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Packages that use SequenceGraph | |
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nct.graph | |
nct.networkblast | |
nct.service.homology |
Uses of SequenceGraph in nct.graph |
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Classes in nct.graph that implement SequenceGraph | |
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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 |
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Classes in nct.networkblast that implement SequenceGraph | |
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class |
InteractionGraph
An implementation of a SequenceGraph that is specified by a SIF file. |
Methods in nct.networkblast with parameters of type SequenceGraph | |
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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 with type arguments of type SequenceGraph | |
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HomologyGraph(HomologyModel homModel,
double exThresh,
java.util.Collection<SequenceGraph<java.lang.String,java.lang.Double>> graphs)
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Uses of SequenceGraph in nct.service.homology |
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Methods in nct.service.homology with parameters of type SequenceGraph | |
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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. |
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. |
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. |
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. |
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