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
Metafunctions
AlphabetAccess to the Alphabet type. (Graph)
CargoType of additional data stored in an object. (Graph)
EdgeDescriptorType of an object that represents an edge descriptor. (Graph)
EdgeIdHandlerType of an object that represents an Id Manager. (Graph)
EdgeTypeEdge type of a graph object. (Graph)
HostType of the object a given object depends on. (Graph)
IteratorType of iterator objects that are used to traverse the container. (Graph)
SpecThe spec of a class. (Graph)
VertexDescriptorType of an object that represents a vertex descriptor. (Graph)
Functions
addEdgeAdds a new edge to the graph, either with or without cargo. (Graph)
addEdgesShortcut to add multiple edges at once. Creates vertices implicitly. (Graph)
addVertexAdds a new vertex to the graph. (Graph)
alignmentEvaluationGiven a multiple alignment, this function calculates all kinds of alignment statistics.
assignStringSetAssigns a new string set to an alignment graph.
clearResets an object. (Graph)
clearEdgesRemoves all edges in a graph. (Graph)
clearVerticesRemoves all vertices in a graph. (Graph)
convertAlignmentConverts an alignment graph into an alignment matrix.
degreeNumber of incident edges for a given vertex. (Graph)
emptyTest a container for being empty. (Graph)
findEdgeFinds an edge. (Graph)
findVertexFinds a vertex given a sequence id and a position.
fragmentBeginGets the begin position for this vertex descriptor in the sequence.
fragmentLengthGets the length of the label of a given vertex descriptor in the sequence.
getAdjacencyMatrixReturns an adjacency matrix representation of the graph. (Graph)
getAlignmentTurns a HSP from a Blast search into an Alignment object.
getDistanceMatrixComputes a pairwise distance matrix from an alignment graph.
getFirstCoveredPositionFinds the first position in a sequence that is not assigned to a nil vertex.
getLastCoveredPositionFinds the last position in a sequence that is not assigned to a nil vertex.
getStringSetGets the string set of an alignment graph.
globalAlignmentComputes the best global alignment of the two sequences.
inDegreeNumber of incoming edges for a given vertex. (Graph)
labelGets the label that is associated with this vertex descriptor.
localAlignmentComputes the best local alignment of two sequences.
matchRefinementRefines (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.
numEdgesNumber of edges in a graph. (Graph)
numVerticesNumber of vertices in a graph. (Graph)
outDegreeNumber of outgoing edges for a given vertex. (Graph)
progressiveAlignmentPerforms a progressive alignment.
removeEdgeRemoves an edge from the graph. For automatons a label is required. (Graph)
removeInEdgesRemoves the incoming edges of a given vertex. (Graph)
removeOutEdgesRemoves the outgoing edges of a given vertex. (Graph)
removeVertexRemoves a vertex. (Graph)
resizeEdgeMapInitializes an edge map (Graph)
resizeVertexMapInitializes a vertex map. (Graph)
sequenceIdGets the sequence id that is associated with this vertex descriptor.
sourceVertexReturns the source vertex of an edge. (Graph)
stringSetGets the string set of an alignment graph.
sumOfPairsScoreGiven a multiple alignment, this function calculates the sum-of-pairs score.
targetVertexReturns the target vertex of an edge. (Graph)
transposeTransposes a graph, either in-place or from source to dest. (Graph)
tripletLibraryExtensionPerforms a full or group-based consistency extension.
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