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A

addReport(RuntimeReport) - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Appends a new report to this summary.
addRun(GraphDataSet, ReportSummaryStatistics) - Method in class dev.roanh.cpqkeys.EvaluationResults
Add a new result for evaluating an algorithm on a specific dataset.
algo - Variable in class dev.roanh.cpqkeys.ReportSummaryStatistics
The algorithm that produced the runtimes for this report summary.
algo - Variable in class dev.roanh.cpqkeys.RuntimeReport
The algorithm these runtimes were measured for.
Algorithm - Class in dev.roanh.cpqkeys
Entry point for an algorithm implementation that can canonize an input graph.
Algorithm(String, Function<Graph<QueryGraphCPQ.Vertex, Predicate>, long[]>) - Constructor for class dev.roanh.cpqkeys.Algorithm
Constructs a new algorithm instance with the given display name and canonization function.
algorithms - Static variable in class dev.roanh.cpqkeys.Main
List of algorithms to evaluate.

B

Bliss - Class in dev.roanh.cpqkeys.algo
Binding for Bliss.
Bliss() - Constructor for class dev.roanh.cpqkeys.algo.Bliss
 

C

canonFun - Variable in class dev.roanh.cpqkeys.Algorithm
The canonization function for this algorithm.
canonize(Graph<QueryGraphCPQ.Vertex, Predicate>) - Method in class dev.roanh.cpqkeys.Algorithm
Runs this algorithm on the given input graph.
canonTime - Variable in class dev.roanh.cpqkeys.ReportSummaryStatistics
Summary of the canonization runtime statistics.
canonTime - Variable in class dev.roanh.cpqkeys.RuntimeReport
Canonization time for the algorithm (nanoseconds)
ColoredGraph(int[][], Collection<List<Integer>>) - Constructor for class dev.roanh.cpqkeys.GraphUtil.ColoredGraph
Constructs a new coloured graph with the given adjacency list and colour information.
colorMap - Variable in class dev.roanh.cpqkeys.GraphUtil.ColoredGraph
A collection of lists where each list has the IDs of nodes with the same colour.
computeCanon(Graph<QueryGraphCPQ.Vertex, Predicate>) - Static method in class dev.roanh.cpqkeys.algo.Bliss
Runs Bliss on the given input graph.
computeCanon(int[], int[]) - Static method in class dev.roanh.cpqkeys.algo.Bliss
Computes the canonical labelling of the given coloured graph.
computeCanon(Graph<QueryGraphCPQ.Vertex, Predicate>) - Static method in class dev.roanh.cpqkeys.algo.Nishe
Runs Nishe on the given input graph.
computeCanon(int[][], int[]) - Static method in class dev.roanh.cpqkeys.algo.Nishe
Computes the canonical trace value and new partition nest for the given graph with the given vertex colouring.
computeCanon(Graph<QueryGraphCPQ.Vertex, Predicate>) - Static method in class dev.roanh.cpqkeys.algo.Traces
Runs Traces on the given input graph.
computeCanon(int[][], int[]) - Static method in class dev.roanh.cpqkeys.algo.Traces
Computes the canonical form of the given coloured graph using traces.
computeCanonDense(int[][], int[]) - Static method in class dev.roanh.cpqkeys.algo.Nauty
Computes the canonical form of the given coloured graph using the dense version of nauty.
computeCanonSparse(int[][], int[]) - Static method in class dev.roanh.cpqkeys.algo.Nauty
Computes the canonical form of the given coloured graph using the sparse version of nauty.

D

data - Variable in class dev.roanh.cpqkeys.GraphDataSet
The graphs for this data set.
DATASET_SIZE - Static variable in class dev.roanh.cpqkeys.Main
Number of graphs in a data set.
DENSE - Static variable in class dev.roanh.cpqkeys.algo.Nauty
Algorithm binding for the dense version of nauty.
dev.roanh.cpqkeys - package dev.roanh.cpqkeys
 
dev.roanh.cpqkeys.algo - package dev.roanh.cpqkeys.algo
 
DIRECTED - Static variable in class dev.roanh.cpqkeys.algo.Scott
Algorithm binding for Scott that accepts directed graphs as input.

E

evaluateAlgorithm(Algorithm) - Static method in class dev.roanh.cpqkeys.Main
Evaluates the given algorithm on randomly generated CPQs.
EvaluationResults - Class in dev.roanh.cpqkeys
Report summarising multiple run of the same algorithm on different data sets.
EvaluationResults() - Constructor for class dev.roanh.cpqkeys.EvaluationResults
 

F

findPython() - Static method in class dev.roanh.cpqkeys.Main
Finds a Python 3 installation on the host system.
formatNanos(double) - Static method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Formats the given number of nanoseconds as a string breaking the time up into units of increasing magnitude as required.
formatNanos(long) - Static method in class dev.roanh.cpqkeys.RuntimeReport
Formats the given number of nanoseconds as a string breaking the time up into units of increasing magnitude as required.
fromCPQ(int, int, int) - Static method in class dev.roanh.cpqkeys.GraphDataSet
Generates a data set consisting of CPQ query graphs using CPQ.generateRandomCPQ(int, int).

G

getAdjacencyList() - Method in class dev.roanh.cpqkeys.GraphUtil.ColoredGraph
Gets the adjacency list representation of this graph.
getAlgorithm() - Method in class dev.roanh.cpqkeys.RuntimeReport
Gets the algorithm that was executed to generate this report.
getCanonizationTime() - Method in class dev.roanh.cpqkeys.RuntimeReport
Gets the time spent by the algorithm computing the canonical representation of the input graph.
getCanonizationTimeAverage() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the average canonization time for all runtime reports.
getCanonizationTimeStdDev() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the sample standard deviation for the canonization runtime.
getColorMap() - Method in class dev.roanh.cpqkeys.GraphUtil.ColoredGraph
Gets the colour map for this coloured graph, each list in the returned collection contains the IDs of nodes with the same colour.
getEdgesAverage() - Method in class dev.roanh.cpqkeys.GraphDataSet
Gets the average number of edges in the graphs for this data set.
getEdgesStdDev() - Method in class dev.roanh.cpqkeys.GraphDataSet
Gets the sample standard deviation of the number of edges in the graphs for this data set.
getName() - Method in class dev.roanh.cpqkeys.Algorithm
Gets the display name of this algorithm.
getNativeSetupTime() - Method in class dev.roanh.cpqkeys.RuntimeReport
Gets the time spent on the side of the native implementation preparing all the input data for the canonization step.
getNativeSetupTimeAverage() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the average native setup time for all runtime reports.
getNativeSetupTimeStdDev() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the sample standard deviation for the native setup runtime.
getNodeCount() - Method in class dev.roanh.cpqkeys.GraphUtil.ColoredGraph
Gets the total number of nodes in this graph.
getNodesAverage() - Method in class dev.roanh.cpqkeys.GraphDataSet
Gets the average number of nodes in the graphs for this data set.
getNodesStdDev() - Method in class dev.roanh.cpqkeys.GraphDataSet
Gets the sample standard deviation of the number of nodes in the graphs for this data set.
getOtherTime() - Method in class dev.roanh.cpqkeys.RuntimeReport
Gets the total time spend on other tasks.
getOtherTimeAverage() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the average 'other' time for all runtime reports.
getOtherTimeStdDev() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the sample standard deviation for the 'other' runtime.
getReports() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the individual runtime reports that make up this summary.
getSetupTime() - Method in class dev.roanh.cpqkeys.RuntimeReport
Gets the time spent Java side transforming the input CPQ query graph into a form suitable for the algorithm.
getSetupTimeAverage() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the average setup time for all runtime reports.
getSetupTimeStdDev() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the sample standard deviation for the setup runtime.
getTotalTime() - Method in class dev.roanh.cpqkeys.RuntimeReport
Gets the total time spent running the Algorithm.time(dev.roanh.gmark.util.Graph) method.
getTotalTimeAverage() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the average total time for all runtime reports.
getTotalTimeStdDev() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Gets the sample standard deviation for the total runtime.
graph - Variable in class dev.roanh.cpqkeys.GraphUtil.ColoredGraph
The adjacency list representing the graph.
GraphDataSet - Class in dev.roanh.cpqkeys
Represents a data set consisting of graph instances.
GraphDataSet(List<Graph<QueryGraphCPQ.Vertex, Predicate>>) - Constructor for class dev.roanh.cpqkeys.GraphDataSet
Constructs a new data set with the given data.
GraphUtil - Class in dev.roanh.cpqkeys
Various utilities for transforming graphs.
GraphUtil() - Constructor for class dev.roanh.cpqkeys.GraphUtil
 
GraphUtil.ColoredGraph - Class in dev.roanh.cpqkeys
Represents a coloured graph.

I

INSTANCE - Static variable in class dev.roanh.cpqkeys.algo.Bliss
Algorithm binding for bliss.
INSTANCE - Static variable in class dev.roanh.cpqkeys.algo.Nishe
Algorithm binding for Nishe.
INSTANCE - Static variable in class dev.roanh.cpqkeys.algo.Traces
Algorithm binding for traces.
iterator() - Method in class dev.roanh.cpqkeys.GraphDataSet
 

L

LABELS - Static variable in class dev.roanh.cpqkeys.Main
Number of labels to use for the data set.
loadNatives() - Static method in class dev.roanh.cpqkeys.Main
Loads the compiled JNI libraries required for certain algorithm implementations.
LOGS - Static variable in class dev.roanh.cpqkeys.Main
Directory to store runtime logs in.

M

Main - Class in dev.roanh.cpqkeys
Main class for the CPQ Keys canonization algorithm evaluation framework.
Main() - Constructor for class dev.roanh.cpqkeys.Main
 
main(String[]) - Static method in class dev.roanh.cpqkeys.Main
Starts the algorithm evaluation process.
MAX_RULES - Static variable in class dev.roanh.cpqkeys.Main
Maximum number of rule applications to use to generate a data set.
MAX_RUNTIME - Static variable in class dev.roanh.cpqkeys.Main
The maximum amount of time in nanoseconds that an algorithm is allowed to spend evaluating a complete data set.
MIN_RULES - Static variable in class dev.roanh.cpqkeys.Main
Number of rule applications to use to generate the initial data set.

N

name - Variable in class dev.roanh.cpqkeys.Algorithm
The display name of this algorithm.
nativeSetupTime - Variable in class dev.roanh.cpqkeys.ReportSummaryStatistics
Summary of the native setup runtime statistics.
nativeSetupTime - Variable in class dev.roanh.cpqkeys.RuntimeReport
Native setup time for the algorithm (nanoseconds).
Nauty - Class in dev.roanh.cpqkeys.algo
Binding for Nauty.
Nauty() - Constructor for class dev.roanh.cpqkeys.algo.Nauty
 
Nishe - Class in dev.roanh.cpqkeys.algo
Binding for Nishe.
Nishe() - Constructor for class dev.roanh.cpqkeys.algo.Nishe
 

O

otherTime - Variable in class dev.roanh.cpqkeys.ReportSummaryStatistics
Summary of other runtime statistics.

P

prepareColors(GraphUtil.ColoredGraph) - Static method in class dev.roanh.cpqkeys.algo.Nauty
Computes a nauty and traces compatible array of color data.
print() - Method in class dev.roanh.cpqkeys.GraphDataSet
Prints some general statistics about this data set, namely the data set size and average number of nodes and edges together with their standard deviation.
print(PrintStream) - Method in class dev.roanh.cpqkeys.GraphDataSet
Prints some general statistics about this data set, namely the data set size and average number of nodes and edges together with their standard deviation.
print() - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Prints a runtime report with all the times formatted together with their sample standard deviation.
print(PrintStream) - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Prints a runtime report with all the times formatted together with their sample standard deviation.
print() - Method in class dev.roanh.cpqkeys.RuntimeReport
Prints a runtime report with all the times formatted.
print(PrintStream) - Method in class dev.roanh.cpqkeys.RuntimeReport
Prints a runtime report with all the times formatted.
PYTHON_COMMAND - Static variable in class dev.roanh.cpqkeys.Main
Command to start a Python process on the host system.

R

readTimes(Process) - Static method in class dev.roanh.cpqkeys.algo.Scott
Reads the final runtime measurements from the Scott subprocess.
reports - Variable in class dev.roanh.cpqkeys.ReportSummaryStatistics
List of individual runtime reports that make up this summary.
ReportSummaryStatistics - Class in dev.roanh.cpqkeys
Report summarising a collection of individual runtime reports.
ReportSummaryStatistics(Algorithm, GraphDataSet) - Constructor for class dev.roanh.cpqkeys.ReportSummaryStatistics
Constructs a new summary report by running the given algorithm on the graphs in the given data set.
results - Variable in class dev.roanh.cpqkeys.EvaluationResults
The evaluation result on different datasets.
RULE_GROWTH_FACTOR - Static variable in class dev.roanh.cpqkeys.Main
Increase in data set size after an algorithm processes a data set within the set time limit.
runDirected(Graph<QueryGraphCPQ.Vertex, Predicate>) - Static method in class dev.roanh.cpqkeys.algo.Scott
Runs Scott on a directed input graph.
runNauty(Graph<QueryGraphCPQ.Vertex, Predicate>, BiFunction<int[][], int[], long[]>) - Static method in class dev.roanh.cpqkeys.algo.Nauty
Runs either the dense or sparse version of nauty on the given input graph.
RuntimeReport - Class in dev.roanh.cpqkeys
Report summarising various runtimes about an algorithm
RuntimeReport(Algorithm, long[], long) - Constructor for class dev.roanh.cpqkeys.RuntimeReport
Constructs a new runtime report for the given algorithm with the given runtime information.
runUndirected(Graph<QueryGraphCPQ.Vertex, Predicate>) - Static method in class dev.roanh.cpqkeys.algo.Scott
Runs Scott on an undirected input graph that is constructed from the given input graph by the undirected transform GraphUtil.toUndirectedGraph(Graph).

S

save(Path) - Method in class dev.roanh.cpqkeys.EvaluationResults
Saves the evaluation results to the given file.
Scott - Class in dev.roanh.cpqkeys.algo
Binding for Scott.
Scott() - Constructor for class dev.roanh.cpqkeys.algo.Scott
 
SEED - Static variable in class dev.roanh.cpqkeys.Main
Random seed to use to generate data sets.
setupTime - Variable in class dev.roanh.cpqkeys.ReportSummaryStatistics
Summary of the setup runtime statistics.
setupTime - Variable in class dev.roanh.cpqkeys.RuntimeReport
Setup time for the algorithm (nanoseconds).
SPARSE - Static variable in class dev.roanh.cpqkeys.algo.Nauty
Algorithm binding for the sparse version of nauty.
startSession(String) - Static method in class dev.roanh.cpqkeys.algo.Scott
Starts a new Scott process and returns it.
stdDev(ToIntFunction<Graph<QueryGraphCPQ.Vertex, Predicate>>) - Method in class dev.roanh.cpqkeys.GraphDataSet
Computes the sample standard deviation of the given field in the data set.
stdDev(LongSummaryStatistics, Function<RuntimeReport, Long>) - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Computes the sample standard deviation of the given field in the data set.

T

time(Graph<QueryGraphCPQ.Vertex, Predicate>) - Method in class dev.roanh.cpqkeys.Algorithm
Runs this algorithm on the given input graph and returns a runtime report with runtime information.
toColoredGraph(Graph<V, E>) - Static method in class dev.roanh.cpqkeys.GraphUtil
Converts the given input graph to a coloured graph instance by grouping vertices with their colour determined by the content of their DataProxy instance.
totalTime - Variable in class dev.roanh.cpqkeys.ReportSummaryStatistics
Summary of the total runtime statistics.
totalTime - Variable in class dev.roanh.cpqkeys.RuntimeReport
Raw execution time (nanoseconds).
toUndirectedGraph(Graph<V, E>) - Static method in class dev.roanh.cpqkeys.GraphUtil
Converts the given directed input graph to a graph where all directed edges are instead represented by labelled vertices.
Traces - Class in dev.roanh.cpqkeys.algo
Binding for Traces.
Traces() - Constructor for class dev.roanh.cpqkeys.algo.Traces
 

U

UNDIRECTED - Static variable in class dev.roanh.cpqkeys.algo.Scott
Algorithm binding for Scott that only accepts undirected graphs as input.

W

writeData(PrintStream) - Method in class dev.roanh.cpqkeys.ReportSummaryStatistics
Writes the data for this summary as a single line to the given stream.
writeData(PrintStream) - Method in class dev.roanh.cpqkeys.RuntimeReport
Writes the data for this report as a single line to the given stream.
writeEdges(PrintWriter, List<Graph.GraphEdge<T, Predicate>>) - Static method in class dev.roanh.cpqkeys.algo.Scott
Writes the given list of edges to the given writer in a format that can be parsed by Scott.
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