Class Specialization

Alignment Graph

An alignment graph.

An alignment graph with 3 sequences. |

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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