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D

DatagraphCleaner - Class in helix.graph.algo.c3part.preprocessor
a class implementing a cleaner for datagraph.
DatagraphCleaner() - Constructor for class helix.graph.algo.c3part.preprocessor.DatagraphCleaner
 
DataGraphCloser - Class in helix.graph.algo.c3part.preprocessor
a class to compute delta closure of datagraphs.
in a datagraph all vertices are assumed to be colored (not necessarily all edges) and monochromatic.
note: color 0 is reserved for the epsilon relation and is specified on edges.
note: this class does not close on the epsilon relation.
DataGraphCloser(List<Integer>) - Constructor for class helix.graph.algo.c3part.preprocessor.DataGraphCloser
close on all colors (except color 0) with deltas given in delta list.
debug - Variable in class helix.graph.algo.c3part.C3PartOptions
 
DegeneracyReporter - Class in helix.graph.program.isofun
a postprocessor to compute and print epsilon degeneracy of syntons
DegeneracyReporter() - Constructor for class helix.graph.program.isofun.DegeneracyReporter
 
degree() - Method in class helix.graph.model.impl.memory.MemVertex
 
degree() - Method in interface helix.graph.model.Vertex
get the number edges that are incident edges to this vertex
DelegateRegistry - Class in helix.graph.model.impl
 
DelegateRegistry() - Constructor for class helix.graph.model.impl.DelegateRegistry
 
DeltaClosure - Class in helix.graph.algo
 
DeltaClosure(Graph, int, DeltaClosure.Constraint) - Constructor for class helix.graph.algo.DeltaClosure
constructor
DeltaClosure.Constraint - Class in helix.graph.algo
class to define edge constraint
DeltaClosure.Constraint() - Constructor for class helix.graph.algo.DeltaClosure.Constraint
 
deltaEps - Variable in class helix.graph.program.isofun.IsofunOptions
 
deltaGap - Variable in class helix.graph.program.isofun.IsofunOptions
 
deltaShuf - Variable in class helix.graph.algo.c3part.C3PartOptions
 
DENSE_AGGREGATOR - Static variable in class helix.graph.algo.c3part.C3PartOptions
 
DENSE_MODE_ABSOLUTE - Static variable in class helix.graph.algo.c3part.C3PartOptions
 
DENSE_MODE_QUANTILE - Static variable in class helix.graph.algo.c3part.C3PartOptions
 
DENSE_MODE_RELATIVE - Static variable in class helix.graph.algo.c3part.C3PartOptions
 
DenseCCAggregator - Class in helix.graph.algo.c3part.aggregator
 
DenseCCAggregator(Graph, C3PartOptions, RColorSet) - Constructor for class helix.graph.algo.c3part.aggregator.DenseCCAggregator
constructor
Dijkstra - Class in helix.graph.algo
Dijkstra's algorithm solves the single-source shortest path problem note1 : this implementation is O(V2 + E) i.e does not use a priority queue note2: Dijkstra's algorithm is only useful if you want the shortest path from one source.
Dijkstra(Graph) - Constructor for class helix.graph.algo.Dijkstra
constructor
DimacsExtendedReader - Class in helix.graph.io
a Dimacs format reader with additional capabilities to read attributes attached to Graph, Vertices or Edges.
Attributes are specified as :
key=value with key = alpha+ value = any+ | "qany+" alpha = [a-z] | [A-Z] | [0-9] | '_' any = [^ |"] qany = [^"] note: Please note that the '-' (dash) character is not allowed in key and is only allowed in values if it is quoted.
note: You cannot backquote the '"' in values...
DimacsExtendedReader(Reader, GraphFactory) - Constructor for class helix.graph.io.DimacsExtendedReader
 
DimacsExtendedReader(Reader, GraphFactory, Logger) - Constructor for class helix.graph.io.DimacsExtendedReader
 
DimacsExtendedWriter - Class in helix.graph.io
Extended Dimacs format :
p [label] : problem line : label is from graph registry Label
n [label] + : vertex lines : label is from vertex registry Label
e index1 index2 [label] : edge line : indexi are 1-based index refereing to
vertices (see below).
DimacsExtendedWriter(Writer) - Constructor for class helix.graph.io.DimacsExtendedWriter
constructor
DimacsReader - Class in helix.graph.io
Extended Dimacs format :
[c [comment]] : comment line : may appear anywhere
[p [label]] : problem line : label is kept in graph registry as Label
[n [label]]+ : vertex line : label is kept in vertex registry as Label
e index1 index2 [label] : edge line : indexi are 1-based index refereing to
vertices (see below).
DimacsReader(Reader, GraphFactory) - Constructor for class helix.graph.io.DimacsReader
default constructor
DimacsReader(Reader, GraphFactory, Logger) - Constructor for class helix.graph.io.DimacsReader
constructor with logging addition
disconnectVertex(Vertex) - Method in interface helix.graph.model.Graph
 
disconnectVertex(Vertex) - Method in class helix.graph.model.impl.AbstractGraph
 
Distance - Static variable in class helix.graph.algo.Dijkstra
 
distance(Vertex) - Method in class helix.graph.algo.Dijkstra
get distance from source to target return -1 if target is not connected to source
distance(Vertex, Vertex) - Method in class helix.graph.algo.Warshall
get shortest path between vertex u and v
DuplicateEdgeException - Exception in helix.graph.model
 
DuplicateEdgeException() - Constructor for exception helix.graph.model.DuplicateEdgeException
 
DuplicateEdgeException(String) - Constructor for exception helix.graph.model.DuplicateEdgeException
 
DuplicateEdgeException(Throwable) - Constructor for exception helix.graph.model.DuplicateEdgeException
 
DuplicateValueException - Exception in helix.graph.model
 
DuplicateValueException() - Constructor for exception helix.graph.model.DuplicateValueException
 
DuplicateValueException(String) - Constructor for exception helix.graph.model.DuplicateValueException
 
DuplicateValueException(Throwable) - Constructor for exception helix.graph.model.DuplicateValueException
 
duplicateVertex(Graph, Vertex) - Static method in class helix.graph.algo.Cloner
duplicate a single vertex in a graph
note: this is quicker than calling duplicateVertices with a singleton
-1- duplicate vertex v to copy(v) -2- foreach edge (v, u) createEdge(copy(v), u)
duplicateVertices(Graph, GSet<Vertex>) - Static method in class helix.graph.algo.Cloner
duplicate a set of vertices within the same graph
-1- duplicate each vertex v in vertices to copy(v) -2- foreach vertex v in vertices foreach edge (v, u) createEdge(copy(v), u') with u' = (hasCopy(u) ? copy(u) : u)

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