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C

c1sigma - Variable in class edu.claflin.finder.algo.clustering.Walktrap.MutualConnectionsRecord

c2sigma - Variable in class edu.claflin.finder.algo.clustering.Walktrap.MutualConnectionsRecord

checkArgument(boolean) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, char, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, char, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, char, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, char, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, int, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, int, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, int, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, int, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, long, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, long, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, long, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, long, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object...) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkArgument(boolean, String, Object, Object, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkElementIndex(int, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkElementIndex(int, int, String) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNode(Node) - Method in class edu.claflin.finder.logic.Graph

Verifies that the node is NOT in the graph.

checkNodeGroupings(Graph) - Method in class edu.claflin.finder.algo.MatrixPatternAnalyzer

Deprecated.

Step 2: Iterate on Step 1 through all contiguous node groupings.

checkNodeIndex(int) - Method in class edu.claflin.finder.logic.Graph

Deprecated.

No replacement. Further operations shall utilize {)}

checkNotNull(T) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, char, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, char, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, char, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, char, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, int, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, int, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, int, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, int, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, long, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, long, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, long, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, long, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object...) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkNotNull(T, String, Object, Object, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkPositionIndex(int, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkPositionIndex(int, int, String) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkPositionIndexes(int, int, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, char, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, char, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, char, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, char, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, int, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, int, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, int, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, int, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, long, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, long, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, long, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, long, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object...) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object, char) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object, int) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object, long) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkState(boolean, String, Object, Object, Object, Object) - Static method in class edu.claflin.finder.algo.jungutils.Preconditions

checkSubGraphs(Graph, int) - Method in class edu.claflin.finder.algo.MatrixPatternAnalyzer

Deprecated.

Step 3: Repeat Step 2 for each "Cornered" Sub-matrix of the original Graph.

checkZeroMatrices(Graph, int) - Method in class edu.claflin.finder.algo.MatrixPatternAnalyzer

Deprecated.

Step 1: Check for valid 0 Sub-matrices.

clazz - Variable in class edu.claflin.finder.algo.jungutils.Predicates.InstanceOfPredicate

clazz - Variable in class edu.claflin.finder.algo.jungutils.Predicates.SubtypeOfPredicate

clear() - Method in class edu.claflin.finder.algo.jungutils.MapBinaryHeap

clear() - Method in class edu.claflin.finder.algo.jungutils.Pair

clear() - Method in class edu.claflin.finder.logic.communities.struct.BinarySearchTree

clearRow(int) - Method in class edu.claflin.finder.logic.communities.struct.fast_greedy_struct.SparseMatrix

Clear the ith tree and heap

CliqueCondition - Class in edu.claflin.finder.logic.cond

Represents a Clique condition.

CliqueCondition() - Constructor for class edu.claflin.finder.logic.cond.CliqueCondition

closestReachableUnvisited(HashMap<Node, Double>, Graph, Set<String>) - Method in class edu.claflin.finder.algo.DijkstraShortestPath

ClusteringAlgorithm - Class in edu.claflin.finder.algo.clustering

ClusteringAlgorithm(ArgumentsBundle) - Constructor for class edu.claflin.finder.algo.clustering.ClusteringAlgorithm

COMMON_ARGS(String) - Constructor for enum edu.claflin.finder.algo.ArgumentsBundle.COMMON_ARGS

CommonMatcher - Class in edu.claflin.finder.algo.jungutils

The subset of the Matcher API which is used by this package, and also shared with the re2j library.

CommonMatcher() - Constructor for class edu.claflin.finder.algo.jungutils.CommonMatcher

CommonPattern - Class in edu.claflin.finder.algo.jungutils

The subset of the Pattern API which is used by this package, and also shared with the re2j library.

CommonPattern() - Constructor for class edu.claflin.finder.algo.jungutils.CommonPattern

CommunicationListener - Interface in edu.claflin.finder.logic.cygrouper

communicator - Static variable in class edu.claflin.finder.logic.cygrouper.Communicator

Communicator - Class in edu.claflin.finder.logic.cygrouper

Communicator() - Constructor for class edu.claflin.finder.logic.cygrouper.Communicator

Communities - Class in edu.claflin.finder.logic.communities

Communities(HashMap<Integer, List<Node>>, Graph) - Constructor for class edu.claflin.finder.logic.communities.Communities

community - Variable in class edu.claflin.finder.logic.communities.struct.fast_greedy_struct.VectorValue

comp - Variable in class edu.claflin.finder.algo.jungutils.MapBinaryHeap

ComparableComparator() - Constructor for class edu.claflin.finder.algo.jungutils.MapBinaryHeap.ComparableComparator

compare(Prim.DistanceRecord, Prim.DistanceRecord) - Method in class edu.claflin.finder.algo.Prim.DistanceRecordComparator

compare(Edge, Edge) - Method in class edu.claflin.finder.algo.DijkstraShortestPath.EdgeComparator

compare(Edge, Edge) - Method in class edu.claflin.finder.logic.comp.EdgeWeightComparator

Compares the edges based on the D data held by the edge.

compare(Graph, Graph) - Method in class edu.claflin.finder.algo.Algorithm

Compares the two graphs based on edges.

compare(Graph, Graph) - Method in class edu.claflin.finder.logic.cygrouper.GraphAverageWeightComparator

compare(Graph, Graph) - Method in class edu.claflin.finder.logic.cygrouper.GraphSizeComparator

compare(T, T) - Method in class edu.claflin.finder.algo.jungutils.MapBinaryHeap.ComparableComparator

compare(V, V) - Method in class edu.claflin.finder.algo.jungutils.BetweennessCentrality.BetweennessComparator

compareTo(HeapNodeFG) - Method in class edu.claflin.finder.logic.communities.struct.fast_greedy_struct.HeapNodeFG

Compare this HeapNode to that HeapNode.

compareTo(HeapNodeFG) - Method in class edu.claflin.finder.logic.communities.struct.fast_greedy_struct.IndexedHeapNode

compareTo(TreeNode) - Method in class edu.claflin.finder.logic.communities.struct.TreeNode

compareTo(TreeNodeInfo) - Method in class edu.claflin.finder.logic.communities.struct.fast_greedy_struct.TreeNodeInfoFG

compareTo(HeapNodeWT) - Method in class edu.claflin.finder.logic.communities.struct.walk_trap_struct.HeapNodeWT

compareTo(Node) - Method in class edu.claflin.finder.logic.Node

compareToQ(HeapNodeFG) - Method in class edu.claflin.finder.logic.communities.struct.fast_greedy_struct.HeapNodeFG

components - Variable in class edu.claflin.finder.algo.jungutils.Predicates.AndPredicate

components - Variable in class edu.claflin.finder.algo.jungutils.Predicates.OrPredicate

compose(Function<B, C>, Function<A, ? extends B>) - Static method in class edu.claflin.finder.algo.jungutils.Functions

compose(Predicate<B>, Function<A, ? extends B>) - Static method in class edu.claflin.finder.algo.jungutils.Predicates

CompositionPredicate(Predicate<B>, Function<A, ? extends B>) - Constructor for class edu.claflin.finder.algo.jungutils.Predicates.CompositionPredicate

computeBetweenness(Queue<V>, Function<? super E, ? extends Number>) - Method in class edu.claflin.finder.algo.jungutils.BetweennessCentrality

Condition - Class in edu.claflin.finder.logic

Represents a graph condition in memory.

Condition() - Constructor for class edu.claflin.finder.logic.Condition

ConditionedGraph - Class in edu.claflin.finder.logic

Represents a "conditioned" graph.

ConditionedGraph(Graph, Collection<Condition>) - Constructor for class edu.claflin.finder.logic.ConditionedGraph

Private constructor used to create copies of ConditionedGraph objects.

ConditionedGraph(String) - Constructor for class edu.claflin.finder.logic.ConditionedGraph

Public constructor for creating a simple ConditionedGraph.

ConditionedGraph(String, Collection<Condition>) - Constructor for class edu.claflin.finder.logic.ConditionedGraph

Public constructor for creating a ConditionedGraph.

ConditionedGraph(String, Collection<Condition>, boolean) - Constructor for class edu.claflin.finder.logic.ConditionedGraph

Public constructor for creating a ConditionedGraph.

conditionOther(Graph) - Method in class edu.claflin.finder.logic.ConditionedGraph

Private method used for copying the ConditionedGraph.

conditions - Variable in class edu.claflin.finder.logic.ConditionedGraph

The List of Conditions applied to this Graph.

conditionsList - Variable in class edu.claflin.finder.algo.ArgumentsBundle

The List of conditions to apply to the Algorithm.

connectedCommunities(List<Node>, List<Node>) - Method in class edu.claflin.finder.logic.communities.Communities

ConnectedComponentsDFS - Class in edu.claflin.finder.algo

Processes a Graph searching for connected components by performing a depth first search on each node.

ConnectedComponentsDFS(ArgumentsBundle) - Constructor for class edu.claflin.finder.algo.ConnectedComponentsDFS

Public constructor for initializing the DepthFirstTraversalSearch with default conditions.

connections - Variable in class edu.claflin.finder.logic.cygrouper.CygrouperNode

constant(E) - Static method in class edu.claflin.finder.algo.jungutils.Functions

ConstantFunction(E) - Constructor for class edu.claflin.finder.algo.jungutils.Functions.ConstantFunction

constructArrayList(Set<Node>, Set<Node>) - Static method in class edu.claflin.finder.logic.BronKerboschBipartiteUtils

Constructs array list of array lists from sets.

contains(Object) - Method in class edu.claflin.finder.algo.jungutils.MapBinaryHeap

contains(Object) - Method in class edu.claflin.finder.algo.jungutils.Pair

contains(Pattern) - Static method in class edu.claflin.finder.algo.jungutils.Predicates

contains(T) - Method in class edu.claflin.finder.logic.communities.struct.BinarySearchTree

Is the specified ElemntType in the BinarySearchTree?

contains(T) - Method in class edu.claflin.finder.struct.DisjointSet

contains(T, TreeNode<T>) - Method in class edu.claflin.finder.logic.communities.struct.BinarySearchTree

containsAll(Collection<?>) - Method in class edu.claflin.finder.algo.jungutils.Pair

containsEdge(E) - Method in interface edu.claflin.finder.algo.jungutils.Hypergraph

Returns true if this graph's edge collection contains edge.

containsEdge(E) - Method in class edu.claflin.finder.algo.jungutils.SparseGraph

containsEdge(E) - Method in class edu.claflin.finder.algo.jungutils.UndirectedSparseGraph

containsNode(Node) - Method in class edu.claflin.finder.logic.Graph

Checks if the graph contains the given node.

ContainsPatternPredicate(CommonPattern) - Constructor for class edu.claflin.finder.algo.jungutils.Predicates.ContainsPatternPredicate

containsVertex(V) - Method in interface edu.claflin.finder.algo.jungutils.Hypergraph

Returns true if this graph's vertex collection contains vertex.

containsVertex(V) - Method in class edu.claflin.finder.algo.jungutils.SparseGraph

containsVertex(V) - Method in class edu.claflin.finder.algo.jungutils.UndirectedSparseGraph

convertCyfinderEdge(String, String) - Method in class edu.claflin.finder.logic.cygrouper.CygrouperAssembler

copy() - Method in class edu.claflin.finder.logic.communities.Communities

copy() - Method in class edu.claflin.finder.logic.ConditionedGraph

Copies this Graph object using the getSubGraph() method.

copy() - Method in class edu.claflin.finder.logic.Graph

Copies this Graph object using the getSubGraph() method.

counter - Variable in class edu.claflin.finder.algo.Algorithm

cprobs(List<Node>, Graph, List<Node>) - Method in class edu.claflin.finder.algo.clustering.Walktrap

Get a probability vector for a community.

createBackbone() - Method in class edu.claflin.finder.logic.communities.struct.BinarySearchTree

Time complexity: O(n)

createPerfectBST() - Method in class edu.claflin.finder.logic.communities.struct.BinarySearchTree

Time complexity: O(n)

cull(ArrayList<Graph>) - Method in class edu.claflin.finder.algo.Algorithm

Removes duplicate subGraphs from the provided ArrayList.

CygrouperAssembler - Class in edu.claflin.finder.logic.cygrouper

CygrouperAssembler(List<Edge>) - Constructor for class edu.claflin.finder.logic.cygrouper.CygrouperAssembler

CygrouperEdge - Class in edu.claflin.finder.logic.cygrouper

CygrouperEdge(String, String) - Constructor for class edu.claflin.finder.logic.cygrouper.CygrouperEdge

CygrouperNode - Class in edu.claflin.finder.logic.cygrouper

CygrouperNode(String) - Constructor for class edu.claflin.finder.logic.cygrouper.CygrouperNode

CytogrouperMain - Class in edu.claflin.finder.logic.cygrouper

CytogrouperMain(List<Graph>, CommunicationListener, int) - Constructor for class edu.claflin.finder.logic.cygrouper.CytogrouperMain

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