Uses of Interface
helix.graph.model.Graph

Packages that use Graph
helix.graph.algo   
helix.graph.algo.c3part   
helix.graph.algo.c3part.aggregator   
helix.graph.algo.c3part.compressor   
helix.graph.algo.c3part.lookahead   
helix.graph.algo.c3part.optimizer   
helix.graph.algo.c3part.preprocessor   
helix.graph.algo.c3part.reporter   
helix.graph.algo.c3part.visitor   
helix.graph.io   
helix.graph.model   
helix.graph.model.impl   
helix.graph.model.impl.memory   
helix.graph.program.isofun   
helix.graph.util   
 

Uses of Graph in helix.graph.algo
 

Methods in helix.graph.algo that return Graph
static Graph Cloner.cloneGraph(Graph src)
          clone a graph completely same as subGraph(g, g.vertices())
 Graph StarGenerator.generate(GraphFactory factory)
           
 Graph Generator.generate(GraphFactory factory)
           
 Graph ErdosGenerator.generate(GraphFactory factory)
           
 Graph CircleGenerator.generate(GraphFactory factory)
           
 Graph BasicGenerator.generate(GraphFactory factory)
           
static Graph Cloner.subGraph(Graph src, Iterable<Vertex> vertices)
          make a subgraph from graph restricted to given vertices
static Graph Cloner.union(Graph g1, Graph g2)
          make union of two disjoints graphs
 

Methods in helix.graph.algo with parameters of type Graph
static Graph Cloner.cloneGraph(Graph src)
          clone a graph completely same as subGraph(g, g.vertices())
static Vertex Cloner.duplicateVertex(Graph graph, Vertex v)
          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)
static GSet<Vertex> Cloner.duplicateVertices(Graph graph, GSet<Vertex> vertices)
          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)
static Graph Cloner.subGraph(Graph src, Iterable<Vertex> vertices)
          make a subgraph from graph restricted to given vertices
static Graph Cloner.union(Graph g1, Graph g2)
          make union of two disjoints graphs
 

Constructors in helix.graph.algo with parameters of type Graph
AbstractCCVisitor(Graph g)
           
CCVisitor(Graph graph)
           
ComponentsFinder(Graph g)
          constructor
DeltaClosure(Graph graph, int delta, DeltaClosure.Constraint constraint)
          constructor
Dijkstra(Graph graph)
          constructor
Warshall(Graph graph)
          constructor
 

Uses of Graph in helix.graph.algo.c3part
 

Methods in helix.graph.algo.c3part that return types with arguments of type Graph
 Set<Graph> C3PartAlgo.run()
          run main algo (with current options)
 Set<Graph> C3PartAbstract.run()
          run algo with current options.
 

Methods in helix.graph.algo.c3part with parameters of type Graph
static int MultiGraphDebugger.checkColors(Graph multi, String prefix, boolean fixme)
          check colors of multigraph pass null as compress to ignore compression
static void MultiGraphDebugger.fixColors(Graph multi)
          fix colors of multigraph
 ColorOptimizer C3PartDTM.getOptimizerFor(Graph Clas)
           
 ColorOptimizer C3PartAlgo.getOptimizerFor(Graph Clas)
          get current optimizer for this algo and (possibly) this particular Clas
 ColorOptimizer C3PartAbstractOTFQuorum.getOptimizerFor(Graph Clas)
           
 ColorOptimizer C3PartAbstract.getOptimizerFor(Graph Clas)
          get optimizer for Clas this abstract class knows :
 

Constructors in helix.graph.algo.c3part with parameters of type Graph
C3PartAbstract(Graph dataGraph)
          default pseudo constructor note: defining the constructor in the abstract class will force its requirement in subclasses : just call super() if you don't need to override.
C3PartAbstractOTF(Graph dataGraph)
           
C3PartAbstractOTFBasic(Graph dataGraph)
           
C3PartAbstractOTFQGlobal(Graph dataGraph)
           
C3PartAbstractOTFQLocal(Graph dataGraph)
           
C3PartAbstractOTFQuorum(Graph dataGraph)
           
C3PartAbstractXFS(Graph dataGraph)
          required pseudo constructor
C3PartBFS(Graph dataGraph)
          constructor
C3PartDFS(Graph dataGraph)
          API
C3PartDFSQ(Graph dataGraph)
          API
C3PartDTM(Graph dataGraph)
           
C3PartOTF(Graph dataGraph)
          constructor
C3PartOTFBasic(Graph dataGraph)
          constructor
C3PartOTFQGlobal(Graph dataGraph)
          constructor
C3PartOTFQLocal(Graph dataGraph)
          constructor
 

Uses of Graph in helix.graph.algo.c3part.aggregator
 

Constructors in helix.graph.algo.c3part.aggregator with parameters of type Graph
CCAggregator(Graph datagraph, C3PartOptions options, RColorSet multicolors)
          constructor
CenteredAggregator(Graph datagraph, C3PartOptions options)
          required constructor
CliqueAggregator(Graph datagraph, C3PartOptions options)
          required constructor
DenseCCAggregator(Graph datagraph, C3PartOptions options, RColorSet multicolors)
          constructor
NodeAggregator(Graph datagraph, C3PartOptions options)
          required constructor
PivotingAggregator(Graph datagraph, C3PartOptions options)
          constructor - same as super
 

Uses of Graph in helix.graph.algo.c3part.compressor
 

Methods in helix.graph.algo.c3part.compressor with parameters of type Graph
 void NoCompressor.compress(Graph graph)
           
 void MultiInSetCompressor.compress(Graph graph)
          compress graph -> avoid recoloring root at each compression
 void GraphCompressor.compress(Graph graph)
          compress graph
 void AbstractCompressor.compress(Graph graph)
          compress graph
 void NoCompressor.compress(Graph graph, Logger logger)
           
 void GraphCompressor.compress(Graph graph, Logger logger)
          same as compress with logging compression rate
 void AbstractCompressor.compress(Graph graph, Logger logger)
          same as compress with logging compression rate
 void NoCompressor.compressVertex(Vertex v, Vertex root, Graph graph)
           
 void MultiInSetCompressor.compressVertex(Vertex V, Vertex Root, Graph multi)
           
 void GraphCompressor.compressVertex(Vertex v, Vertex root, Graph graph)
          compress single vertex v on root vertex
 void AbstractCompressor.compressVertex(Vertex v, Vertex root, Graph graph)
          compress single vertex v on root vertex root
 void NoCompressor.expand(Graph graph)
           
 void GraphCompressor.expand(Graph graph)
          expand graph to its uncompressed (initial) state
 void AbstractCompressor.expand(Graph graph)
          expand graph to its uncompressed state
 void NoCompressor.expandVertex(Vertex v, Graph graph)
           
 void MultiInSetCompressor.expandVertex(Vertex V, Graph multi)
          expand single vertex and recompute root colors
 void GraphCompressor.expandVertex(Vertex v, Graph graph)
          restore compressed alias vertex v to its initial state
 void AbstractMultiCompressor.expandVertex(Vertex V, Graph multi)
          restore compressed vertex v to its initial state
 void NoCompressor.flatten(Graph graph)
           
 void GraphCompressor.flatten(Graph graph)
          expand graph without edges AV TODO temporary placeholder
 void AbstractCompressor.flatten(Graph graph)
          expand graph without edges
 Iterable<Vertex> NoCompressor.getVertices(Graph graph)
           
 Iterable<Vertex> GraphCompressor.getVertices(Graph graph)
          return all vertices in compressed graph.
 Iterable<Vertex> AbstractCompressor.getVertices(Graph graph)
          return all vertices in compressed graph.
 int NoCompressor.nbVertices(Graph graph)
           
 int GraphCompressor.nbVertices(Graph graph)
          return the number of vertices in graph (including compressed one)
 int AbstractCompressor.nbVertices(Graph graph)
          return the number of vertices in graph (including compressed one)
 Iterable<Vertex> MultiInSetCompressor.patternSet_(Vertex V, Graph multi)
          delegate patternSet
 Iterable<Vertex> MultiInSetColorsCompressor.patternSet_(Vertex V, Graph multi)
          delegate patternSet
 Iterable<Vertex> MultiInColorsCompressor.patternSet_(Vertex V, Graph multi)
          delegate patternSet
 Iterable<Vertex> MultiIdentCompressor.patternSet_(Vertex V, Graph multi)
          delegate patternSet
abstract  Iterable<Vertex> AbstractMultiCompressor.patternSet_(Vertex V, Graph multi)
          delegate pattern set
 void MultiInSetCompressor.restoreEdge_(Vertex V, Vertex W, Vertex Root, Graph multi)
          delegate restoration restore (if needed) edge between V and W
 void MultiInSetColorsCompressor.restoreEdge_(Vertex V, Vertex W, Vertex Root, Graph multi)
          delegate restoration restore (if needed) edge between V and W
 void MultiInColorsCompressor.restoreEdge_(Vertex V, Vertex W, Vertex Root, Graph multi)
          delegate restoration restore (if needed) edge between V and W
 void MultiIdentCompressor.restoreEdge_(Vertex V, Vertex W, Vertex Root, Graph multi)
          delegate restoration restore (if needed) edge between V and W
abstract  void AbstractMultiCompressor.restoreEdge_(Vertex V, Vertex W, Vertex Root, Graph multi)
          delegate edge restoration restore (if needed) edge between V and W
 boolean MultiInSetCompressor.subsumes_(Vertex V, Vertex U, Graph graph)
          delegate subsumption
 boolean MultiInSetColorsCompressor.subsumes_(Vertex V, Vertex U, Graph graph)
          delegate subsumption
 boolean MultiInColorsCompressor.subsumes_(Vertex V, Vertex U, Graph graph)
          delegate subsumption
 boolean MultiIdentCompressor.subsumes_(Vertex V, Vertex U, Graph multi)
          delegate subsumption
abstract  boolean AbstractMultiCompressor.subsumes_(Vertex V, Vertex U, Graph multi)
          delegate subsumption
 boolean NoCompressor.subsumes(Vertex v, Vertex u, Graph graph)
           
 boolean GraphCompressor.subsumes(Vertex v, Vertex u, Graph graph)
          tells if vertex v subsumes vertex u
 boolean AbstractMultiCompressor.subsumes(Vertex V, Vertex U, Graph multi)
          tells if vertex V subsumes vertex U
 

Uses of Graph in helix.graph.algo.c3part.lookahead
 

Methods in helix.graph.algo.c3part.lookahead with parameters of type Graph
 GSet<Vertex> LookaheadConnector.getLookahead(Graph datagraph, Graph multigraph, int color)
          get the pseudoterminals and return a new GSet[Vertex]
 void TwoWayPathConnector.getLookAhead(Graph datagraph, Graph multigraph, int color, GSet<Vertex> store)
           
 void TerminalsConnector.getLookAhead(Graph datagraph, Graph multigraph, int color, GSet<Vertex> store)
           
 void OneWayPathConnector.getLookAhead(Graph datagraph, Graph multigraph, int color, GSet<Vertex> store)
           
abstract  void LookaheadConnector.getLookAhead(Graph datagraph, Graph multigraph, int color, GSet<Vertex> store)
          get the pseudoterminals and append them into 'store'.
 void FullColorConnector.getLookAhead(Graph datagraph, Graph multigraph, int color, GSet<Vertex> store)
           
 void ColorPathConnector.getLookAhead(Graph datagraph, Graph multigraph, int color, GSet<Vertex> store)
          get the connected component of all datanodes in multigraph terminals following only links of terminal color.
 void AllPathConnector.getLookAhead(Graph datagraph, Graph multigraph, int color, GSet<Vertex> store)
           
 

Uses of Graph in helix.graph.algo.c3part.optimizer
 

Constructors in helix.graph.algo.c3part.optimizer with parameters of type Graph
EmbeddedColorOptimizer(C3PartAlgo algo, Graph datagraph, Graph clas)
          required constructor
GlobalColorOptimizer(C3PartAlgo algo, Graph datagraph, Graph clas)
           
TerminalsColorOptimizer(C3PartAlgo algo, Graph datagraph, Graph clas)
           
TerminalsStarColorOptimizer(C3PartAlgo algo, Graph datagraph, Graph clas)
           
 

Uses of Graph in helix.graph.algo.c3part.preprocessor
 

Methods in helix.graph.algo.c3part.preprocessor with parameters of type Graph
 void TandemCleaner.run(Graph graph)
          run cleaner
 void NoCleaner.run(Graph graph)
           
 void MultiGraphCloser.run(Graph graph)
          implement our run() operation
 void IterativeCleaner.run(Graph graph)
           
abstract  void GraphPreprocessor.run(Graph graph)
          preprocess datagraph note: the datagraph argument is modified
 void EpsilonCloser.run(Graph graph)
          implement our run() operation
 void DataGraphCloser.run(Graph graph)
          implement our run() operation
 void ColorCleaner.run(Graph graph)
           
 void Chromatizer.run(Graph graph)
          implement our run() operation
 void CCColorCleaner.run(Graph graph)
           
 void GraphPreprocessor.run(Graph graph, Logger logger)
          same but with logging information
 

Uses of Graph in helix.graph.algo.c3part.reporter
 

Methods in helix.graph.algo.c3part.reporter with parameters of type Graph
static boolean GraphChecker.checkGraph(Graph g)
           
static boolean GraphChecker.checkGraph(Graph g, GraphChecker.Level level)
          full check
static int[] GraphStatistics.componentsPerColor(Graph g)
          compute number of connected components per color
static int[][] GraphStatistics.epsilonMatrix(Graph g)
          count the number of epsilon links between each datasubgraph return the matrix of occurences (diagonal contains the number of internal links)
static void GraphStatistics.logStatistics(Graph g)
          report graph statistics
static void CCCReporterDebug.printSynton(Graph synton, C3PartOptions options)
           
static void CCCReporter.printSynton(Graph synton, C3PartOptions options)
          print out a synton in Dimacs format
static int[] GraphStatistics.verticesPerColor(Graph g)
          compute number of vertices per color
 

Uses of Graph in helix.graph.algo.c3part.visitor
 

Constructors in helix.graph.algo.c3part.visitor with parameters of type Graph
CCByColorsVisitor(Graph datagraph)
           
CCByColorVisitor(Graph multigraph, int color)
           
CCByEpsilonVisitor(Graph datagraph)
           
CCDatagraphVisitor(Graph datagraph)
           
CCMultigraphVisitor(Graph multigraph)
           
CCStarByColorVisitor(Graph multigraph, int color, int colorIndex, Vertex star)
           
CCSuperStarByColorVisitor(Graph multigraph, int color, int colorIndex, Vertex star)
           
 

Uses of Graph in helix.graph.io
 

Methods in helix.graph.io that return Graph
 Graph GraphReader.read()
           
 Graph DimacsReader.read()
           
 Graph DimacsExtendedReader.read()
           
abstract  Graph AbstractGraphReader.read()
           
 

Methods in helix.graph.io with parameters of type Graph
 void GraphWriter.write(Graph graph)
           
 void DimacsExtendedWriter.write(Graph graph)
          writer
abstract  void AbstractGraphWriter.write(Graph graph)
           
 

Uses of Graph in helix.graph.model
 

Methods in helix.graph.model that return Graph
 Graph GraphFactory.make()
           
 

Methods in helix.graph.model that return types with arguments of type Graph
 Set<Graph> Graph.physicalSplit(Iterable<GSet<Vertex>> splits)
           
 

Uses of Graph in helix.graph.model.impl
 

Classes in helix.graph.model.impl that implement Graph
 class AbstractGraph
           
 

Methods in helix.graph.model.impl that return types with arguments of type Graph
 Set<Graph> AbstractGraph.physicalSplit(Iterable<GSet<Vertex>> splits)
          TODO a documenter serieusement en particulier : destroy the current graph accepte un visiteur a classes recouvrantes et non totalement couvrant
 

Uses of Graph in helix.graph.model.impl.memory
 

Classes in helix.graph.model.impl.memory that implement Graph
 class MemGraph
           
 

Methods in helix.graph.model.impl.memory that return Graph
 Graph MemGraphFactory.make()
           
 

Uses of Graph in helix.graph.program.isofun
 

Methods in helix.graph.program.isofun with parameters of type Graph
static C3PartAlgo IsofunOptions.getAlgoForName(String name, Graph graph)
          get proper algorithm from name
static void DegeneracyReporter.logDegeneracy(Graph datagraph)
          compute and print epsilon degeneracy information for input datagraph
static void ContiguityReporter.printContiguity(Graph synton)
          print synton contiguity
static void OGReporter.printOGs(Graph synton, List<Integer> deltagap)
          print POGs
 

Method parameters in helix.graph.program.isofun with type arguments of type Graph
static void DegeneracyReporter.logDegeneracy(Set<Graph> result)
          compute and print epsilon degeneracy information for multigraph results (i.e.
 

Uses of Graph in helix.graph.util
 

Methods in helix.graph.util with parameters of type Graph
 Vertex GraphDebugger.checkIntegrity(Graph g, String header)
           
 void GraphDebugger.log(Graph g)
           
 void GraphDebugger.log(Graph g, boolean withEdges, String header)
          print graph
 void GraphDebugger.log(Graph g, String header)
          simplified versions