Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Z
N
nct.filter
- package nct.filter
nct.graph
- package nct.graph
nct.graph.basic
- package nct.graph.basic
nct.graph.util
- package nct.graph.util
nct.networkblast
- package nct.networkblast
nct.networkblast.filter
- package nct.networkblast.filter
nct.networkblast.graph
- package nct.networkblast.graph
nct.networkblast.graph.compatibility
- package nct.networkblast.graph.compatibility
nct.networkblast.score
- package nct.networkblast.score
nct.networkblast.search
- package nct.networkblast.search
nct.output
- package nct.output
nct.parsers
- package nct.parsers
nct.service.homology
- package nct.service.homology
nct.service.homology.blast
- package nct.service.homology.blast
nct.service.homology.sif
- package nct.service.homology.sif
nct.service.interactions
- package nct.service.interactions
nct.service.sequences
- package nct.service.sequences
nct.service.synonyms
- package nct.service.synonyms
nct.visualization.cytoscape.dual
- package nct.visualization.cytoscape.dual
nct.xml
- package nct.xml
NetworkBlast
- Class in
nct.networkblast
The main program (NetworkBlast.java) will create all the objects needed to run the NetworkBlast algorithm.
NetworkBlast(String[])
- Constructor for class nct.networkblast.
NetworkBlast
This is the main class that initializes and executes everything.
NewComplexSearch
<
NodeType
extends java.lang.Comparable<? super
NodeType
>> - Class in
nct.networkblast.search
This class implements the SearchGraph interface.
NewComplexSearch(int, int)
- Constructor for class nct.networkblast.search.
NewComplexSearch
Sets the max and min sizes for complexes.
NewComplexSearch(int, int, boolean, List<Graph<NodeType, Double>>)
- Constructor for class nct.networkblast.search.
NewComplexSearch
node2Index
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
node2Species
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nodeCount
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nodeDistanceRestLengthConstant
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nodeDistanceSpringRestLengths
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nodeDistanceSpringScalars
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nodeDistanceSpringStrengths
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nodeDistanceStrengthConstant
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
nodeId
- Variable in class nct.service.interactions.
DIPInteractionNetwork
nodeOrganismMap
- Variable in class nct.service.interactions.
DIPInteractionNetwork
NodePairSet
- Class in
nct.visualization.cytoscape.dual
This class keeps track of a set of unordered pairs of nodes
NodePairSet()
- Constructor for class nct.visualization.cytoscape.dual.
NodePairSet
normalize
- Variable in class nct.service.homology.blast.
LocalBlast
Whether or not to normalize e-values based on database size.
notationDecl(String, String, String)
- Method in class nct.xml.
XMLSaxEventDistributor
numberOfEdges()
- Method in class nct.graph.basic.
BasicGraph
Returns the number of edges in the graph.
numberOfEdges()
- Method in interface nct.graph.
Graph
Returns the number of edges in the graph.
numberOfNodes()
- Method in class nct.graph.basic.
BasicGraph
Returns the number of nodes in the graph.
numberOfNodes()
- Method in interface nct.graph.
Graph
Returns the number of nodes in the graph.
numEdges
- Variable in class nct.graph.basic.
BasicGraph
The number of edges in the graph.
numLayoutPasses
- Variable in class nct.visualization.cytoscape.dual.
SpringEmbeddedLayouter
numSimulations
- Variable in class nct.networkblast.
NetworkBlast
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
Q
R
S
T
U
V
W
X
Z