Class Specialization
Alignment Graph
An alignment graph.

An alignment graph with 3 sequences.

Graph

Alignment Graph

Graph<Alignment<TStringSet, TCargo, TSpec> >
Include Headers
seqan/refinement.h
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)
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.
createIntervalTree | Create an interval tree. (Graph)
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 fragment or 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.
globalMsaAlignment | Computes a global multiple alignment.
inDegree | Number of incoming edges for a given vertex. (Graph)
label | Gets the label that is associated with this vertex descriptor or the sequence that is associated with a fragment.
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.
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.
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.
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 or with a sequence of a fragment.
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)
transpose | Transposes a graph, either in-place or from source to dest. (Graph)
tripletLibraryExtension | Performs a full or group-based consistency extension.
write | 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
SeqAn - Sequence Analysis Library - www.seqan.de

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