- checkConsistency() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Check the consistency of a graph.
- checkForPositiveInteger(String) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Checks if a String is a positive integer.
- cloneByteBuffer(ByteBuffer) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Deep copy of ByteBuffer.
- cluster(ArrayList<FastGraph>) - Method in class uk.ac.kent.dover.fastGraph.KMedoids
-
Clusters the subgraphs
- compareAndExportResults(int, int, int) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Compares the results from the reference set to the real set.
Exports these in a user friendly manner
- compareByEigenvalues(FastGraph) - Method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Compare graphs by their eigenvalues
- compareEigenValues(double[]) - Method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Compare eigenvalues
- compareMotifDatas(int, int) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Runs the comparison of motif data for each size given
- comparisonScore(FastGraph, FastGraph) - Method in class uk.ac.kent.dover.fastGraph.KMedoids
-
Returns the comparison score of the two graphs.
- Connected - Class in uk.ac.kent.dover.fastGraph
-
Class to test graph connectivity.
- Connected() - Constructor for class uk.ac.kent.dover.fastGraph.Connected
-
- connected(FastGraph) - Static method in class uk.ac.kent.dover.fastGraph.Connected
-
Breadth first search through the graph.
- CONNECTION_EDGE_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- CONNECTION_NODE_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- CONNECTION_PAIR_SIZE - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- convertArray(int[]) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts an int[] to a LinkedList of Integer using streams
- convertArray(int[], LinkedList<Integer>) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts an int[] to a LinkedList of Integer using streams
- convertArray(int[], HashSet<Integer>) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts an int[] to a HashSet of Integer using streams
- convertArrayList(ArrayList<Integer>) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts a ArrayList of Integer to an int[] using streams
- convertGraphToBuffers(int, int, String, String, boolean) - Method in class uk.ac.kent.dover.fastGraph.Launcher
-
Calls the conversion method to convert an Adjacency List to Buffers
- convertHashSet(HashSet<Integer>) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts a HashSet of Integer to int[]
- convertHashSet(int[], HashSet<Integer>) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts a HashSet of Integer to a given int[]
- convertLinkedList(LinkedList<Integer>) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts a LinkedList of Integer to an int[] using streams
- convertLinkedList(LinkedList<Integer>, int[]) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts a LinkedList of Integer to a given int[] using streams
- convertLinkedListObject(LinkedList<T>, T[]) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Converts a LinkedList of any given object into an array of that object
- countInstancesOfNodeDegrees(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Counts the number of instances of nodes with various degrees.
- countNodesOfAge(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Counts the number of nodes at the given age
- createInducedSubgraph(LinkedList<Integer>, LinkedList<Integer>, int) - Method in class uk.ac.kent.dover.fastGraph.InducedSubgraph
-
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.
- createTime() - Static method in class uk.ac.kent.dover.fastGraph.Debugger
-
Returns the current time for time keeping
- EDGE_AGE_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- EDGE_BYTE_SIZE - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- EDGE_LABEL_LENGTH_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- EDGE_LABEL_START_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- EDGE_NODE1_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- EDGE_NODE2_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- EDGE_TYPE_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- EDGE_WEIGHT_OFFSET - Static variable in class uk.ac.kent.dover.fastGraph.FastGraph
-
- edgesBetween(int, int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Find the edges between two nodes
- EdgeStructure - Class in uk.ac.kent.dover.fastGraph
-
A class for storing information about an edge when modifying a fast graph.
- EdgeStructure(int, String, int, byte, byte, int, int) - Constructor for class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- enabled - Static variable in class uk.ac.kent.dover.fastGraph.Debugger
-
- EnumerateSubgraphFanmod - Class in uk.ac.kent.dover.fastGraph
-
Algorithm to generate subgraphs for motif detection, based on: A Faster Algorithm for Detecting Network Motifs, Sebastian Wernicke (2005)
Variable names in this class are an attempt to match those in the algorithm in the paper
- EnumerateSubgraphFanmod(FastGraph) - Constructor for class uk.ac.kent.dover.fastGraph.EnumerateSubgraphFanmod
-
- EnumerateSubgraphNeighbourhood - Class in uk.ac.kent.dover.fastGraph
-
Creates subgraphs based on neighbourhood sampling
- EnumerateSubgraphNeighbourhood(FastGraph) - Constructor for class uk.ac.kent.dover.fastGraph.EnumerateSubgraphNeighbourhood
-
Trivial constructor
- EnumerateSubgraphRandom - Class in uk.ac.kent.dover.fastGraph
-
Generates subgraphs randomly
- EnumerateSubgraphRandom(FastGraph) - Constructor for class uk.ac.kent.dover.fastGraph.EnumerateSubgraphRandom
-
Trivial constructor
- enumerateSubgraphs(int, double) - Method in class uk.ac.kent.dover.fastGraph.EnumerateSubgraphFanmod
-
ESU - Returns all size-k subgraphs in the FastGraph.
- enumerateSubgraphs(int, int, int) - Method in class uk.ac.kent.dover.fastGraph.EnumerateSubgraphNeighbourhood
-
Generates a set of subgraphs based on neighbourhoods.
The system will generate a neighbourhood for each node.
- enumerateSubgraphsFromNode(int, int, int, int, Random, HashSet<FastGraph>) - Method in class uk.ac.kent.dover.fastGraph.EnumerateSubgraphNeighbourhood
-
Generates a set of subgraphs from a given node
- ExactIsomorphism - Class in uk.ac.kent.dover.fastGraph
-
Testing the structural similarity of two FastGraphs
- ExactIsomorphism(FastGraph) - Constructor for class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Create an ExactIsomorphism before running isomorphic.
- ExactMotifFinder - Class in uk.ac.kent.dover.fastGraph
-
- ExactMotifFinder(FastGraph, boolean) - Constructor for class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Trivial contructor
- ExactMotifFinder(FastGraph, MotifTask, boolean) - Constructor for class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Trivial constructor
- ExactMotifFinder.IsoHolder - Class in uk.ac.kent.dover.fastGraph
-
Class to hold a FastGraph key and the number of instances of that FastGraph for a particular key.
Graphs are loaded from disk.
- ExactMotifFinder.MotifResultHolder - Class in uk.ac.kent.dover.fastGraph
-
Inner class to hold details of motifs ready for output
- ExactSubgraphIsomorphism - Class in uk.ac.kent.dover.fastGraph
-
Testing the containment of a FastGraph inside another FastGraph.
- ExactSubgraphIsomorphism(FastGraph, FastGraph, NodeComparator, EdgeComparator) - Constructor for class uk.ac.kent.dover.fastGraph.ExactSubgraphIsomorphism
-
- exactSubgraphs(FastGraph, FastGraph) - Method in class uk.ac.kent.dover.fastGraph.Launcher
-
Calls the method to find subgraphs using the exact subgraph finder
- extractGraphLists(HashMap<String, LinkedList<ExactMotifFinder.IsoHolder>>) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
This extracts the lists of isomorphic graphs.
- FastGraph - Class in uk.ac.kent.dover.fastGraph
-
Graph class with redundant node connections.
- FastGraphEdgeType - Enum in uk.ac.kent.dover.fastGraph
-
Enum to hold the various edge types in the data.
- FastGraphException - Exception in uk.ac.kent.dover.fastGraph
-
Exception thrown and caught when an error within Fast Graph occurs that can't be described by the other
exception types, but needs to be reported.
- FastGraphException() - Constructor for exception uk.ac.kent.dover.fastGraph.FastGraphException
-
Creates Exception with no message
- FastGraphException(String) - Constructor for exception uk.ac.kent.dover.fastGraph.FastGraphException
-
Creates Exception with a message
- FastGraphException(String, Throwable) - Constructor for exception uk.ac.kent.dover.fastGraph.FastGraphException
-
Creates Exception with a message
- FastGraphException(Throwable) - Constructor for exception uk.ac.kent.dover.fastGraph.FastGraphException
-
Creates Exception with a message
- FastGraphNodeType - Enum in uk.ac.kent.dover.fastGraph
-
Enum to hold the various node types in the data.
- findAllEdgesOfAge(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Finds a list of all edges of the given age
- findAllNodesOfAge(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Finds a list of all nodes of the given age
- findDegreeBuckets(int[], int[]) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
populate buckets index with the number of nodes that have degree index
- findDegrees() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Finds the the degrees of each node.
- findDegreesOfAge(int, ArrayList<Integer>) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Finds the the degrees of each node at a certain age.
- findEigenvalues(int[][]) - Method in class uk.ac.kent.dover.fastGraph.AdjacencyMatrix
-
Finds the eigenvalue of a matrix
Taken from: http://introcs.cs.princeton.edu/java/95linear/Eigenvalues.java.html
- findEigenvalues(boolean[][]) - Method in class uk.ac.kent.dover.fastGraph.AdjacencyMatrix
-
Finds the eigenvalue of a matrix
Taken from: http://introcs.cs.princeton.edu/java/95linear/Eigenvalues.java.html
- findEigenvalues(double[][]) - Method in class uk.ac.kent.dover.fastGraph.AdjacencyMatrix
-
Finds the eigenvalue of a matrix
Taken from: http://introcs.cs.princeton.edu/java/95linear/Eigenvalues.java.html
- findGenerationSubGraph(byte, boolean) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Return a new FastGraph that is the nodes and edges of a particular generation
of this FastGraph.
- findMaximumEdgeAge() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- findMaximumNodeAge() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- findMinimumEdgeAge() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- findMinimumNodeAge() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- findMotifs(int, double, HashMap<String, LinkedList<ExactMotifFinder.IsoHolder>>) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Run the motif finder.
- findMotifs(MotifTask, String, String, int, int, boolean, File) - Method in class uk.ac.kent.dover.fastGraph.Launcher
-
Calls the method to find all motifs with the parameters given
- findMotifsRealSet(int, int) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Finds all motifs from the real set.
- findMotifsReferenceSet(int, int, int) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Finds all motifs from the reference set.
- findNeighbours(FastGraph, int) - Static method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
gives the neighbours of nodes in g, without duplicates and without self sourcing.
- findParallelEdges() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Outputs a list where each element is a list of parallel edges
- gedTime - Variable in class uk.ac.kent.dover.fastGraph.KMedoids
-
- generateDifference() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
Generates the difference of these results.
- generateDisplayGraph() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Creates a displayGraph.Graph which can then be accessed, manipulated and visualized
using that package.
- generateGraphByDeletingItems(int[], int[], boolean) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Generates a new graph from the subgraph specified by the parameters.
- generateGraphFromSubgraph(int[], int[]) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Generates a new graph from the subgraph specified by the parameters.
- generateRandomGraph(File, int, int, boolean, boolean) - Method in class uk.ac.kent.dover.fastGraph.Launcher
-
Generates a random graph
- generateRandomIsomorphicGraph(FastGraph, long, boolean) - Static method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Generates a random graph isomorphic to the input one.
- generateRandomRewiredGraph(int, long) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
This generates a new random graph based on the existing graph, but with rewired edges.
- generateRewiredBehaviourGraphWithRandomGenerations(int, long, double, double, int, int, boolean, boolean) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Create a graph.
- generateRewiredGraph(List<int[]>) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Generates a new graph from the changes in edge wiring specified.
- generateSignificance() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
Generates the significance of this result.
- generateStringForHash() - Method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Generate a string that can be used to put graph in buckets before final brute force comparison.
- generateTimeString() - Method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Generates a count of the nodes at each age.
Uses relative ages, so if a graph had 1 node of age 4, 2 of age 5 and 3 of age 6, would be represented as [1,2,3]
- getAge() - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- getAge() - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
-
- getConnectionBuf() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getDirect() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeAge(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeBuf() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeLabel(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeLabelBuf() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeLabelString() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Gets a big string of the edge labels.
- getEdgeMapping() - Method in class uk.ac.kent.dover.fastGraph.SubgraphMapping
-
- getEdgeNode1(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeNode2(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeType(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getEdgeWeight(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getForename() - Method in class uk.ac.kent.dover.fastGraph.NamePicker
-
Returns a forename, based on weighted probabilities.
- getFoundMappings() - Method in class uk.ac.kent.dover.fastGraph.ExactSubgraphIsomorphism
-
Call this after subGraphIsomorphismFinder.
- getFromHashSet(HashSet<T>, int) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Gets a specific numbered item from the HashSet given.
There is no guarantee this may pick the same entry if run multiple times.
- getGeneration() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getGraph() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.IsoHolder
-
Loads the graph from disk
- getHashBuckets() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Returns the hashbuckets from this instance
- getId() - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- getId() - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
-
- getKey() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.IsoHolder
-
Gets the key
- getKey() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
- getLabel() - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- getLabel() - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
-
- getLastMatch() - Method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Call this after getting true from a call to isomorphism().
- getName() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getName() - Method in class uk.ac.kent.dover.fastGraph.Name
-
- getName() - Method in class uk.ac.kent.dover.fastGraph.NamePicker
-
Returns a full name, using the getForename() and getSurname() methods;
- getNames(int) - Method in class uk.ac.kent.dover.fastGraph.NamePicker
-
Returns a list of full names
- getNode1() - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- getNode2() - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- getNodeAge(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeBuf() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeConnectingEdges(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeConnectingEdges(int[], int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
This version puts the connecting edges in the argument array, to avoid repeated object creation and so speed up multiple accesses.
- getNodeConnectingInEdges(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeConnectingInEdges(int[], int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeConnectingInNodes(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeConnectingInNodes(int[], int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeConnectingNodes(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeConnectingNodes(int[], int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
This version puts the connecting nodes in the argument array, to avoid repeated object creation and so speed up multiple accesses.
- getNodeConnectingNodesOfSameAge(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeConnectingOutEdges(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeConnectingOutEdges(int[], int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeConnectingOutNodes(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeConnectingOutNodes(int[], int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
For directed graphs.
- getNodeDegree(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeInDegree(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeLabel(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeLabelBuf() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeLabelString() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Gets a big string of the node labels.
- getNodeMapping() - Method in class uk.ac.kent.dover.fastGraph.SubgraphMapping
-
- getNodeOutDegree(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeType(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNodeWeight(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNumber() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.IsoHolder
-
Gets the number
- getNumber() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
Gets the total number
- getNumberOfEdges() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNumberOfNodes() - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
- getNumOfResults() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
- getProb() - Method in class uk.ac.kent.dover.fastGraph.Name
-
- getRealPercentage() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
- getReferenceGraph() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
- getReferencePercentage() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
- getSingleEdgeMapping(int) - Method in class uk.ac.kent.dover.fastGraph.SubgraphMapping
-
- getSingleNodeMapping(int) - Method in class uk.ac.kent.dover.fastGraph.SubgraphMapping
-
- getSurname() - Method in class uk.ac.kent.dover.fastGraph.NamePicker
-
Returns a surname, based on weighted probabilities.
- getTimeEdgeType() - Static method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Creates the Display EdgeType for time edges.
- getTimeSinceInSeconds(long) - Static method in class uk.ac.kent.dover.fastGraph.Debugger
-
Outputs the difference between the current time and the one given
- getType() - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- getType() - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
-
- getValue() - Method in enum uk.ac.kent.dover.fastGraph.FastGraphEdgeType
-
Gets the value of this type
- getValue() - Method in enum uk.ac.kent.dover.fastGraph.FastGraphNodeType
-
Gets the value of this type
- getWeight() - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
-
- getWeight() - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
-
- getzScore() - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
Gets the z score
- randomGraphFactory(int, int, boolean) - Static method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Generate a random graph of the desired size.
- randomGraphFactory(int, int, long, boolean) - Static method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Generate a random graph of the desired size.
- randomGraphFactory(int, int, long, boolean, boolean) - Static method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Generate a random graph of the desired size.
- randomSampleSubgraph(int, int) - Method in class uk.ac.kent.dover.fastGraph.EnumerateSubgraphRandom
-
- randomSelection(Random, int, ArrayList<T>) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Picks a random sublist of a list.
- randomTimeSeriesFactory(double, double, int, int, boolean, boolean) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Creates a random time slice based on the current graph.
- relabelFastGraph(int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Relabels the current FastGraph with the family groups in subgraphs/families folder.
Any remaining nodes and edges are labelled randomly.
- removeNodesAndEdgesFromGraph(LinkedList<Integer>, LinkedList<Integer>, int, int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
This method creates a new FastGraph of the rough size given in targetNodes and targetEdges.
- reportFailRatios() - Static method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Output counts
- reportTimes() - Static method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
Output timing
- resetProfiling() - Static method in class uk.ac.kent.dover.fastGraph.ExactIsomorphism
-
sets all the profiling counts and timing to zero
- resetTime() - Static method in class uk.ac.kent.dover.fastGraph.Debugger
-
Resets the timing system
- round(double, int) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Round to the given number of decimal places.
- roundAndConvert(double[], int) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Rounds and Converts a double[].
- roundAndConvert(int[], double[], int) - Static method in class uk.ac.kent.dover.fastGraph.Util
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Rounds and Converts a double[].
- roundAndConvert(double, int) - Static method in class uk.ac.kent.dover.fastGraph.Util
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Rounds and Converts a double.
- roundArray(double[][]) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Rounds and sorts a double[][] to an int[][]
- roundArray(double[]) - Static method in class uk.ac.kent.dover.fastGraph.Util
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Rounds and sorts a double[] to an int[]
- roundArray(double[], int) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Rounds and a double[] to a less precise double[]
- saveBuffers(String, String) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
-
saves the current graph to several files, in directory given to base name given (i.e.
- saveClusters(ArrayList<ArrayList<FastGraph>>) - Method in class uk.ac.kent.dover.fastGraph.KMedoids
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Save clusters to disk
- saveResult() - Method in class uk.ac.kent.dover.fastGraph.Profiler
-
Saves the profiling results to file
- saveSubgraph(FastGraph, FastGraph, int, File) - Method in class uk.ac.kent.dover.fastGraph.SubgraphIsomorphism
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Saves the given subgraph into the relevant folder with the key of count
- setAge(byte) - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
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- setAge(byte) - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
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- setAllEdgeLabels(String[]) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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Change all the edge labels in the graph.
- setAllNodeLabels(String[]) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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Change all the node labels in the graph.
- setEdgeAge(int, byte) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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- setEdgeType(int, byte) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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- setEdgeWeight(int, int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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- setId(int) - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
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- setId(int) - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
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- setKey(String) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.IsoHolder
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Sets the key
- setKey(String) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
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- setLabel(String) - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
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- setLabel(String) - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
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- setName(String) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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Names should be simple alphanumeric.
- setNode1(int) - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
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- setNode2(int) - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
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- setNodeAge(int, byte) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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- setNodeType(int, byte) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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- setNodeWeight(int, int) - Method in class uk.ac.kent.dover.fastGraph.FastGraph
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- setNumber(int) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.IsoHolder
-
Sets the number
- setRealPercentage(double) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
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- setReferenceGraph(FastGraph) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
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- setReferencePercentage(double) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
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- setSaveAll(boolean) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder
-
Sets if the saveAll option is specified
- setType(byte) - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
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- setType(byte) - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
-
- setWeight(int) - Method in class uk.ac.kent.dover.fastGraph.EdgeStructure
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- setWeight(int) - Method in class uk.ac.kent.dover.fastGraph.NodeStructure
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- setzScore(double) - Method in class uk.ac.kent.dover.fastGraph.ExactMotifFinder.MotifResultHolder
-
Sets the z score
- standardDeviation(double[], double) - Static method in class uk.ac.kent.dover.fastGraph.Util
-
Returns the standard deviation of an array
- standardDeviation(ArrayList<T>, double) - Static method in class uk.ac.kent.dover.fastGraph.Util
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Returns the standard deviation of an array
- startingWorkingDirectory - Static variable in class uk.ac.kent.dover.fastGraph.Launcher
-
- structureFactory(String, byte, List<NodeStructure>, List<EdgeStructure>, boolean) - Static method in class uk.ac.kent.dover.fastGraph.FastGraph
-
Given a collection of NodeStructure and EdgeStructure, create a new graph.
- SubgraphIsomorphism - Class in uk.ac.kent.dover.fastGraph
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- SubgraphIsomorphism() - Constructor for class uk.ac.kent.dover.fastGraph.SubgraphIsomorphism
-
- subgraphIsomorphismFinder() - Method in class uk.ac.kent.dover.fastGraph.ApproximateSubgraphIsomorphism
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Performs the approximate subgraph isomorphism
- subgraphIsomorphismFinder() - Method in class uk.ac.kent.dover.fastGraph.ExactSubgraphIsomorphism
-
Find the pattern graph in the target graph.
- SubgraphMapping - Class in uk.ac.kent.dover.fastGraph
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For mapping a graph to a subgraph of a larger graph
The nodeMapping and edgeMapping indexes are those of the smaller graph
The contents are the corresponding nodes and edges in the larger graph
- SubgraphMapping(FastGraph, FastGraph, int[], int[]) - Constructor for class uk.ac.kent.dover.fastGraph.SubgraphMapping
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- subList(ArrayList<T>, int, int) - Static method in class uk.ac.kent.dover.fastGraph.Util
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Returns a sublist.
A copy of List.sublist() except the end is checked and shortened if too long