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## C

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 {)}
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.
CliqueCondition - Class in edu.claflin.finder.logic.cond
  Represents a Clique condition.
CliqueCondition() - Constructor for class edu.claflin.finder.logic.cond.CliqueCondition
COMMON_ARGS(String) - Constructor for enum edu.claflin.finder.algo.ArgumentsBundle.COMMON_ARGS
CommunicationListener - Interface in edu.claflin.finder.logic.cygrouper
Communicator - Class in edu.claflin.finder.logic.cygrouper
Communicator() - Constructor for class edu.claflin.finder.logic.cygrouper.Communicator
communicator - Static variable in class edu.claflin.finder.logic.cygrouper.Communicator
compare(Graph, Graph) - Method in class edu.claflin.finder.algo.Algorithm
  Compares the two graphs based on edges.
compare(Edge, Edge) - Method in class edu.claflin.finder.logic.comp.EdgeWeightComparator
  Compares the edges based on the D data held by the edge.
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(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.
ConditionedGraph(Graph, Collection<Condition>) - Constructor for class edu.claflin.finder.logic.ConditionedGraph
  Private constructor used to create copies of ConditionedGraph objects.
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.
connections - Variable in class edu.claflin.finder.logic.cygrouper.CygrouperNode
convertCyfinderEdge(String, String) - Method in class edu.claflin.finder.logic.cygrouper.CygrouperAssembler
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
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) - Constructor for class edu.claflin.finder.logic.cygrouper.CytogrouperMain

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