Class Specialization
Alignment Graph
An alignment graph.
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| An alignment graph with 3 sequences. |
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Alignment Graph | |||||||
Include Headers
seqan/graph_align.h
Parameters
The type of the string set containing the sequence information, must be a Dependent StringSet Default: Dependent StringSet | |
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) | |
| Return type of stringSet function. | |
| 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. | |
| Initializes a vertex map with values of an array. (Graph) | |
| Assigns a new string set to an alignment graph. | |
| Initializes a vertex map with values of an array. (Graph) | |
| Computes the best global pairwise alignment between two sequences given a non-empty seed chain. | |
| Builds an Alignment Graph from a set of input alignments. | |
| Resets an object. (Graph) | |
| Removes all edges in a graph. (Graph) | |
| Removes all vertices in a graph. (Graph) | |
| Compute consensus alignment. | |
| Converts an alignment graph into an alignment matrix. | |
| Create an interval tree. (Graph) | |
| Number of incident edges for a given vertex. (Graph) | |
| Test a container for being empty. (Graph) | |
| Finds an edge. (Graph) | |
| Finds a vertex given a sequence id and a position. | |
| Gets the begin position for this fragment or 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) | |
| 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. | |
| Projects a position of one sequence taking part in a pairwise match onto the other sequence. | |
| Gets the string set of an alignment graph. | |
| Computes the best global pairwise alignment. | |
| Computes a global multiple alignment. | |
| Computes the heaviest common subsequence between two strings using the match information given in an alignment graph. | |
| Number of incoming edges for a given vertex. (Graph) | |
| Gets the label that is associated with this vertex descriptor or the sequence that is associated with a fragment. | |
| 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. | |
| Number of edges in a graph. (Graph) | |
| Number of vertices in a graph. (Graph) | |
| Number of outgoing edges for a given vertex. (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 or with a sequence of a fragment. | |
| 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) | |
| Transposes a graph, either in-place or from source to dest. (Graph) | |
| Performs a full or group-based consistency extension. | |
| 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, Floyd-Warshall Algorithm, Heaviest Increasing Subsequence, Prims Algorithm, Global Alignments, Maximum Flow, Shortest Path in DAGs, HMM, Kruskals Algorithm, All Pairs Shortest Path, Depth-First Search, Dijkstras Algorithm, Longest Common Subsequence
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