All Classes Interface Summary Class Summary Enum Summary
| Class |
Description |
| AbstractGraph<V,E> |
Abstract implementation of the Graph interface.
|
| AbstractTypedGraph<V,E> |
An abstract class for graphs whose edges all have the same EdgeType.
|
| Algorithm |
Abstraction of the algorithm classes used for finding subgraphs.
|
| Algorithm.GraphSortOrder |
|
| ArgumentsBundle |
Used to supply arguments to Algorithms in a generalized manner.
|
| ArgumentsBundle.COMMON_ARGS |
An enumeration containing common arguments used by the program.
|
| BatchProcessor<T,S> |
Used to process one or multiple objects.
|
| BetweennessCentrality<V,E> |
Computes betweenness centrality for each vertex and edge in the graph.
|
| BinarySearchTree<T extends TreeNodeInfo> |
|
| BipartiteCondition |
Represents a bipartite graph as a Condition object.
|
| BreadthFirstTraversalSearch |
Processes a Graph searching for subgraphs by performing a breadth
first search on each node of the graph. |
| BronKerbosch |
Finds Maximum Cliques and Bicliques with Bron Kersboch Algorithm.
|
| BronKerboschBipartiteUtils |
Provides methods to mark graphs as bipartite using the basic Graph, Edge, and
Node classes.
|
| Bundle |
Processes a Graph searching for subgraphs. |
| CliqueCondition |
Represents a Clique condition.
|
| ClusteringAlgorithm |
|
| CommonMatcher |
The subset of the Matcher API which is used by this
package, and also shared with the re2j library.
|
| CommonPattern |
The subset of the Pattern API which is used by this
package, and also shared with the re2j library.
|
| CommunicationListener |
|
| Communicator |
|
| Communities |
|
| Condition |
Represents a graph condition in memory.
|
| ConditionedGraph |
Represents a "conditioned" graph.
|
| ConnectedComponentsDFS |
Processes a Graph searching for connected components by performing a
depth first search on each node. |
| CygrouperAssembler |
|
| CygrouperEdge |
|
| CygrouperNode |
|
| CytogrouperMain |
|
| DepthFirstTraversalSearch |
Processes a Graph searching for bipartite subgraphs by performing a
depth first search on each node. |
| DijkstraShortestPath |
|
| DirectedCliqueCondition |
Represents a Directed Clique condition.
|
| DisjointSet<T extends java.lang.Comparable<T>> |
A LinkedList-based Disjoint Set data structure.
|
| Edge<D> |
Represents an Edge in memory.
|
| EdgeBetweennessClusterer<V,E> |
An algorithm for computing clusters (community structure) in graphs based on
edge betweenness.
|
| EdgeScorer<E,S> |
An interface for algorithms that assign scores to edges.
|
| EdgeType |
Defines the possible edge types for graphs which assign types to edges.
|
| EdgeWeightComparator |
A simple edge weight comparator in which the edge data is considered a
numeric value and used as the comparison benchmark.
|
| FastGreedy |
FastGreedu Algorithm
https://ece-research.unm.edu/ifis/papers/community-moore.pdf
|
| Function<F,T> |
|
| Functions |
|
| Functions.ConstantFunction<E> |
|
| Functions.ForMapWithDefault<K,V> |
|
| Functions.FunctionComposition<A,B,C> |
|
| Functions.FunctionForMapNoDefault<K,V> |
|
| Functions.IdentityFunction |
|
| Functions.PredicateFunction<T> |
|
| Functions.SupplierFunction<T> |
|
| Functions.ToStringFunction |
|
| GirvanNewman |
Edge Betweenness clustering with Girvan Newman Algorithm
https://en.wikipedia.org/wiki/Girvan%E2%80%93Newman_algorithm
|
| Global |
Holds "Global" data that needs to be accessed by multiple parts of the
program.
|
| Graph<V,E> |
A graph consisting of a set of vertices of type V set and a set
of edges of type E.
|
| Graph |
Used to represent a graph in memory.
|
| GraphAverageWeight |
|
| GraphAverageWeightComparator |
|
| GraphReader |
Interface used for classes designed to read graphs from memory.
|
| GraphSizeComparator |
|
| GraphWriter |
Interface used by classes that write graphs to memory.
|
| HeapNodeFG |
|
| HeapNodeWT |
|
| Hypergraph<V,E> |
A hypergraph, consisting of a set of vertices of type V and a
set of hyperedges of type E which connect the vertices.
|
| IndexedHeapNode |
|
| IndexedHeapQueue |
|
| JdkPattern |
|
| JdkPattern.JdkMatcher |
|
| Kruskal |
|
| LogLevel |
Enumeration of the logging levels for the user.
|
| LogType |
Enumeration of the logging types used by the logging utility.
|
| LogUtil |
Logging utility for documenting the state of the program.
|
| Main |
Interprets the command line arguments provided to the program.
|
| ManifestParser |
Reads manifest files.
|
| MapBinaryHeap<T> |
|
| MatrixPatternAnalyzer |
Deprecated.
|
| NOABatchIO |
A class for writing graphs in the NOA batch format.
|
| Node |
Represents a node in memory.
|
| Pair<T> |
An implementation of Collection that stores exactly 2 non-null
objects and is not mutable.
|
| Preconditions |
|
| Predicate<T> |
|
| Predicates |
|
| Predicates.AndPredicate<T> |
|
| Predicates.CompositionPredicate<A,B> |
|
| Predicates.ContainsPatternPredicate |
|
| Predicates.InPredicate<T> |
|
| Predicates.InstanceOfPredicate |
|
| Predicates.IsEqualToPredicate<T> |
|
| Predicates.NotPredicate<T> |
|
| Predicates.ObjectPredicate |
|
| Predicates.OrPredicate<T> |
|
| Predicates.SubtypeOfPredicate |
|
| Prim |
|
| PrioritySet<T> |
Represents a PrioritySet.
|
| Processable<T,S> |
Represents an operation that can be carried out on a specific type of data.
|
| ShortestPath |
|
| SIFGraphIO |
A class for reading and writing graphs in the SIF format.
|
| SimpleGraphIO |
A class for reading and writing graphs.
|
| SparseGraph<V,E> |
An implementation of Graph that is suitable for sparse graphs
and permits both directed and undirected edges.
|
| SparseMatrix |
SparseMatrix is a sparse matrix with row format.
|
| TreeNode<T extends TreeNodeInfo> |
The basic unit of the BinarySearchTree.
|
| TreeNodeInfo |
|
| TreeNodeInfoFG |
|
| UndirectedGraph<V,E> |
A tagging interface for extensions of Graph that accept only
undirected edges.
|
| UndirectedSparseGraph<V,E> |
An implementation of UndirectedGraph that is suitable for sparse
graphs.
|
| VectorValue |
|
| VertexScorer<V,S> |
An interface for algorithms that assign scores to vertices.
|
| Walktrap |
Community detection with the Walktrap Algorithm.
|
| WeakComponentClusterer<V,E> |
Finds all weak components in a graph as sets of vertex sets.
|