Uses of Interface
nct.graph.DistanceGraph

Packages that use DistanceGraph
nct.graph   
nct.graph.basic   
nct.networkblast.graph   
nct.networkblast.graph.compatibility   
 

Uses of DistanceGraph in nct.graph
 

Subinterfaces of DistanceGraph in nct.graph
 interface SequenceGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An interface that describes accessing a sequence database associated with the graph.
 

Uses of DistanceGraph in nct.graph.basic
 

Classes in nct.graph.basic that implement DistanceGraph
 class BasicDistanceGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An extension of BasicGraph that calculates the minimum distance between nodes.
 class BlastGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An extension of BasicDistanceGraph that implements SequenceGraph and contains a pointer to a Blast database.
 class FastaGraph<NodeType extends Comparable<? super NodeType>,WeightType extends Comparable<? super WeightType>>
          An extension of BasicDistanceGraph that implements the SequenceGraph interface and contains a (pointer to a) fasta database.
 

Uses of DistanceGraph in nct.networkblast.graph
 

Classes in nct.networkblast.graph that implement DistanceGraph
 class InteractionGraph
          An implementation of a SequenceGraph that is specified by a SIF file.
 

Fields in nct.networkblast.graph with type parameters of type DistanceGraph
protected  KPartiteGraph<java.lang.String,java.lang.Double,? extends DistanceGraph<java.lang.String,java.lang.Double>> CompatibilityGraph.homologyGraph
           
protected  java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> CompatibilityGraph.interactionGraphs
           
 

Constructor parameters in nct.networkblast.graph with type arguments of type DistanceGraph
CompatibilityGraph(KPartiteGraph<java.lang.String,java.lang.Double,? extends DistanceGraph<java.lang.String,java.lang.Double>> homologyGraph, java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> interactionGraphs, ScoreModel<java.lang.String,java.lang.Double> scoreModel, CompatibilityCalculator compatCalc)
          Constructor.
CompatibilityGraph(KPartiteGraph<java.lang.String,java.lang.Double,? extends DistanceGraph<java.lang.String,java.lang.Double>> homologyGraph, java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> interactionGraphs, ScoreModel<java.lang.String,java.lang.Double> scoreModel, CompatibilityCalculator compatCalc)
          Constructor.
 

Uses of DistanceGraph in nct.networkblast.graph.compatibility
 

Method parameters in nct.networkblast.graph.compatibility with type arguments of type DistanceGraph
 boolean CompatibilityCalculator.calculate(Graph<java.lang.String,java.lang.Double> compatGraph, java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> partitionGraphs, java.lang.String[] nodeBase, java.lang.String[] nodeBranch)
          The method that determines which nodes to add, adds them if appropriate, and calculates the edge score.
 boolean AdditiveCompatibilityCalculator.calculate(Graph<java.lang.String,java.lang.Double> compatGraph, java.util.List<? extends DistanceGraph<java.lang.String,java.lang.Double>> partitionGraphs, java.lang.String[] nodeBase, java.lang.String[] nodeBranch)
          The method that determines which nodes to add, adds them if appropriate, and calculates the edge score.