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E
E_VALUE
- Static variable in class nct.service.homology.
BiojavaLocalBlast
Sentinel used to specify the expectation value threshold.
E_VALUE
- Static variable in class nct.service.homology.
LocalBlast
Sentinel used to specify the expectation value threshold.
Edge
<
NodeType
extends java.lang.Comparable<? super
NodeType
>,
WeightType
extends java.lang.Comparable<? super
WeightType
>> - Interface in
nct.graph
An generic interface describing the basic components of an edge: source and target nodes, edge weight, and description.
edgeCount
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
edgeDescMap
- Variable in class nct.networkblast.
CompatibilityGraph
EdgeWeightShuffle
<
NodeType
extends java.lang.Comparable<? super
NodeType
>,
WeightType
extends java.lang.Comparable<? super
WeightType
>> - Class in
nct.graph.util
This class performs a basic Fisher-Yates shuffle of the edge weights.
EdgeWeightShuffle(Random)
- Constructor for class nct.graph.util.
EdgeWeightShuffle
endDocument()
- Method in class nct.service.interactions.
DIPInteractionNetwork
Basic SAX event handler.
endDocument()
- Method in class nct.service.synonyms.
DIPSynonyms
Standard SAX event handler.
endDocument()
- Method in class nct.xml.
XMLSaxEventDistributor
endElement(String, String, String)
- Method in class nct.service.interactions.
DIPInteractionNetwork
Basic SAX event handler.
endElement(String, String, String)
- Method in class nct.service.synonyms.
DIPSynonyms
Standard SAX event handler.
endElement(String, String, String)
- Method in class nct.xml.
XMLSaxEventDistributor
endPrefixMapping(String)
- Method in class nct.xml.
XMLSaxEventDistributor
epsilon
- Variable in class nct.networkblast.
NetworkBlast
equals(Object)
- Method in class nct.graph.
BasicEdge
error(SAXParseException)
- Method in class nct.xml.
XMLSaxEventDistributor
evalues
- Variable in class nct.service.homology.
BiojavaLocalBlast
The map where the evalues between proteins are stored.
evalues
- Variable in class nct.service.homology.
LocalBlast
The map where the evalues between proteins are stored.
eValueThreshold
- Variable in class nct.service.homology.
BiojavaLocalBlast
A string representation of a double value that is the expectation value threshold for the blastall command (-e argument).
eValueThreshold
- Variable in class nct.service.homology.
LocalBlast
A string representation of a double value that is the expectation value threshold for the blastall command (-e argument).
expectation
- Variable in class nct.networkblast.
NetworkBlast
expectationDefault
- Static variable in class nct.networkblast.
NetworkBlast
expectationValues(SequenceGraph, SequenceGraph)
- Method in class nct.service.homology.
BiojavaLocalBlast
Returns a map of expectation values between nodes of the specified graphs.
expectationValues(SequenceGraph<String, Double>, SequenceGraph<String, Double>)
- Method in interface nct.service.homology.
HomologyModel
A method that returns a mapping of expectation values between nodes of the two graphs.
expectationValues(SequenceGraph, SequenceGraph)
- Method in class nct.service.homology.
LocalBlast
Returns a map of expectation values between nodes of the specified graphs.
expectationValues(SequenceGraph<String, Double>, SequenceGraph<String, Double>)
- Method in class nct.service.homology.
SIFHomologyReader
Returns a map of expectation values between nodes of the specified graphs.
exThresh
- Variable in class nct.networkblast.
HomologyGraph
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