A B C D E F G H I K L M N O P Q R S T U V W X

C

C3PartAbstract - Class in helix.graph.algo.c3part
 
C3PartAbstract(Graph) - Constructor for class helix.graph.algo.c3part.C3PartAbstract
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 - Class in helix.graph.algo.c3part
 
C3PartAbstractOTF(Graph) - Constructor for class helix.graph.algo.c3part.C3PartAbstractOTF
 
C3PartAbstractOTFBasic - Class in helix.graph.algo.c3part
 
C3PartAbstractOTFBasic(Graph) - Constructor for class helix.graph.algo.c3part.C3PartAbstractOTFBasic
 
C3PartAbstractOTFQGlobal - Class in helix.graph.algo.c3part
 
C3PartAbstractOTFQGlobal(Graph) - Constructor for class helix.graph.algo.c3part.C3PartAbstractOTFQGlobal
 
C3PartAbstractOTFQLocal - Class in helix.graph.algo.c3part
 
C3PartAbstractOTFQLocal(Graph) - Constructor for class helix.graph.algo.c3part.C3PartAbstractOTFQLocal
 
C3PartAbstractOTFQuorum - Class in helix.graph.algo.c3part
 
C3PartAbstractOTFQuorum(Graph) - Constructor for class helix.graph.algo.c3part.C3PartAbstractOTFQuorum
 
C3PartAbstractXFS - Class in helix.graph.algo.c3part
 
C3PartAbstractXFS(Graph) - Constructor for class helix.graph.algo.c3part.C3PartAbstractXFS
required pseudo constructor
C3PartAlgo - Interface in helix.graph.algo.c3part
interface for all C3Part algorithms
C3PartBFS - Class in helix.graph.algo.c3part
 
C3PartBFS(Graph) - Constructor for class helix.graph.algo.c3part.C3PartBFS
constructor
C3PartDFS - Class in helix.graph.algo.c3part
 
C3PartDFS(Graph) - Constructor for class helix.graph.algo.c3part.C3PartDFS
API
C3PartDFSQ - Class in helix.graph.algo.c3part
 
C3PartDFSQ(Graph) - Constructor for class helix.graph.algo.c3part.C3PartDFSQ
API
C3PartDTM - Class in helix.graph.algo.c3part
 
C3PartDTM(Graph) - Constructor for class helix.graph.algo.c3part.C3PartDTM
 
C3PartOptions - Class in helix.graph.algo.c3part
options values for C3Part algorithms
C3PartOptions(String[]) - Constructor for class helix.graph.algo.c3part.C3PartOptions
default constructor with user's command line arguments.
C3PartOptions() - Constructor for class helix.graph.algo.c3part.C3PartOptions
constructor without any command line (used to make default options) note: of course you don't need to call parse() just after
C3PartOptions(C3PartOptions) - Constructor for class helix.graph.algo.c3part.C3PartOptions
constructor to copy existing options
C3PartOTF - Class in helix.graph.algo.c3part
 
C3PartOTF(Graph) - Constructor for class helix.graph.algo.c3part.C3PartOTF
constructor
C3PartOTFBasic - Class in helix.graph.algo.c3part
 
C3PartOTFBasic(Graph) - Constructor for class helix.graph.algo.c3part.C3PartOTFBasic
constructor
C3PartOTFQGlobal - Class in helix.graph.algo.c3part
 
C3PartOTFQGlobal(Graph) - Constructor for class helix.graph.algo.c3part.C3PartOTFQGlobal
constructor
C3PartOTFQLocal - Class in helix.graph.algo.c3part
 
C3PartOTFQLocal(Graph) - Constructor for class helix.graph.algo.c3part.C3PartOTFQLocal
constructor
C3PartUtil - Class in helix.graph.algo.c3part
Utilities for C3Part algorithms Note: for readability, we use uppercase characters for parameters holding nodes of the multigraph (e.g.
CC_AGGREGATOR - Static variable in class helix.graph.algo.c3part.C3PartOptions
 
CCAggregator - Class in helix.graph.algo.c3part.aggregator
 
CCAggregator(Graph, C3PartOptions, RColorSet) - Constructor for class helix.graph.algo.c3part.aggregator.CCAggregator
constructor
CCByColorsVisitor - Class in helix.graph.algo.c3part.visitor
 
CCByColorsVisitor(Graph) - Constructor for class helix.graph.algo.c3part.visitor.CCByColorsVisitor
 
CCByColorVisitor - Class in helix.graph.algo.c3part.visitor
 
CCByColorVisitor(Graph, int) - Constructor for class helix.graph.algo.c3part.visitor.CCByColorVisitor
 
CCByEpsilonVisitor - Class in helix.graph.algo.c3part.visitor
 
CCByEpsilonVisitor(Graph) - Constructor for class helix.graph.algo.c3part.visitor.CCByEpsilonVisitor
 
CCColorCleaner - Class in helix.graph.algo.c3part.preprocessor
a class to remove vertices of a datagraph that belong to partially colored epsilon CC.
CCColorCleaner(int) - Constructor for class helix.graph.algo.c3part.preprocessor.CCColorCleaner
constructor: specify minimum number of colors
CCCReporter - Class in helix.graph.algo.c3part.reporter
a clas to report CCCs in Dimacs-like format : q #vertices #node1 ...
CCCReporter() - Constructor for class helix.graph.algo.c3part.reporter.CCCReporter
 
CCCReporterDebug - Class in helix.graph.algo.c3part.reporter
a temporary debug extension of CCCReporter a clas to report CCCs in Dimacs-like format : q #vertices #node1 ...
CCCReporterDebug() - Constructor for class helix.graph.algo.c3part.reporter.CCCReporterDebug
 
CCDatagraphVisitor - Class in helix.graph.algo.c3part.visitor
 
CCDatagraphVisitor(Graph) - Constructor for class helix.graph.algo.c3part.visitor.CCDatagraphVisitor
 
ccDenseMode - Variable in class helix.graph.algo.c3part.C3PartOptions
 
ccDensity - Variable in class helix.graph.algo.c3part.C3PartOptions
 
CCMultigraphVisitor - Class in helix.graph.algo.c3part.visitor
 
CCMultigraphVisitor(Graph) - Constructor for class helix.graph.algo.c3part.visitor.CCMultigraphVisitor
 
CCStarByColorVisitor - Class in helix.graph.algo.c3part.visitor
 
CCStarByColorVisitor(Graph, int, int, Vertex) - Constructor for class helix.graph.algo.c3part.visitor.CCStarByColorVisitor
 
CCSuperStarByColorVisitor - Class in helix.graph.algo.c3part.visitor
the superstar version of CCStarByColorVisitor -1- keep red stars apart (red star is a vertex having a star on specified color) -2- compute normal CCs -3- fadd red stars as a separate CC
CCSuperStarByColorVisitor(Graph, int, int, Vertex) - Constructor for class helix.graph.algo.c3part.visitor.CCSuperStarByColorVisitor
 
CCVisitor - Class in helix.graph.algo
 
CCVisitor(Graph) - Constructor for class helix.graph.algo.CCVisitor
 
CENTER_AGGREGATOR - Static variable in class helix.graph.algo.c3part.C3PartOptions
 
CenteredAggregator - Class in helix.graph.algo.c3part.aggregator
 
CenteredAggregator(Graph, C3PartOptions) - Constructor for class helix.graph.algo.c3part.aggregator.CenteredAggregator
required constructor
CenteredQuorumCleaner - Class in helix.graph.algo.c3part.preprocessor
 
CenteredQuorumCleaner(int, int) - Constructor for class helix.graph.algo.c3part.preprocessor.CenteredQuorumCleaner
 
check - Variable in class helix.graph.program.isofun.IsofunOptions
 
checkColors(Vertex, Vertex, String, boolean) - Static method in class helix.graph.algo.c3part.MultiGraphDebugger
check colors of edge U-V
checkColors(Graph, String, boolean) - Static method in class helix.graph.algo.c3part.MultiGraphDebugger
check colors of multigraph pass null as compress to ignore compression
checkGraph(Graph, GraphChecker.Level) - Static method in class helix.graph.algo.c3part.reporter.GraphChecker
full check
checkGraph(Graph) - Static method in class helix.graph.algo.c3part.reporter.GraphChecker
 
checkIntegrity(Graph, String) - Method in class helix.graph.util.GraphDebugger
 
Chromatizer - Class in helix.graph.algo.c3part.preprocessor
 
Chromatizer(RColorSet, int) - Constructor for class helix.graph.algo.c3part.preprocessor.Chromatizer
default constructor
Chromatizer(RColorSet, int, List<Integer>) - Constructor for class helix.graph.algo.c3part.preprocessor.Chromatizer
alternate constructor : use the delta values in user's delta list to specify which colors are required.
CircleGenerator - Class in helix.graph.algo
 
CircleGenerator(int) - Constructor for class helix.graph.algo.CircleGenerator
 
cleanup - Variable in class helix.graph.program.isofun.IsofunOptions
 
clear() - Method in interface helix.graph.model.Graph
 
clear() - Method in class helix.graph.model.impl.AbstractGraph
 
clear() - Method in class helix.graph.model.impl.RVertexList
 
clear() - Method in class helix.graph.model.impl.RVertexSet
 
clearColor(int) - Method in class helix.graph.model.impl.RColorSet
unset color in this ColorSet same as : setColor(i, false)
clearColors() - Method in class helix.graph.model.impl.RColorSet
clear all colors in this ColorSet
CLIQUE_AGGREGATOR - Static variable in class helix.graph.algo.c3part.C3PartOptions
 
CliqueAggregator - Class in helix.graph.algo.c3part.aggregator
 
CliqueAggregator(Graph, C3PartOptions) - Constructor for class helix.graph.algo.c3part.aggregator.CliqueAggregator
required constructor
cloneGraph(Graph) - Static method in class helix.graph.algo.Cloner
clone a graph completely same as subGraph(g, g.vertices())
Cloner - Class in helix.graph.algo
a class to duplicate graphs or parts of graph
Color - Static variable in interface helix.graph.model.Registry
 
ColorCleaner - Class in helix.graph.algo.c3part.preprocessor
a class to remove some colors from datagraph and shift remaining colors accordingly
ColorCleaner(Iterable<Integer>) - Constructor for class helix.graph.algo.c3part.preprocessor.ColorCleaner
 
ColorOptimizer - Interface in helix.graph.algo.c3part.optimizer
 
ColorPathConnector - Class in helix.graph.algo.c3part.lookahead
 
colors - Variable in class helix.graph.algo.c3part.C3PartOptions
 
Colors - Static variable in interface helix.graph.model.Registry
 
CommandLine - Class in helix.graph.util
 
CommandLine(String[]) - Constructor for class helix.graph.util.CommandLine
constructor
CommandLineException - Exception in helix.graph.util
 
CommandLineException() - Constructor for exception helix.graph.util.CommandLineException
 
CommandLineException(String) - Constructor for exception helix.graph.util.CommandLineException
 
CommandLineException(Throwable) - Constructor for exception helix.graph.util.CommandLineException
 
Comment - Static variable in interface helix.graph.model.Registry
 
component(Vertex) - Method in class helix.graph.algo.ComponentsFinder
return component containing vertex v
ComponentsFinder - Class in helix.graph.algo
a class to compute connected components.
ComponentsFinder(Graph) - Constructor for class helix.graph.algo.ComponentsFinder
constructor
componentsPerColor(Graph) - Static method in class helix.graph.algo.c3part.reporter.GraphStatistics
compute number of connected components per color
compress(Graph) - Method in class helix.graph.algo.c3part.compressor.AbstractCompressor
compress graph
compress(Graph, Logger) - Method in class helix.graph.algo.c3part.compressor.AbstractCompressor
same as compress with logging compression rate
compress(Graph) - Method in interface helix.graph.algo.c3part.compressor.GraphCompressor
compress graph
compress(Graph, Logger) - Method in interface helix.graph.algo.c3part.compressor.GraphCompressor
same as compress with logging compression rate
compress(Graph) - Method in class helix.graph.algo.c3part.compressor.MultiInSetCompressor
compress graph -> avoid recoloring root at each compression
compress(Graph) - Method in class helix.graph.algo.c3part.compressor.NoCompressor
 
compress(Graph, Logger) - Method in class helix.graph.algo.c3part.compressor.NoCompressor
 
compressor - Variable in class helix.graph.algo.c3part.C3PartOptions
 
compressVertex(Vertex, Vertex, Graph) - Method in class helix.graph.algo.c3part.compressor.AbstractCompressor
compress single vertex v on root vertex root
compressVertex(Vertex, Vertex, Graph) - Method in interface helix.graph.algo.c3part.compressor.GraphCompressor
compress single vertex v on root vertex
compressVertex(Vertex, Vertex, Graph) - Method in class helix.graph.algo.c3part.compressor.MultiInSetCompressor
 
compressVertex(Vertex, Vertex, Graph) - Method in class helix.graph.algo.c3part.compressor.NoCompressor
 
concthresh - Variable in class helix.graph.algo.c3part.C3PartOptions
 
ConcurrentService - Class in helix.graph.util
 
ConcurrentService(int) - Constructor for class helix.graph.util.ConcurrentService
 
ConcurrentService() - Constructor for class helix.graph.util.ConcurrentService
 
connectedComponents() - Method in class helix.graph.algo.ComponentsFinder
return all connected components of graph
containsAll(Iterable<Integer>) - Method in class helix.graph.util.IPermutation
check if permutation contains the set of integers given as argument
ContiguityReporter - Class in helix.graph.program.isofun
a reporter to compute and print gene contiguity in syntons.
ContiguityReporter() - Constructor for class helix.graph.program.isofun.ContiguityReporter
 
copy(Registry) - Method in class helix.graph.model.impl.AbstractRegistry
 
copy(Registry) - Method in interface helix.graph.model.Registry
 
countColors() - Method in class helix.graph.model.impl.RColorSet
count the number of colors in this ColorSet
countStars(Vertex) - Static method in class helix.graph.algo.c3part.C3PartUtil
count number of stars in multinode V

A B C D E F G H I K L M N O P Q R S T U V W X