traverse (biograph) - Traverse biograph object by following adjacent nodes

Syntax

[disc, pred, closed] = traverse(BGObj, S) [...] = traverse(BGObj, S, ...'Depth', DepthValue, ...) [...] = traverse(BGObj, S, ...'Directed', DirectedValue, ...) [...] = traverse(BGObj, S, ...'Method', MethodValue, ...)

Arguments

`BGObj`	Biograph object created by `biograph` (object constructor).
`S`	Integer that indicates the source node in `BGObj`.
`DepthValue`	Integer that indicates a node in `BGObj` that specifies the depth of the search. Default is `Inf` (infinity).
`DirectedValue`	Property that indicates whether graph represented by an N-by-N adjacency matrix extracted from a biograph object, `BGObj` is directed or undirected. Enter `false` for an undirected graph. This results in the upper triangle of the sparse matrix being ignored. Default is `true`.
`MethodValue`	String that specifies the algorithm used to traverse the graph. Choices are: `'BFS'` — Breadth-first search. Time complexity is `O(N+E)`, where `N` and `E` are number of nodes and edges respectively. `'DFS'` — Default algorithm. Depth-first search. Time complexity is `O(N+E)`, where `N` and `E` are number of nodes and edges respectively.

Description

Tip For introductory information on graph theory functions, see Graph Theory Functions in the Bioinformatics Toolbox User's Guide.

[disc, pred, closed] = traverse(BGObj, S) traverses the directed graph represented by an N-by-N adjacency matrix extracted from a biograph object, BGObj, starting from the node indicated by integer S. In the N-by-N sparse matrix, all nonzero entries indicate the presence of an edge. disc is a vector of node indices in the order in which they are discovered. pred is a vector of predecessor node indices (listed in the order of the node indices) of the resulting spanning tree. closed is a vector of node indices in the order in which they are closed.

[...] = traverse(BGObj, S, ...'PropertyName', PropertyValue, ...) calls traverse with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotes and is case insensitive. These property name/property value pairs are as follows:

[...] = traverse(BGObj, S, ...'Depth', DepthValue, ...) specifies the depth of the search. DepthValue is an integer indicating a node in the graph represented by the N-by-N adjacency matrix extracted from a biograph object, BGObj. Default is Inf (infinity).

[...] = traverse(BGObj, S, ...'Directed', DirectedValue, ...) indicates whether the graph represented by the N-by-N adjacency matrix extracted from a biograph object, BGObj is directed or undirected. Set DirectedValue to false for an undirected graph. This results in the upper triangle of the sparse matrix being ignored. Default is true.

[...] = traverse(BGObj, S, ...'Method', MethodValue, ...) lets you specify the algorithm used to traverse the graph represented by the N-by-N adjacency matrix extracted from a biograph object, BGObj. Choices are:

'BFS' — Breadth-first search. Time complexity is O(N+E), where N and E are number of nodes and edges respectively.
'DFS' — Default algorithm. Depth-first search. Time complexity is O(N+E), where N and E are number of nodes and edges respectively.

References

[1] Sedgewick, R., (2002). Algorithms in C++, Part 5 Graph Algorithms (Addison-Wesley).

[2] Siek, J.G., Lee, L-Q, and Lumsdaine, A. (2002). The Boost Graph Library User Guide and Reference Manual, (Upper Saddle River, NJ:Pearson Education).

traverse (biograph) - Traverse biograph object by following adjacent nodes

Syntax

Arguments

Description

References

See Also

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