Uses of Interface
nct.graph.SequenceGraph

Packages that use SequenceGraph
nct.graph.basic   
nct.networkblast.graph   
nct.service.homology   
nct.service.homology.blast   
nct.service.homology.sif   
 

Uses of SequenceGraph in nct.graph.basic
 

Classes in nct.graph.basic that implement SequenceGraph
 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 SequenceGraph in nct.networkblast.graph
 

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

Methods in nct.networkblast.graph with parameters of type SequenceGraph
 boolean HomologyGraph.addGraph(SequenceGraph<java.lang.String,java.lang.Double> sg)
          Adds the nodes of the specified graph to this graph and adds the graph as a partition.
 

Constructor parameters in nct.networkblast.graph with type arguments of type SequenceGraph
HomologyGraph(HomologyModel homModel, double exThresh, java.util.Collection<SequenceGraph<java.lang.String,java.lang.Double>> graphs)
           
 

Uses of SequenceGraph in nct.service.homology
 

Methods in nct.service.homology with parameters of type SequenceGraph
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> HomologyModel.expectationValues(SequenceGraph<java.lang.String,java.lang.Double> sg1, SequenceGraph<java.lang.String,java.lang.Double> sg2)
          A method that returns a mapping of expectation values between nodes of the two graphs.
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> HomologyModel.expectationValues(SequenceGraph<java.lang.String,java.lang.Double> sg1, SequenceGraph<java.lang.String,java.lang.Double> sg2)
          A method that returns a mapping of expectation values between nodes of the two graphs.
 

Uses of SequenceGraph in nct.service.homology.blast
 

Methods in nct.service.homology.blast with parameters of type SequenceGraph
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> LocalBlast.expectationValues(SequenceGraph sg1, SequenceGraph sg2)
          Returns a map of expectation values between nodes of the specified graphs.
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> LocalBlast.expectationValues(SequenceGraph sg1, SequenceGraph sg2)
          Returns a map of expectation values between nodes of the specified graphs.
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> BiojavaLocalBlast.expectationValues(SequenceGraph sg1, SequenceGraph sg2)
          Returns a map of expectation values between nodes of the specified graphs.
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> BiojavaLocalBlast.expectationValues(SequenceGraph sg1, SequenceGraph sg2)
          Returns a map of expectation values between nodes of the specified graphs.
 

Uses of SequenceGraph in nct.service.homology.sif
 

Methods in nct.service.homology.sif with parameters of type SequenceGraph
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> SIFHomologyReader.expectationValues(SequenceGraph<java.lang.String,java.lang.Double> sg1, SequenceGraph<java.lang.String,java.lang.Double> sg2)
          Returns a map of expectation values between nodes of the specified graphs.
 java.util.Map<java.lang.String,java.util.Map<java.lang.String,java.lang.Double>> SIFHomologyReader.expectationValues(SequenceGraph<java.lang.String,java.lang.Double> sg1, SequenceGraph<java.lang.String,java.lang.Double> sg2)
          Returns a map of expectation values between nodes of the specified graphs.