| Class Specialization Alignment Graph An alignment graph.
An alignment graph with 3 sequences.
Graph
Alignment Graph
Graph<Alignment<TStringSet, TCargo, TSpec> > Parameters
TStringSet | The type of the string set containing the sequence information. Default: Class.StringSet
TCargo | The cargo type that can be attached to the edges. Metafunctions: Cargo Default: void Remarks: Use Cargo to get the cargo type of an undirected graph.
TSpec | The specializing type for the graph. Metafunctions: Spec Default: Default, see Default. Remarks: Use WithoutEdgeId here to omit edge ids. Note: If edges do not store ids external property maps do not work.
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)
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
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)
alignmentEvaluation | Given a multiple alignment, this function calculates all kinds of alignment statistics.
assignStringSet | Assigns a new string set to an alignment graph.
clear | Resets an object. (Graph)
clearEdges | Removes all edges in a graph. (Graph)
clearVertices | Removes all vertices in a graph. (Graph)
convertAlignment | Converts an alignment graph into an alignment matrix.
degree | Number of incident edges for a given vertex. (Graph)
empty | Test a container for being empty. (Graph)
findEdge | Finds an edge. (Graph)
findVertex | Finds a vertex given a sequence id and a position.
fragmentBegin | Gets the begin position for this vertex descriptor in the sequence.
fragmentLength | Gets the length of the label of a given vertex descriptor in the sequence.
getAdjacencyMatrix | Returns an adjacency matrix representation of the graph. (Graph)
getAlignment | Turns a HSP from a Blast search into an Alignment object.
getDistanceMatrix | Computes a pairwise distance matrix from an alignment graph.
getFirstCoveredPosition | Finds the first position in a sequence that is not assigned to a nil vertex.
getLastCoveredPosition | Finds the last position in a sequence that is not assigned to a nil vertex.
getStringSet | Gets the string set of an alignment graph.
globalAlignment | Computes the best global alignment of the two sequences.
inDegree | Number of incoming edges for a given vertex. (Graph)
label | Gets the label that is associated with this vertex descriptor.
localAlignment | Computes the best local alignment of two sequences.
matchRefinement | 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. 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.
numEdges | Number of edges in a graph. (Graph)
numVertices | Number of vertices in a graph. (Graph)
outDegree | Number of outgoing edges for a given vertex. (Graph)
progressiveAlignment | Performs a progressive alignment.
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)
sequenceId | Gets the sequence id that is associated with this vertex descriptor.
sourceVertex | Returns the source vertex of an edge. (Graph)
stringSet | Gets the string set of an alignment graph.
sumOfPairsScore | Given a multiple alignment, this function calculates the sum-of-pairs score.
targetVertex | Returns the target vertex of an edge. (Graph)
transpose | Transposes a graph, either in-place or from source to dest. (Graph)
tripletLibraryExtension | Performs a full or group-based consistency extension.
Example Programs All Pairs Shortest Path, Bellman-Ford Algorithm, Breadth-First Search, Depth-First Search, Dijkstras Algorithm, Floyd-Warshall Algorithm, Global Alignments, Heaviest Increasing Subsequence, HMM, HMM Silent States, Kruskals Algorithm, Longest Common Subsequence, Longest Increasing Subsequence, Maximum Flow, Prims Algorithm, Shortest Path in DAGs, Strongly Connected Components, Topological Sort, Transitive Closure SeqAn - Sequence Analysis Library - www.seqan.de