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Hierarchy For All Packages
Package Hierarchies:
nct.filter
,
nct.graph
,
nct.graph.util
,
nct.networkblast
,
nct.output
,
nct.parsers
,
nct.score
,
nct.search
,
nct.service.homology
,
nct.service.interactions
,
nct.service.sequences
,
nct.service.synonyms
,
nct.visualization.cytoscape
,
nct.visualization.cytoscape.dual
,
nct.xml
Class Hierarchy
java.lang.Object
nct.graph.
BasicEdge
<NodeType,WeightType> (implements nct.graph.
Edge
<NodeType,WeightType>)
nct.graph.
BasicGraph
<NodeType,WeightType> (implements java.lang.Cloneable, java.lang.Comparable<T>, nct.graph.
Graph
<NodeType,WeightType>)
nct.graph.
BasicDistanceGraph
<NodeType,WeightType> (implements nct.graph.
DistanceGraph
<NodeType,WeightType>)
nct.graph.
BlastGraph
<NodeType,WeightType> (implements nct.graph.
SequenceGraph
<NodeType,WeightType>)
nct.graph.
FastaGraph
<NodeType,WeightType> (implements nct.graph.
SequenceGraph
<NodeType,WeightType>)
nct.networkblast.
InteractionGraph
(implements nct.graph.
SequenceGraph
<NodeType,WeightType>)
nct.graph.
BasicKPartiteGraph
<NodeType,WeightType,PartitionType> (implements java.lang.Cloneable, java.lang.Comparable<T>, nct.graph.
KPartiteGraph
<NodeType,WeightType,PartitionType>)
nct.networkblast.
HomologyGraph
nct.networkblast.
CompatibilityGraph
nct.graph.
BasicWeightedNode
<IDType,WeightType> (implements nct.graph.
WeightedNode
<IDType,WeightType>)
nct.service.homology.
BiojavaLocalBlast
(implements nct.service.homology.
HomologyModel
)
nct.search.
ColorCodingPathSearch
<NodeType> (implements nct.visualization.cytoscape.
Monitorable
, nct.search.
SearchGraph
<NodeType,WeightType>)
nct.networkblast.
CompatColorCodingPathSearch
<NodeType> (implements nct.search.
SearchGraph
<NodeType,WeightType>)
nct.networkblast.
CompatComplexSearch
<NodeType> (implements nct.search.
SearchGraph
<NodeType,WeightType>)
nct.networkblast.
CompatibilityNode
<NodeType,WeightType> (implements java.lang.Comparable<T>)
nct.networkblast.
CompatibilityScoreModel
(implements nct.score.
ScoreModel
<NodeType,WeightType>)
nct.visualization.cytoscape.
CytoscapeConverter
org.xml.sax.helpers.DefaultHandler (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
nct.service.interactions.
DIPInteractionNetwork
(implements nct.service.interactions.
InteractionNetwork
<NodeType,WeightType>)
nct.service.synonyms.
DIPSynonyms
(implements nct.service.synonyms.
SynonymMapper
)
nct.graph.util.
DegreePreservingRandomizer
<NodeType,WeightType> (implements nct.graph.util.
GraphRandomizer
<NodeType,WeightType>)
nct.networkblast.
ThresholdRandomizer
nct.service.sequences.
DIPSequenceDatabase
(implements nct.service.sequences.
SequenceDatabase
)
nct.visualization.cytoscape.dual.
DualLayout
nct.filter.
DuplicateThresholdFilter
<NodeType,WeightType> (implements nct.filter.
Filter
<NodeType,WeightType>)
nct.graph.util.
EdgeWeightShuffle
<NodeType,WeightType> (implements nct.graph.util.
GraphRandomizer
<NodeType,WeightType>)
nct.parsers.
FastaProteinParser
java.io.InputStream (implements java.io.Closeable)
java.io.FilterInputStream
nct.service.homology.
BlastXMLFileFilterInputStream
nct.service.homology.
LocalBlast
(implements nct.service.homology.
HomologyModel
)
nct.score.
LogLikelihoodScoreModel
<NodeType> (implements nct.score.
ScoreModel
<NodeType,WeightType>)
nct.visualization.cytoscape.
Monitor
nct.networkblast.
NetworkBlast
nct.search.
NewComplexSearch
<NodeType> (implements nct.visualization.cytoscape.
Monitorable
, nct.search.
SearchGraph
<NodeType,WeightType>)
nct.visualization.cytoscape.dual.
NodePairSet
nct.networkblast.
PathGraph
<NodeType> (implements java.lang.Cloneable, java.lang.Comparable<T>, nct.graph.
Graph
<NodeType,WeightType>)
nct.service.homology.
SIFHomologyReader
(implements nct.service.homology.
HomologyModel
)
nct.service.interactions.
SIFInteractionNetwork
(implements nct.service.interactions.
InteractionNetwork
<NodeType,WeightType>)
nct.parsers.
SIFParser
nct.output.
SIFWriter
<NodeType,WeightType>
nct.score.
SimpleEdgeScoreModel
<NodeType> (implements nct.score.
ScoreModel
<NodeType,WeightType>)
nct.score.
SimpleNodeScoreModel
<NodeType> (implements nct.score.
ScoreModel
<NodeType,WeightType>)
nct.score.
SimpleScoreModel
<NodeType> (implements nct.score.
ScoreModel
<NodeType,WeightType>)
nct.filter.
SortFilter
<NodeType,WeightType> (implements nct.filter.
Filter
<NodeType,WeightType>)
nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nct.networkblast.
TestSearch
java.lang.Thread (implements java.lang.Runnable)
nct.visualization.cytoscape.dual.
DualLayoutTask
nct.filter.
UniqueCompatNodeFilter
(implements nct.filter.
Filter
<NodeType,WeightType>)
nct.xml.
XMLSaxEventDistributor
<HandlerType> (implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.ErrorHandler)
nct.output.
ZIPSIFWriter
<NodeType,WeightType>
Interface Hierarchy
java.lang.Cloneable
nct.graph.
DistanceGraph
<NodeType,WeightType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
nct.graph.
Graph
<NodeType,WeightType> (also extends java.lang.Comparable<T>)
nct.graph.
DistanceGraph
<NodeType,WeightType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
nct.graph.
KPartiteGraph
<NodeType,WeightType,PartitionType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
nct.graph.
KPartiteGraph
<NodeType,WeightType,PartitionType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
java.lang.Comparable<T>
nct.graph.
DistanceGraph
<NodeType,WeightType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
nct.graph.
Edge
<NodeType,WeightType>
nct.graph.
Graph
<NodeType,WeightType> (also extends java.lang.Cloneable)
nct.graph.
DistanceGraph
<NodeType,WeightType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
nct.graph.
KPartiteGraph
<NodeType,WeightType,PartitionType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
nct.graph.
KPartiteGraph
<NodeType,WeightType,PartitionType>
nct.graph.
SequenceGraph
<NodeType,WeightType>
nct.graph.
WeightedNode
<IDType,WeightType>
nct.filter.
Filter
<NodeType,WeightType>
nct.graph.util.
GraphRandomizer
<NodeType,WeightType>
nct.service.homology.
HomologyModel
nct.service.interactions.
InteractionNetwork
<NodeType,WeightType>
nct.visualization.cytoscape.
Monitorable
nct.score.
ScoreModel
<NodeType,WeightType>
nct.search.
SearchGraph
<NodeType,WeightType>
nct.service.sequences.
SequenceDatabase
nct.service.synonyms.
SynonymMapper
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