## Uses of Class
edu.claflin.finder.logic.Graph

- Packages that use Graph
  Package | Description
  --- | ---
  edu.claflin.finder | Subgraph Finder - Used to find and locate subgraphs within a network.
  edu.claflin.finder.algo | Contains the Algorithm code for finding bipartite subgraphs.
  edu.claflin.finder.io.graph | Contains the specific graph formats supported by the SNBA program family.
  edu.claflin.finder.io.graph.sub | Contains the general classes used to support extensibility of the IO classes.
  edu.claflin.finder.logic | Contains the data structure and processing code-base.
  edu.claflin.finder.logic.cond | Contains Condition implementations for identifying subgraph types.
  edu.claflin.finder.logic.cygrouper |

- - ### Uses of Graph in edu.claflin.finder

    Method parameters in edu.claflin.finder with type arguments of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `private static void` | Main.`writeGraphs(java.util.ArrayList<Graph> graphs, java.lang.String output, GraphWriter writer)` Writes Graph objects to memory.

  - ### Uses of Graph in edu.claflin.finder.algo

    Methods in edu.claflin.finder.algo that return Graph
    Modifier and Type | Method and Description
    --- | ---
    `private Graph` | MatrixPatternAnalyzer.`checkSubGraphs(Graph inGraph, int transpositions)` Deprecated. Step 3: Repeat Step 2 for each "Cornered" Sub-matrix of the original Graph.
    `private Graph` | DepthFirstTraversalSearch.`searchNode(Graph graph, Graph subGraph, Node node, java.util.List<Node> visited)` Helper method to search for the SubGraphs.
    `private Graph` | BreadthFirstTraversalSearch.`searchNode(Graph graph, Node node)` Helper method to search for the SubGraphs.

    Methods in edu.claflin.finder.algo that return types with arguments of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `protected java.util.ArrayList<Graph>` | Algorithm.`cull(java.util.ArrayList<Graph> subGraphs)` Removes duplicate subGraphs from the provided ArrayList.
    `java.util.ArrayList<Graph>` | BreadthFirstTraversalSearch.`process(Graph graph)` Processes data.
    `java.util.ArrayList<Graph>` | Bundle.`process(Graph graph)` Processes data.
    `java.util.ArrayList<Graph>` | DepthFirstTraversalSearch.`process(Graph graph)` Processes data.
    `java.util.ArrayList<Graph>` | MatrixPatternAnalyzer.`process(Graph graph)` Deprecated. Processes data.

    Methods in edu.claflin.finder.algo with parameters of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `private boolean` | MatrixPatternAnalyzer.`checkNodeGroupings(Graph inGraph)` Deprecated. Step 2: Iterate on Step 1 through all contiguous node groupings.
    `private Graph` | MatrixPatternAnalyzer.`checkSubGraphs(Graph inGraph, int transpositions)` Deprecated. Step 3: Repeat Step 2 for each "Cornered" Sub-matrix of the original Graph.
    `private boolean` | MatrixPatternAnalyzer.`checkZeroMatrices(Graph inGraph, int nodeCap)` Deprecated. Step 1: Check for valid 0 Sub-matrices.
    `private boolean` | Algorithm.`compare(Graph base, Graph match)` Compares the two graphs based on edges.
    `java.util.ArrayList<Graph>` | BreadthFirstTraversalSearch.`process(Graph graph)` Processes data.
    `java.util.ArrayList<Graph>` | Bundle.`process(Graph graph)` Processes data.
    `java.util.ArrayList<Graph>` | DepthFirstTraversalSearch.`process(Graph graph)` Processes data.
    `java.util.ArrayList<Graph>` | MatrixPatternAnalyzer.`process(Graph graph)` Deprecated. Processes data.
    `private boolean` | Algorithm.`reorder(Graph base, Graph match)` Deprecated. No replacement. There is no longer a need to reorder graphs to test equality.
    `private Graph` | DepthFirstTraversalSearch.`searchNode(Graph graph, Graph subGraph, Node node, java.util.List<Node> visited)` Helper method to search for the SubGraphs.
    `private Graph` | BreadthFirstTraversalSearch.`searchNode(Graph graph, Node node)` Helper method to search for the SubGraphs.

    Method parameters in edu.claflin.finder.algo with type arguments of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `protected java.util.ArrayList<Graph>` | Algorithm.`cull(java.util.ArrayList<Graph> subGraphs)` Removes duplicate subGraphs from the provided ArrayList.

  - ### Uses of Graph in edu.claflin.finder.io.graph

    Methods in edu.claflin.finder.io.graph that return Graph
    Modifier and Type | Method and Description
    --- | ---
    `Graph` | SIFGraphIO.`parseGraph(java.io.File source, boolean undirected)` Reads a graph from memory.
    `Graph` | SimpleGraphIO.`parseGraph(java.io.File source, boolean undirected)` Reads a graph from memory.

    Methods in edu.claflin.finder.io.graph with parameters of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `void` | NOABatchIO.`writeGraph(Graph toWrite)` Writes graphs to memory.
    `void` | SIFGraphIO.`writeGraph(Graph toWrite)` Writes graphs to memory.
    `void` | SimpleGraphIO.`writeGraph(Graph toWrite)` Writes graphs to memory.

  - ### Uses of Graph in edu.claflin.finder.io.graph.sub

    Methods in edu.claflin.finder.io.graph.sub that return Graph
    Modifier and Type | Method and Description
    --- | ---
    `Graph` | GraphReader.`parseGraph(java.io.File source, boolean undirected)` Reads a graph from memory.

    Methods in edu.claflin.finder.io.graph.sub with parameters of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `void` | GraphWriter.`writeGraph(Graph toWrite)` Writes graphs to memory.

  - ### Uses of Graph in edu.claflin.finder.logic

    Subclasses of Graph in edu.claflin.finder.logic
    Modifier and Type | Class and Description
    --- | ---
    `class` | `ConditionedGraph` Represents a "conditioned" graph.

    Methods in edu.claflin.finder.logic that return Graph
    Modifier and Type | Method and Description
    --- | ---
    `Graph` | Graph.`copy()` Copies this Graph object using the getSubGraph() method.
    `Graph` | Graph.`getSubGraph(java.util.ArrayList<java.lang.String> subStringSet, java.lang.String nameQualifier)` Deprecated. Outdated since v3. Replaced by `getSubGraph(java.util.List, java.lang.String)`
    `Graph` | Graph.`getSubGraph(int startNode, int stopNode, java.lang.String nameQualifier)` Deprecated. Outdated since v3. Replaced by `getSubGraph(java.util.List, java.lang.String)`
    `Graph` | Graph.`getSubGraph(java.util.List<Node> nodes, java.lang.String nameQualifier)` Returns a subGraph of this graph.
    `Graph` | Graph.`uniqueCopy()` Copies this Graph producing a unique copy in which there is no entanglement between the two Graph objects.

    Methods in edu.claflin.finder.logic with parameters of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `private ConditionedGraph` | ConditionedGraph.`conditionOther(Graph graph)` Private method used for copying the ConditionedGraph.
    `abstract boolean` | Condition.`satisfies(Graph existingGraph)` Used to test if the supplied graph is within the bounds of the condition's implementation.

    Constructors in edu.claflin.finder.logic with parameters of type Graph
    Constructor and Description
    `ConditionedGraph(Graph graph, java.util.Collection<Condition> conditions)` Private constructor used to create copies of ConditionedGraph objects.

  - ### Uses of Graph in edu.claflin.finder.logic.cond

    Methods in edu.claflin.finder.logic.cond with parameters of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `boolean` | BipartiteCondition.`satisfies(Graph existingGraph)`
    `boolean` | CliqueCondition.`satisfies(Graph existingGraph)` Used to test if the supplied graph is within the bounds of the condition's implementation.
    `boolean` | DirectedCliqueCondition.`satisfies(Graph existingGraph)` Used to test if the supplied graph is within the bounds of the condition's implementation.
    `private boolean` | BipartiteCondition.`satisfies(Graph existingGraph, java.util.Set<Node> addSet, java.util.Set<Node> compareSet, Node current)` Private method for stepping through the adjacency lists and determining if the graph is bipartite.

  - ### Uses of Graph in edu.claflin.finder.logic.cygrouper

    Fields in edu.claflin.finder.logic.cygrouper with type parameters of type Graph
    Modifier and Type | Field and Description
    --- | ---
    `static java.util.ArrayList<Graph>` | Communicator.`uniqueSubgraphs`

    Method parameters in edu.claflin.finder.logic.cygrouper with type arguments of type Graph
    Modifier and Type | Method and Description
    --- | ---
    `void` | CommunicationListener.`setUniqueSubGraphs(java.util.ArrayList<Graph> subgraphs)`
    `void` | Communicator.`setUniqueSubGraphs(java.util.ArrayList<Graph> subgraphs)`

    Constructor parameters in edu.claflin.finder.logic.cygrouper with type arguments of type Graph
    Constructor and Description
    `CytogrouperMain(java.util.List<Graph> subgraphs, CommunicationListener listener)`