Class Specialization
Alignment Graph
An alignment graph.
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| An alignment graph with 3 sequences. |
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Alignment Graph | |||||||
Parameters
The type of the string set containing the sequence information. Default: | |
The cargo type that can be attached to the edges. Metafunctions: Cargo Default: Remarks: Use Cargo to get the cargo type of an undirected graph. | |
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) | |
| Given a multiple alignment, this function calculates all kinds of alignment statistics. | |
| Finds shortest paths between all pairs of vertices in a graph. (Graph) | |
| Assigns a new string set to an alignment graph. | |
| Computes shortest paths from a single source in a graph. (Graph) | |
| Implements a breadth-first search on a graph. (Graph) | |
| Resets an object. (Graph) | |
| Removes all edges in a graph. (Graph) | |
| Removes all vertices in a graph. (Graph) | |
| Combines multiple alignment graphs into one single graph. | |
| Converts an alignment graph into an alignment matrix. | |
| Number of incident edges for a given vertex. (Graph) | |
| Implements a depth-first search on a graph. (Graph) | |
| Computes shortest paths from a single source in a graph. (Graph) | |
| Test a container for being empty. (Graph) | |
| Finds an edge. (Graph) | |
| Finds a vertex given a sequence id and a position. | |
| Finds shortest paths between all pairs of vertices in a graph. (Graph) | |
| Gets the begin position for this vertex descriptor in the sequence. | |
| Gets the length of the label of a given vertex descriptor in the sequence. | |
| Returns an adjacency matrix representation of the graph. (Graph) | |
| Turns a HSP from a Blast search into an Alignment object. | |
| Computes a pairwise distance matrix from an alignment graph. | |
| Finds the first position in a sequence that is not assigned to a nil vertex. | |
| Finds the last position in a sequence that is not assigned to a nil vertex. | |
| Gets the string set of an alignment graph. | |
| Computes the best global alignment of the two sequences. | |
| Number of incoming edges for a given vertex. (Graph) | |
| Computes a minimum spanning tree on a graph. (Graph) | |
| Gets the label that is associated with this vertex descriptor. | |
| Computes the best local alignment of two sequences. | |
| Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. | |
| Computes multiple local alignments of two sequences. | |
| Number of edges in a graph. (Graph) | |
| Number of vertices in a graph. (Graph) | |
| Number of outgoing edges for a given vertex. (Graph) | |
| Computes a minimum spanning tree on a graph. (Graph) | |
| Performs a progressive alignment. | |
| 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) | |
| Gets the sequence id that is associated with this vertex descriptor. | |
| Returns the source vertex of an edge. (Graph) | |
| Gets the string set of an alignment graph. | |
| Given a multiple alignment, this function calculates the sum-of-pairs score. | |
| Returns the target vertex of an edge. (Graph) | |
| Determines whether there is a path between any two given vertices or not. (Graph) | |
| Transposes a graph, either in-place or from source to dest. (Graph) | |
| Performs the consistency extension proposed in T-Coffee. |
Example Programs
All Pairs Shortest Path, Bellman-Ford Algorithm, Breadth-First Search, Depth-First Search, Dijkstras Algorithm, Floyd-Warshall Algorithm, Global Alignments, Gotohs Algorithm, Heaviest Increasing Subsequence, Hirschbergs Algorithm, Kruskals Algorithm, Longest Common Subsequence, Longest Increasing Subsequence, Maximum Flow, Needleman-Wunsch Algorithm, Prims Algorithm, Shortest Path in DAGs, Smith-Waterman Algorithm, Strongly Connected Components, T-Coffee, Topological Sort, Transitive Closure
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