| Modifier and Type | Method and Description |
|---|---|
void |
Launcher.approximateMotifs(FastGraph targetGraph,
int minSize,
int maxSize,
int numOfClusters,
int iterations,
int subgraphsPerNode,
int attemptsToFindSubgraph)
Finds motifs using the approximate method
|
java.util.ArrayList<java.util.ArrayList<FastGraph>> |
KMedoids.cluster(java.util.ArrayList<FastGraph> subgraphs)
Clusters the subgraphs
|
void |
InducedSubgraph.createInducedSubgraph(java.util.LinkedList<java.lang.Integer> nodes,
java.util.LinkedList<java.lang.Integer> edges,
int numOfNodes)
Will populated nodes and edges with the nodeIndex and edgeIndex of all the nodes and edges of this subgraph.
Will create a subgraph with the required number of nodes in. |
void |
ExactMotifFinder.findMotifs(int k,
double q,
java.util.HashMap<java.lang.String,java.util.LinkedList<ExactMotifFinder.IsoHolder>> hashBuckets)
Run the motif finder.
|
void |
Launcher.findMotifs(uk.ac.kent.dover.fastGraph.Gui.MotifTask mt,
java.lang.String directory,
java.lang.String fileBaseName,
int minNum,
int maxNum,
boolean saveAll,
java.io.File reference)
Calls the method to find all motifs with the parameters given
|
void |
ExactMotifFinder.findMotifsRealSet(int minSize,
int maxSize)
Finds all motifs from the real set.
|
void |
ExactMotifFinder.findMotifsReferenceSet(int rewires,
int minSize,
int maxSize)
Finds all motifs from the reference set.
|
boolean |
ExactIsomorphism.isomorphic(FastGraph g)
Equality of graphs.
|
static boolean |
ExactIsomorphism.isomorphic(FastGraph g1,
FastGraph g2)
Check if two graphs have the same structure.
|
boolean |
ExactIsomorphism.isomorphic(FastGraph g,
int[] nodes,
int[] edges)
Check if the two graphs have the same structure.
|
void |
FastGraph.populateRandomGraph(boolean simple,
long seed)
Creates a graph with the size specified by numberOfNodes and numberOfEdges.
|
void |
Profiler.profileExactMotif(int size)
Profiles the exact motif finder for a given size
|
void |
Profiler.profileExactMotifMultiple(int minSize,
int maxSize)
This will run the exact motif finder multiple times, rather than finding a range.
|
static <T> java.util.ArrayList<T> |
Util.randomSelection(java.util.Random r,
int number,
java.util.ArrayList<T> target)
Picks a random sublist of a list.
|
FastGraph |
FastGraph.removeNodesAndEdgesFromGraph(java.util.LinkedList<java.lang.Integer> nodes,
java.util.LinkedList<java.lang.Integer> edges,
int targetNodes,
int targetEdges)
This method creates a new FastGraph of the rough size given in targetNodes and targetEdges.
|
| Constructor and Description |
|---|
ExactIsomorphism(FastGraph fastGraph)
Create an ExactIsomorphism before running isomorphic.
|