether a given vertex is a leaf or not.
isRoot | Tests whether a given vertex is the root or not.
numChildren | Number of children of a given tree vertex.
numEdges | Number of edges in a graph. (Graph)
numTreeEdges | Number of tree edges.
numVertices | Number of vertices in a graph. (Graph)
outDegree | Number of outgoing edges for a given vertex. (Graph)
parentVertex | Returns the parent vertex of an edge.
progressiveAlignment | Performs a progressive alignment.
removeAllChildren | Removes all children from the tree given a parent.
removeChild | Removes a child from the tree given a parent.
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)
root | Gets a reference to the root of the tree.
slowNjTree | Computes a guide tree from a distance matrix.
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)
upgmaTree | Computes a guide tree from a distance matrix.
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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