Index (Broadwick 1.2 API)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

AbcAbsDistance - Class in broadwick.abc: Create a default controller that run 1000 samples from the prior.
AbcAbsDistance() - Constructor for class broadwick.abc.AbcAbsDistance
AbcController - Interface in broadwick.abc: AbcController class for running abc.
AbcDistance - Interface in broadwick.abc: Create the distance measure required for the ABC rejection algorithm.
AbcMaxNumStepController - Class in broadwick.abc: Create a default controller that run 1000 samples from the prior.
AbcMaxNumStepController() - Constructor for class broadwick.abc.AbcMaxNumStepController
AbcModel - Interface in broadwick.abc: A simple model class thats runs a model and creates named quantities, i.e.
AbcNamedQuantity - Class in broadwick.abc: An ABC named quantity is an order maintaining store of key-value pairs that can be used to store parameters for a model or the summary statistic calculated by a model.
AbcNamedQuantity(Map<String, Double>) - Constructor for class broadwick.abc.AbcNamedQuantity: Create a single set of named quantities.
AbcPriorsSampler - Interface in broadwick.abc: This interface determines how the Prior distribution(s) should be sampled.
AbstractTauLeapingBase - Class in broadwick.stochastic.algorithms: Abstract base class for tau leaping classes.
AbstractTauLeapingBase(AmountManager, TransitionKernel) - Constructor for class broadwick.stochastic.algorithms.AbstractTauLeapingBase: Create the tau-leaping object.
accept(MonteCarloResults, MonteCarloResults) - Method in class broadwick.montecarlo.acceptor.MetropolisHastings
accept(MonteCarloResults, MonteCarloResults) - Method in interface broadwick.montecarlo.acceptor.MonteCarloAcceptor: Accept a step in a Monte Carlo path/chain based on the ratio of the results at each step.
acceptor - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
add(Vector) - Method in class broadwick.math.Vector: Add a vector to this one.
add(IntegerDistribution) - Method in class broadwick.statistics.distributions.IntegerDistribution: Adds the content of the argument to the current object.
add(double) - Method in class broadwick.statistics.Samples: Add an observable (value) to the accumulator.
add(Samples) - Method in class broadwick.statistics.Samples: Add the contents of anther accumulator to this accumulator.
addAttribute(EdgeAttribute) - Method in class broadwick.graph.Edge: Add an attribute to the edge.
addAttribute(VertexAttribute) - Method in class broadwick.graph.Vertex: Add an attribute to the vertex, overwriting any attribute of the same name.
addConsoleLogger(String, String) - Method in class broadwick.LoggingFacade: Add a console logger to the list of loggers of the project.
addData(double, double) - Method in class broadwick.statistics.regression.SimpleLinearRegression: Adds the observation (x,y) to the regression data set.
addEdge(E, V, V) - Method in class broadwick.graph.DirectedGraph
addEdge(E, V, V, EdgeType) - Method in class broadwick.graph.DirectedGraph
addEdge(E, V, V) - Method in interface broadwick.graph.Graph: Adds edge e to this graph such that it connects vertex v1 to v2.
addEdge(E, V, V, EdgeType) - Method in interface broadwick.graph.Graph: Adds edge e to this graph such that it connects vertex v1 to v2.
addEdge(E, V, V) - Method in class broadwick.graph.Tree
addEdge(E, V, V, EdgeType) - Method in class broadwick.graph.Tree
addEdge(E, V, V) - Method in class broadwick.graph.UndirectedGraph
addEdge(E, V, V, EdgeType) - Method in class broadwick.graph.UndirectedGraph
addEdge(Edge, Element) - Static method in class broadwick.graph.writer.GraphMl: Add an edge to the graphML document.
addEdgeAttribute(String, Class, String) - Method in class broadwick.graph.DirectedGraph
addEdgeAttribute(String, Class, String) - Method in interface broadwick.graph.Graph: Add a new node attribute to the network.
addEdgeAttribute(String, Class, String) - Method in class broadwick.graph.Tree
addEdgeAttribute(String, Class, String) - Method in class broadwick.graph.UndirectedGraph
addError(String) - Method in class broadwick.config.ConfigValidationErrors: Add an error to the list of validation errors.
addError(ConfigValidationErrors.Status, String) - Method in class broadwick.config.ConfigValidationErrors: Add an error to the list of validation errors.
addFileLogger(String, String, String, Boolean) - Method in class broadwick.LoggingFacade: Add a file logger to the list of loggers of the project.
addNode(Vertex, Element) - Static method in class broadwick.graph.writer.GraphMl: Add a node to the graphML document.
addNodeToTree(String, Tree<PhyloNode, Edge<PhyloNode>>, PhyloNode, boolean) - Method in class broadwick.phylo.NewickTreeParser: Given a string that represents a node in the tree, split in into its constituent name and distance components and add it to the tree.
addObserver(MarkovChainObserver) - Method in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo: Add an observer to the list of observers.
addObserver(Observer) - Method in class broadwick.odesolver.OdeSolver: Add an observer to the engines list of observers.
addObserver(Observer) - Method in class broadwick.stochastic.StochasticSimulator: Add an observer to the engines list of observers.
addSubtree(Tree<V, E>, V, E) - Method in class broadwick.graph.Tree: Add a [sub]tree to the current tree.
addToKernel(SimulationEvent, Double) - Method in class broadwick.stochastic.TransitionKernel: Add the transition rate for a given event.
addVertex(V) - Method in class broadwick.graph.DirectedGraph
addVertex(V) - Method in interface broadwick.graph.Graph: Adds a vertex to the graph.
addVertex(V) - Method in class broadwick.graph.Tree
addVertex(V) - Method in class broadwick.graph.UndirectedGraph
addVertexAttribute(String, Class, String) - Method in class broadwick.graph.DirectedGraph
addVertexAttribute(String, Class, String) - Method in interface broadwick.graph.Graph: Add a new node attribute to the network.
addVertexAttribute(String, Class, String) - Method in class broadwick.graph.Tree
addVertexAttribute(String, Class, String) - Method in class broadwick.graph.UndirectedGraph
alias - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
alias - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
alias - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
alias - Variable in class broadwick.config.generated.DataFiles.LocationsFile
alias - Variable in class broadwick.config.generated.DataFiles.PopulationFile
alias - Variable in class broadwick.config.generated.DataFiles.TestsFile
AmountManager - Interface in broadwick.stochastic: An amount manager is responsible for keeping track of the populations within the simulation.
amountManager - Variable in class broadwick.stochastic.StochasticSimulator
Animal - Class in broadwick.data: Utility class for location data.
Animal() - Constructor for class broadwick.data.Animal
animalsCache - Variable in class broadwick.data.Lookup
ApproxBayesianComp - Class in broadwick.abc: This class runs an approximate Bayesian computation, sampling from the posterior.
ApproxBayesianComp(AbcNamedQuantity, AbcModel, AbcPriorsSampler, double) - Constructor for class broadwick.abc.ApproxBayesianComp: Create an ABC instance.
ArrayUtils - Class in broadwick.utils: Useful methods for acting on arrays.
ArrayUtils() - Constructor for class broadwick.utils.ArrayUtils: Hidden Utility constructor.
asCsv(Collection<String>) - Method in class broadwick.data.readers.DataFileReader: Convert a collection of elements read from the data file (the column names in the internal database) into a CSV string.
asQuestionCsv(Collection<String>) - Method in class broadwick.data.readers.DataFileReader: Convert a collection of elements read from the data file (the column names in the internal database) into a CSV string of question marks.
attributes - Variable in class broadwick.graph.Edge
attributes - Variable in class broadwick.graph.Vertex

B

BATCH_SIZE - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
BatchedMovementsFileReader - Class in broadwick.data.readers: Reader for the files describing the batched movements (i.e.
BatchedMovementsFileReader(DataFiles.BatchMovementFile, DatabaseImpl) - Constructor for class broadwick.data.readers.BatchedMovementsFileReader: Create the movement file reader.
batchMovementFile - Variable in class broadwick.config.generated.DataFiles
BatchMovementFile() - Constructor for class broadwick.config.generated.DataFiles.BatchMovementFile
batchSize - Variable in class broadwick.data.Movement
batchSizeColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
bins - Variable in class broadwick.statistics.distributions.IntegerDistribution
branchLabel - Variable in class broadwick.phylo.NewickTreeParser
broadwick - package broadwick: Provides for entry into Broadwick, the framework for epidemiological modelling.
Broadwick - Class in broadwick: Broadwick: Project for Scientific Computing.
Broadwick(String[]) - Constructor for class broadwick.Broadwick: Create the Broadwick project to read and verify the configuration files and initialise the project.
broadwick.abc - package broadwick.abc: Package for Approximate Bayesian Computation.
broadwick.concurrent - package broadwick.concurrent: The package contains several classes for concurrent programming.
broadwick.config - package broadwick.config: The package contains several classes for interacting with the configuration files for Broadwick.
broadwick.config.generated - package broadwick.config.generated
broadwick.data - package broadwick.data: Package to provide an interface to the data files for the project.
broadwick.data.readers - package broadwick.data.readers: Package to provide an interface to the data files for the project.
broadwick.graph - package broadwick.graph: This package contains classes for reading and manipulating graphs.
broadwick.graph.algorithms - package broadwick.graph.algorithms: This package contains several useful algorithms for acting on graphs.
broadwick.graph.writer - package broadwick.graph.writer: This package contains classes for saving graphs in various formats.
broadwick.grid - package broadwick.grid: This package contains classes to utilise the grid capcbilities of Broadwick.
broadwick.io - package broadwick.io: Provides useful IO utilities.
broadwick.math - package broadwick.math: Provides various math functions.
broadwick.model - package broadwick.model: This package contains the base classes and interfaces for the definition of models for the Broadwick framework.
broadwick.montecarlo - package broadwick.montecarlo: Monte Carlo simulation package.
broadwick.montecarlo.acceptor - package broadwick.montecarlo.acceptor: All Monte Carlo acceptance criteria can be found in this package.
broadwick.montecarlo.markovchain - package broadwick.montecarlo.markovchain: This package contains classes for generating Monte Carlo Markov Chains.
broadwick.montecarlo.markovchain.controller - package broadwick.montecarlo.markovchain.controller: This package contains classes for controlling the Markov chain e.g determining when to terminate the chain.
broadwick.montecarlo.markovchain.observer - package broadwick.montecarlo.markovchain.observer: This package contains classes for observing Markov Chains.
broadwick.montecarlo.markovchain.proposal - package broadwick.montecarlo.markovchain.proposal: This package contains classes for generating paths or chains for Monte Carlo Markov Chains.
broadwick.odesolver - package broadwick.odesolver: A package for ODE solvers.
broadwick.phylo - package broadwick.phylo: This package contains parsers for phylogenetic trees.
broadwick.rng - package broadwick.rng: Provides simple API for generating random numbers.
broadwick.statistics - package broadwick.statistics: This package contains classes for performing simple statistical analysis.
broadwick.statistics.distributions - package broadwick.statistics.distributions: This package contains classes for defining distributions, including user defined ones.
broadwick.statistics.regression - package broadwick.statistics.regression: Statistical routines for Broadwick involving multivariate data.
broadwick.stochastic - package broadwick.stochastic: Provides classes for solving models stochastically.
broadwick.stochastic.algorithms - package broadwick.stochastic.algorithms: Provides algorithms to implement the stochastic processes.
broadwick.utils - package broadwick.utils: Provides algorithms to implement the stochastic processes.
broadwick.xml - package broadwick.xml: Provides useful classes for manipulating the XML used in Broadwick.
BroadwickConstants - Class in broadwick: All the constants for the Broadwick framework are defined here.
BroadwickConstants() - Constructor for class broadwick.BroadwickConstants: Utility constructor (hidden).
BroadwickException - Exception in broadwick: A general RuntimeException for the Broadwick framework.
BroadwickException() - Constructor for exception broadwick.BroadwickException: Constructs a new exception with null as its detail message.
BroadwickException(String) - Constructor for exception broadwick.BroadwickException: Constructs a new exception with the specified detail message.
BroadwickException(Throwable) - Constructor for exception broadwick.BroadwickException: Constructs a new exception by wrapping a specified throwable.
BroadwickIOException - Exception in broadwick.io: A RuntimeException for I/O classes.
BroadwickIOException() - Constructor for exception broadwick.io.BroadwickIOException: Constructs a new io exception with null as its detail message.
BroadwickIOException(String) - Constructor for exception broadwick.io.BroadwickIOException: Constructs a new io exception with the specified detail message.
BroadwickVersion - Class in broadwick: This is a simple class to obtain the version number of the project from the manifest file of the packaged jar.
BroadwickVersion() - Constructor for class broadwick.BroadwickVersion: Private constructor to provide a singleton instance.
buffer - Variable in class broadwick.io.FileOutput
BUILD_STRING_FORMAT - Static variable in class broadwick.BroadwickVersion
BUILD_TIMESTAMP - Static variable in class broadwick.BroadwickVersion
buildCommandLineArguments() - Method in class broadwick.CliOptions: Construct and provide GNU-compatible Options.
burnIn - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo

C

calculate(AbcNamedQuantity, AbcNamedQuantity) - Method in class broadwick.abc.AbcAbsDistance
calculate(AbcNamedQuantity, AbcNamedQuantity) - Method in interface broadwick.abc.AbcDistance: Calculated the distance between the observed data and the generated data.
calculateDistance(V, V) - Method in class broadwick.graph.algorithms.ShortestPath: Returns the length of a shortest path from the source to the target vertex, or null if the target is not reachable from the source.
calculateRTotal() - Method in class broadwick.stochastic.algorithms.GillespieSimple: Calculate the h's described in (14) page 413 and the sum a (26) page 418.
calculateRTotal() - Method in class broadwick.stochastic.algorithms.TauLeaping: Calculate the h's described in (14) page 413 and the sum a (26) page 418.
chainLength - Variable in class broadwick.montecarlo.markovchain.MarkovChain
changed - Variable in class broadwick.stochastic.algorithms.GillespieSimple
classname - Variable in class broadwick.config.generated.Models.Model
clear() - Method in class broadwick.statistics.distributions.IntegerDistribution: Clear all the data from the distribution, after this method the distribution has no denominator or frequency.
clear() - Method in class broadwick.statistics.Samples: Clear the contents of the accumulator.
clear() - Method in class broadwick.stochastic.TransitionKernel: Clear all the events from the kernel.
CliOptions - Class in broadwick: Construct and read command line arguments.
CliOptions(String[]) - Constructor for class broadwick.CliOptions: Construct and provide GNU-compatible Options.
clone() - Method in class broadwick.stochastic.TransitionKernel: Copy this kernel object.
CloneUtils - Class in broadwick.utils: Utility for object cloning using serialization.
CloneUtils() - Constructor for class broadwick.utils.CloneUtils: Hide utility class constructor.
close() - Method in interface broadwick.data.DatabaseImpl: Close the database connection.
close() - Method in class broadwick.data.DataReader
close() - Method in class broadwick.data.H2Database
close() - Method in class broadwick.io.FileInput
close() - Method in class broadwick.io.FileOutput
cmdLine - Variable in class broadwick.CliOptions
column - Variable in class broadwick.config.generated.CustomTags.CustomTag
columns() - Method in class broadwick.math.Matrix: Get the number of columns in the matrix.
COMMENT_CHAR - Static variable in class broadwick.io.FileInput
compare(Movement, Movement) - Method in class broadwick.data.MovementsComparator
compareTo(MarkovChainObserver) - Method in class broadwick.montecarlo.markovchain.observer.MarkovChainObserver
compareTo(Observer) - Method in class broadwick.odesolver.Observer
compareTo(Observer) - Method in class broadwick.stochastic.Observer
computeDerivatives(double, List<Double>) - Method in interface broadwick.odesolver.Ode: Get the current time derivative of the state vector.
configFileOpt - Variable in class broadwick.CliOptions
ConfigValidationErrors - Class in broadwick.config: This class encapsulates errors found during the validation of configuration files.
ConfigValidationErrors() - Constructor for class broadwick.config.ConfigValidationErrors: Constructs a new exception with null as its detail message.
ConfigValidationErrors.Status - Enum in broadwick.config: Error status of the configuration status.
ConfigValidator - Class in broadwick.config: Validator class for configuration files supplied to Broadwick, the framework for epidemiological modelling.
ConfigValidator(Project) - Constructor for class broadwick.config.ConfigValidator: Create an validator instance that is capable of checking the content of a configuration file.
configXml - Variable in class broadwick.Broadwick
connection - Variable in class broadwick.data.H2Database
connection - Variable in class broadwick.data.Lookup
connectionPool - Variable in class broadwick.data.H2Database
console - Variable in class broadwick.config.generated.Logs
Console() - Constructor for class broadwick.config.generated.Logs.Console
Constants - Class in broadwick: Definition of all global constants.
Constants() - Constructor for class broadwick.Constants: Hide utility constructor.
Consumer - Class in broadwick.montecarlo: This class takes (or consumes) the results of a single simulation of the model and saves the results in a manner to allow statistics to be generated from the Monte Carlo simulation.
Consumer(ArrayBlockingQueue<MonteCarloResults>, MonteCarloResults) - Constructor for class broadwick.montecarlo.Consumer: Create the consumer object.
consumer - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
ContinuousDistribution - Interface in broadwick.statistics.distributions: Interface defining all continuous distribution classes.
ContinuousMultivariateDistribution - Interface in broadwick.statistics.distributions: Interface defining all distribution classes.
controller - Variable in class broadwick.abc.ApproxBayesianComp
controller - Variable in class broadwick.odesolver.OdeSolver
controller - Variable in class broadwick.stochastic.StochasticSimulator
coordinates - Variable in class broadwick.montecarlo.MonteCarloStep
copy() - Method in class broadwick.math.Matrix: Create a copy of the matrix.
copy() - Method in class broadwick.statistics.distributions.IntegerDistribution: Creates a copy of this histogram and returns it.
copyOf() - Method in class broadwick.montecarlo.MonteCarloScenario: Create a copy of the MonteCarloScenario object.
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.CustomTags
copyTo(Object) - Method in class broadwick.config.generated.CustomTags
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.CustomTags.CustomTag
copyTo(Object) - Method in class broadwick.config.generated.CustomTags.CustomTag
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Databases
copyTo(Object) - Method in class broadwick.config.generated.Databases
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
copyTo(Object) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.DataFiles
copyTo(Object) - Method in class broadwick.config.generated.DataFiles
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
copyTo(Object) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.DataFiles.FullMovementFile
copyTo(Object) - Method in class broadwick.config.generated.DataFiles.FullMovementFile
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.DataFiles.LocationsFile
copyTo(Object) - Method in class broadwick.config.generated.DataFiles.LocationsFile
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.DataFiles.PopulationFile
copyTo(Object) - Method in class broadwick.config.generated.DataFiles.PopulationFile
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.DataFiles.TestsFile
copyTo(Object) - Method in class broadwick.config.generated.DataFiles.TestsFile
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.GaussianPrior
copyTo(Object) - Method in class broadwick.config.generated.GaussianPrior
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.LifeHistoryType
copyTo(Object) - Method in class broadwick.config.generated.LifeHistoryType
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Logs.Console
copyTo(Object) - Method in class broadwick.config.generated.Logs.Console
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Logs
copyTo(Object) - Method in class broadwick.config.generated.Logs
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Logs.File
copyTo(Object) - Method in class broadwick.config.generated.Logs.File
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Models
copyTo(Object) - Method in class broadwick.config.generated.Models
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Models.Model
copyTo(Object) - Method in class broadwick.config.generated.Models.Model
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Models.Model.Priors
copyTo(Object) - Method in class broadwick.config.generated.Models.Model.Priors
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Parameter
copyTo(Object) - Method in class broadwick.config.generated.Parameter
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.PopulationType
copyTo(Object) - Method in class broadwick.config.generated.PopulationType
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Prior
copyTo(Object) - Method in class broadwick.config.generated.Prior
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Project
copyTo(Object) - Method in class broadwick.config.generated.Project
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.Project.Data
copyTo(Object) - Method in class broadwick.config.generated.Project.Data
copyTo(Object, CopyBuilder) - Method in class broadwick.config.generated.UniformPrior
copyTo(Object) - Method in class broadwick.config.generated.UniformPrior
covariances - Variable in class broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution
createAnimal(Record) - Method in class broadwick.data.Lookup: Create an animal object from the node object defining it in the graph database.
createCopy() - Method in class broadwick.config.generated.CustomTags
createCopy() - Method in class broadwick.config.generated.CustomTags.CustomTag
createCopy() - Method in class broadwick.config.generated.Databases
createCopy() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
createCopy() - Method in class broadwick.config.generated.DataFiles
createCopy() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
createCopy() - Method in class broadwick.config.generated.DataFiles.FullMovementFile
createCopy() - Method in class broadwick.config.generated.DataFiles.LocationsFile
createCopy() - Method in class broadwick.config.generated.DataFiles.PopulationFile
createCopy() - Method in class broadwick.config.generated.DataFiles.TestsFile
createCopy() - Method in class broadwick.config.generated.GaussianPrior
createCopy() - Method in class broadwick.config.generated.LifeHistoryType
createCopy() - Method in class broadwick.config.generated.Logs.Console
createCopy() - Method in class broadwick.config.generated.Logs
createCopy() - Method in class broadwick.config.generated.Logs.File
createCopy() - Method in class broadwick.config.generated.Models
createCopy() - Method in class broadwick.config.generated.Models.Model
createCopy() - Method in class broadwick.config.generated.Models.Model.Priors
createCopy() - Method in class broadwick.config.generated.Parameter
createCopy() - Method in class broadwick.config.generated.PopulationType
createCopy() - Method in class broadwick.config.generated.Project
createCopy() - Method in class broadwick.config.generated.Project.Data
createCopy() - Method in class broadwick.config.generated.UniformPrior
createCustomTags() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of CustomTags
createCustomTagsCustomTag() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of CustomTags.CustomTag
createDatabases() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Databases
createDataFiles() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of DataFiles
createDataFilesBatchMovementFile() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of DataFiles.BatchMovementFile
createDataFilesDirectedMovementFile() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of DataFiles.DirectedMovementFile
createDataFilesFullMovementFile() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of DataFiles.FullMovementFile
createDataFilesLocationsFile() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of DataFiles.LocationsFile
createDataFilesPopulationFile() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of DataFiles.PopulationFile
createDataFilesTestsFile() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of DataFiles.TestsFile
createGaussianPrior() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of GaussianPrior
createLifeHistoryType() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of LifeHistoryType
createLocation(Record) - Method in class broadwick.data.Lookup: Create a location object from the node object defining it in the graph database.
createLogs() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Logs
createLogsConsole() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Logs.Console
createLogsFile() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Logs.File
createModels() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Models
createModelsModel() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Models.Model
createModelsModelPriors() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Models.Model.Priors
createMovement(Record) - Method in class broadwick.data.Lookup: Create a movement object from the relationship object defining it in the graph database.
createObject(Class<T>, String) - Method in class broadwick.config.ConfigValidator: Create an object through reflection, to use this method to create a solver object Solver solverObj = this.createObject(Solver.class, "RungeKutta4");
createParameter() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Parameter
createPatternLayoutEncoder(String) - Method in class broadwick.LoggingFacade: Create a pattern layout encoder for a given pattern.
createPopulationType() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of PopulationType
createProject() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Project
createProjectData() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of Project.Data
createTable(String, String, Connection) - Method in class broadwick.data.readers.DataFileReader: Execute a command to create a table.
createTableCommand - Variable in class broadwick.data.readers.BatchedMovementsFileReader
createTableCommand - Variable in class broadwick.data.readers.DirectedMovementsFileReader
createTableCommand - Variable in class broadwick.data.readers.FullMovementsFileReader
createTableCommand - Variable in class broadwick.data.readers.LocationsFileReader
createTableCommand - Variable in class broadwick.data.readers.PopulationsFileReader
createTableCommand - Variable in class broadwick.data.readers.TestsFileReader
createTest(Record) - Method in class broadwick.data.Lookup: Create a Test object from the node object defining it in the graph database.
createThresholdFilter(String) - Method in class broadwick.LoggingFacade: Create a thresholdFilter for a given level.
createUniformPrior() - Method in class broadwick.config.generated.ObjectFactory: Create an instance of UniformPrior
currentStep - Variable in class broadwick.montecarlo.markovchain.MarkovChain
currentTime - Variable in class broadwick.odesolver.OdeSolver
currentTime - Variable in class broadwick.stochastic.StochasticSimulator
customTag - Variable in class broadwick.config.generated.CustomTags
CustomTag() - Constructor for class broadwick.config.generated.CustomTags.CustomTag
CustomTags - Class in broadwick.config.generated: Java class for CustomTags complex type.
CustomTags() - Constructor for class broadwick.config.generated.CustomTags
customTags - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
customTags - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
customTags - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
customTags - Variable in class broadwick.config.generated.DataFiles.LocationsFile
customTags - Variable in class broadwick.config.generated.DataFiles.PopulationFile
customTags - Variable in class broadwick.config.generated.DataFiles.TestsFile
CustomTags.CustomTag - Class in broadwick.config.generated: Java class for anonymous complex type.

D

data - Variable in class broadwick.config.generated.Project
Data() - Constructor for class broadwick.config.generated.Project.Data
data - Variable in class broadwick.data.DataReader
data - Variable in class broadwick.math.Matrix
data - Variable in class broadwick.math.Vector
database - Variable in class broadwick.data.readers.BatchedMovementsFileReader
database - Variable in class broadwick.data.readers.DirectedMovementsFileReader
database - Variable in class broadwick.data.readers.FullMovementsFileReader
database - Variable in class broadwick.data.readers.LocationsFileReader
database - Variable in class broadwick.data.readers.PopulationsFileReader
database - Variable in class broadwick.data.readers.TestsFileReader
DatabaseImpl - Interface in broadwick.data: Interface defining the database implementations.
Databases - Class in broadwick.config.generated: Java class for Databases complex type.
Databases() - Constructor for class broadwick.config.generated.Databases
databases - Variable in class broadwick.config.generated.Project.Data
dataFile - Variable in class broadwick.data.readers.BatchedMovementsFileReader
dataFile - Variable in class broadwick.data.readers.DirectedMovementsFileReader
dataFile - Variable in class broadwick.data.readers.FullMovementsFileReader
dataFile - Variable in class broadwick.data.readers.LocationsFileReader
dataFile - Variable in class broadwick.data.readers.PopulationsFileReader
dataFile - Variable in class broadwick.data.readers.TestsFileReader
DataFileReader - Class in broadwick.data.readers: Base class for all data file readers, containing useful common functionality..
DataFileReader() - Constructor for class broadwick.data.readers.DataFileReader
DataFiles - Class in broadwick.config.generated: Java class for DataFiles complex type.
DataFiles() - Constructor for class broadwick.config.generated.DataFiles
datafiles - Variable in class broadwick.config.generated.Project.Data
DataFiles.BatchMovementFile - Class in broadwick.config.generated: Java class for anonymous complex type.
DataFiles.DirectedMovementFile - Class in broadwick.config.generated: Java class for anonymous complex type.
DataFiles.FullMovementFile - Class in broadwick.config.generated: Java class for anonymous complex type.
DataFiles.LocationsFile - Class in broadwick.config.generated: Java class for anonymous complex type.
DataFiles.PopulationFile - Class in broadwick.config.generated: Java class for anonymous complex type.
DataFiles.TestsFile - Class in broadwick.config.generated: Java class for anonymous complex type.
DataReader - Class in broadwick.data: Utility class to read, store and manipulate the data files.
DataReader(Project.Data) - Constructor for class broadwick.data.DataReader: Create the object that will read the data element of the configuration file.
DATE_LC - Static variable in class broadwick.data.readers.PopulationsFileReader
DATE_OF_BIRTH - Static variable in class broadwick.data.readers.PopulationsFileReader
DATE_OF_DEATH - Static variable in class broadwick.data.readers.PopulationsFileReader
dateFields - Variable in class broadwick.data.readers.BatchedMovementsFileReader
dateFields - Variable in class broadwick.data.readers.DirectedMovementsFileReader
dateFields - Variable in class broadwick.data.readers.FullMovementsFileReader
dateFields - Variable in class broadwick.data.readers.LocationsFileReader
dateFields - Variable in class broadwick.data.readers.PopulationsFileReader
dateFields - Variable in class broadwick.data.readers.TestsFileReader
dateFormat - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
dateFormat - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
dateFormat - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
dateFormat - Variable in class broadwick.config.generated.DataFiles.LocationsFile
dateFormat - Variable in class broadwick.config.generated.DataFiles.PopulationFile
dateFormat - Variable in class broadwick.config.generated.DataFiles.TestsFile
dateFormat - Variable in class broadwick.data.readers.BatchedMovementsFileReader
dateFormat - Variable in class broadwick.data.readers.DirectedMovementsFileReader
dateFormat - Variable in class broadwick.data.readers.FullMovementsFileReader
dateFormat - Variable in class broadwick.data.readers.LocationsFileReader
dateFormat - Variable in class broadwick.data.readers.PopulationsFileReader
dateFormat - Variable in class broadwick.data.readers.TestsFileReader
dateOfBirth - Variable in class broadwick.data.Animal
dateOfBirthColumn - Variable in class broadwick.config.generated.LifeHistoryType
dateOfDeath - Variable in class broadwick.data.Animal
dateOfDeathColumn - Variable in class broadwick.config.generated.LifeHistoryType
dbImpl - Variable in class broadwick.data.DataReader
dbName - Variable in class broadwick.data.DataReader
deepClone(T) - Static method in class broadwick.utils.CloneUtils: Deep clones an object.
DEFAULT_ENCODING - Static variable in class broadwick.io.FileInput
DEFAULT_ENCODING - Static variable in class broadwick.io.FileOutput
DEFAULT_SEP - Static variable in class broadwick.io.FileInput
DefaultController - Class in broadwick.stochastic: A simple implementation of a SimulationController causing the simulation to stop after a given time.
DefaultController(double) - Constructor for class broadwick.stochastic.DefaultController: Creates the controller for a given time where the simulation has to stop.
DefaultOdeController - Class in broadwick.odesolver: A simple controller object that will stop the solver at a specific time.
DefaultOdeController(double) - Constructor for class broadwick.odesolver.DefaultOdeController: Create the controller, specifying the time at which the solver should stop.
defaultValue - Variable in class broadwick.graph.EdgeAttribute
defaultValue - Variable in class broadwick.graph.VertexAttribute
DEPARTURE_DATE - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
DEPARTURE_DATE - Static variable in class broadwick.data.readers.FullMovementsFileReader
DEPARTURE_ID - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
DEPARTURE_ID - Static variable in class broadwick.data.readers.FullMovementsFileReader
departureDate - Variable in class broadwick.data.Movement
departureDateColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
departureDateColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
departureId - Variable in class broadwick.data.Movement
departureLocationIdColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
departureLocationIdColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
dependentVariables - Variable in class broadwick.odesolver.OdeSolver
DepthFirstIterator<V extends Vertex,E extends Edge<V>> - Class in broadwick.graph: Iterator over all the vertices in a graph using a depth first traversal algorithm.
DepthFirstIterator(Tree<V, E>) - Constructor for class broadwick.graph.DepthFirstIterator: Create the iterator over a tree.
destination - Variable in class broadwick.graph.Edge
DESTINATION_DATE - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
DESTINATION_DATE - Static variable in class broadwick.data.readers.FullMovementsFileReader
DESTINATION_ID - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
DESTINATION_ID - Static variable in class broadwick.data.readers.FullMovementsFileReader
destinationDate - Variable in class broadwick.data.Movement
destinationDateColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
destinationDateColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
destinationId - Variable in class broadwick.data.Movement
destinationLocationIdColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
destinationLocationIdColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
deviation - Variable in class broadwick.config.generated.GaussianPrior
difference(Set<T>, Set<T>) - Static method in class broadwick.math.SetOperations: Get the set difference A\B of the sets A and B.
dimension - Variable in class broadwick.statistics.distributions.MultinomialDistribution
DirectedGraph<V extends Vertex,E extends Edge<V>> - Class in broadwick.graph: A DirectedGraph, suitable for sparse graphs, that permits parallel edges..
DirectedGraph() - Constructor for class broadwick.graph.DirectedGraph: Creates an instance of the graph.
directedMovementFile - Variable in class broadwick.config.generated.DataFiles
DirectedMovementFile() - Constructor for class broadwick.config.generated.DataFiles.DirectedMovementFile
DirectedMovementsFileReader - Class in broadwick.data.readers: Reader for the files describing the directed movements (i.e.
DirectedMovementsFileReader(DataFiles.DirectedMovementFile, DatabaseImpl) - Constructor for class broadwick.data.readers.DirectedMovementsFileReader: Create the movement file reader.
directMCReaction() - Method in class broadwick.stochastic.algorithms.GillespieSimple: obtains a random (but following a specific distribution) reaction as described by the direct method in chapter 5A page 417ff.
directMCTau(double) - Method in class broadwick.stochastic.algorithms.GillespieSimple: obtains a random (but following a specific distribution) timestep as described by the direct method in chapter 5A page 417ff.
DiscreteDistribution - Interface in broadwick.statistics.distributions: Interface defining all continuous distribution classes.
dist - Variable in class broadwick.statistics.distributions.HypergeometricDistribution
distance - Variable in class broadwick.abc.ApproxBayesianComp
distance - Variable in class broadwick.phylo.PhyloNode
doEvent(SimulationEvent, double) - Method in class broadwick.stochastic.StochasticSimulator: Fires a reaction.
doEvent(SimulationEvent, double, int) - Method in class broadwick.stochastic.StochasticSimulator: Perform an event by informing the subscribed observers and the amountManager.
DOT - Static variable in class broadwick.io.FileUtils
doThetaEvent() - Method in class broadwick.odesolver.OdeSolver: Gets called when the simulator reaches the predetermined time of a theta event.
doThetaEvent() - Method in class broadwick.stochastic.StochasticSimulator: Gets called when the simulator reaches the predetermined time of a theta event.

E

easting - Variable in class broadwick.data.Location
EASTING - Static variable in class broadwick.data.readers.LocationsFileReader
eastingColumn - Variable in class broadwick.config.generated.DataFiles.LocationsFile
Edge<V extends Vertex> - Class in broadwick.graph: This class represents a generic edge in a graph.
Edge(String) - Constructor for class broadwick.graph.Edge: A generic edge for a graph object.
Edge(String, V, V) - Constructor for class broadwick.graph.Edge: A generic edge for a graph object.
Edge(V, V) - Constructor for class broadwick.graph.Edge: A generic edge for a graph object.
Edge(V, V, Double) - Constructor for class broadwick.graph.Edge: A generic edge for a graph object.
Edge(String, V, V, Double) - Constructor for class broadwick.graph.Edge: A generic edge for a graph object.
EdgeAttribute - Class in broadwick.graph: A generic edge attribute.
EdgeAttribute(String, Class, String) - Constructor for class broadwick.graph.EdgeAttribute: Create a edge attribute object setting the value to be the default value.
edgeAttributes - Variable in class broadwick.graph.DirectedGraph
edgeAttributes - Variable in class broadwick.graph.Tree
edgeAttributes - Variable in class broadwick.graph.UndirectedGraph
EdgeList - Class in broadwick.graph.writer: Simple class to write the nodes/edges of a network in edgelist format.
EdgeList() - Constructor for class broadwick.graph.writer.EdgeList: hidden constructor for static class.
edgemaps - Variable in class broadwick.graph.DirectedGraph
edgemaps - Variable in class broadwick.graph.Tree
edgemaps - Variable in class broadwick.graph.UndirectedGraph
EdgeType - Enum in broadwick.graph: Defines the possible edge types for graphs which assign types to edges.
EdgeType() - Constructor for enum broadwick.graph.EdgeType
EdgeWeightTransformer() - Constructor for class broadwick.graph.algorithms.ShortestPath.EdgeWeightTransformer
element(int, int) - Method in class broadwick.math.Matrix: Get the contents of the matrix.
element(int) - Method in class broadwick.math.Vector: Get the element at the given index.
epsilon - Variable in class broadwick.abc.ApproxBayesianComp
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.CustomTags.CustomTag
equals(Object) - Method in class broadwick.config.generated.CustomTags.CustomTag
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.CustomTags
equals(Object) - Method in class broadwick.config.generated.CustomTags
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Databases
equals(Object) - Method in class broadwick.config.generated.Databases
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
equals(Object) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
equals(Object) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.DataFiles
equals(Object) - Method in class broadwick.config.generated.DataFiles
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.DataFiles.FullMovementFile
equals(Object) - Method in class broadwick.config.generated.DataFiles.FullMovementFile
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.DataFiles.LocationsFile
equals(Object) - Method in class broadwick.config.generated.DataFiles.LocationsFile
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.DataFiles.PopulationFile
equals(Object) - Method in class broadwick.config.generated.DataFiles.PopulationFile
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.DataFiles.TestsFile
equals(Object) - Method in class broadwick.config.generated.DataFiles.TestsFile
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.GaussianPrior
equals(Object) - Method in class broadwick.config.generated.GaussianPrior
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.LifeHistoryType
equals(Object) - Method in class broadwick.config.generated.LifeHistoryType
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Logs.Console
equals(Object) - Method in class broadwick.config.generated.Logs.Console
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Logs
equals(Object) - Method in class broadwick.config.generated.Logs
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Logs.File
equals(Object) - Method in class broadwick.config.generated.Logs.File
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Models
equals(Object) - Method in class broadwick.config.generated.Models
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Models.Model
equals(Object) - Method in class broadwick.config.generated.Models.Model
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Models.Model.Priors
equals(Object) - Method in class broadwick.config.generated.Models.Model.Priors
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Parameter
equals(Object) - Method in class broadwick.config.generated.Parameter
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.PopulationType
equals(Object) - Method in class broadwick.config.generated.PopulationType
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Prior
equals(Object) - Method in class broadwick.config.generated.Prior
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Project.Data
equals(Object) - Method in class broadwick.config.generated.Project.Data
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.Project
equals(Object) - Method in class broadwick.config.generated.Project
equals(Object, EqualsBuilder) - Method in class broadwick.config.generated.UniformPrior
equals(Object) - Method in class broadwick.config.generated.UniformPrior
equals(Object) - Method in class broadwick.phylo.PhyloNode
errors - Variable in class broadwick.config.ConfigValidationErrors
errors - Variable in class broadwick.config.ConfigValidator
errorString - Variable in class broadwick.config.ConfigValidationErrors
Executor - Interface in broadwick.concurrent: Interface for all Broadwick executors, these include a LocalPoolExecutor, which runs and monitors jobs on a local machine, GridPoolExecutor which runs and monitors jobs on a grid environment and DistributedPoolExecutor which runs and monitors jobs in a distributed pool.
Executor.Status - Enum in broadwick.concurrent: Status of the executor.

F

Factorial - Class in broadwick.math: A recursive program to calculate the factorial of a number.
Factorial() - Constructor for class broadwick.math.Factorial: Hiding constructor for utility class.
factorial(int) - Static method in class broadwick.math.Factorial: Calculate the factorial of n.
fieldSep - Variable in class broadwick.io.FileInput
file - Variable in class broadwick.config.generated.Logs
File() - Constructor for class broadwick.config.generated.Logs.File
fileEncoding - Variable in class broadwick.io.FileInput
fileEncoding - Variable in class broadwick.io.FileOutput
FileInput - Class in broadwick.io: Simple interface for reading from a file.
FileInput(String) - Constructor for class broadwick.io.FileInput: Open a handle to a file with the given name.
FileInput(String, String) - Constructor for class broadwick.io.FileInput: Open a handle to a file with the given name.
FileInput(String, String, Charset) - Constructor for class broadwick.io.FileInput: Open a handle to a file with the given name.
fileInput - Variable in class broadwick.io.FileInputIterator
FileInputIterator - Class in broadwick.io: Iterator object for a FileInput object.
FileInputIterator(FileInput) - Constructor for class broadwick.io.FileInputIterator: Create a iterator over the contents of a file.
FileOutput - Class in broadwick.io: Simple interface to printing values to a file.
FileOutput() - Constructor for class broadwick.io.FileOutput: Create a null file output object similar to writing to /dev/null.
FileOutput(String) - Constructor for class broadwick.io.FileOutput: Create a file with the given name.
FileOutput(String, boolean) - Constructor for class broadwick.io.FileOutput: Create a file with the given name.
FileOutput(String, boolean, boolean) - Constructor for class broadwick.io.FileOutput: Create a file with the given name.
FileOutput(String, boolean, boolean, String) - Constructor for class broadwick.io.FileOutput: Create a file with the given name.
FileUtils - Class in broadwick.io: Simple utilities for file objects.
FileUtils() - Constructor for class broadwick.io.FileUtils: Constructor; hidden.
finalise() - Method in class broadwick.model.Model: End the model.
finalize() - Method in class broadwick.graph.DirectedGraph
finalize() - Method in class broadwick.graph.Edge
finalize() - Method in class broadwick.graph.Tree
finalize() - Method in class broadwick.graph.UndirectedGraph
finalize() - Method in class broadwick.graph.Vertex
finalize() - Method in class broadwick.montecarlo.Consumer
finalize() - Method in class broadwick.montecarlo.MonteCarlo
finalize() - Method in class broadwick.montecarlo.Producer
finalState - Variable in class broadwick.stochastic.SimulationEvent
findNodes(String) - Method in class broadwick.phylo.NewickTreeParser: Parse a tree splitting it into top level nodes and subtrees.
finished() - Method in class broadwick.montecarlo.markovchain.observer.MarkovChainObserver: Gets called when a simulation has finished, directly after the termination check.
finished() - Method in class broadwick.odesolver.Observer: Gets called when the ODE solver has finished, directly after the termination check.
finished() - Method in class broadwick.stochastic.Observer: Gets called when a simulation has finished, directly after the termination check.
first - Variable in class broadwick.utils.Pair
flush() - Method in class broadwick.io.FileOutput: Flushes the file stream.
fullMovementFile - Variable in class broadwick.config.generated.DataFiles
FullMovementFile() - Constructor for class broadwick.config.generated.DataFiles.FullMovementFile
FullMovementsFileReader - Class in broadwick.data.readers: Reader for the files describing the full movements (i.e.
FullMovementsFileReader(DataFiles.FullMovementFile, DatabaseImpl) - Constructor for class broadwick.data.readers.FullMovementsFileReader: Create the movement file reader.

G

GaussianPrior - Class in broadwick.config.generated: Java class for GaussianPrior complex type.
GaussianPrior() - Constructor for class broadwick.config.generated.GaussianPrior
gaussianPriorAndUniformPrior - Variable in class broadwick.config.generated.Models.Model.Priors
generate(MonteCarloStep) - Method in class broadwick.montecarlo.markovchain.proposal.MarkovNormalProposal
generate(MonteCarloStep) - Method in interface broadwick.montecarlo.markovchain.proposal.MarkovProposalFunction: Generate a new step in the Markov Chain based only on the supplied step.
GENERATED_CONFIG_CLASSES_DIR - Static variable in class broadwick.Constants
generateNextStep(MonteCarloStep) - Method in class broadwick.montecarlo.markovchain.MarkovChain
generateNextStep(MonteCarloStep) - Method in interface broadwick.montecarlo.markovchain.MarkovStepGenerator: Generate the next step in the path.
GENERATOR - Static variable in class broadwick.montecarlo.acceptor.MetropolisHastings
generator - Variable in class broadwick.montecarlo.markovchain.MarkovChain
GENERATOR - Static variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
GENERATOR - Static variable in class broadwick.montecarlo.markovchain.proposal.MarkovNormalProposal
generator - Variable in class broadwick.rng.RNG: Random number generator type.
Generator() - Constructor for enum broadwick.rng.RNG.Generator
GENERATOR - Static variable in class broadwick.statistics.distributions.IntegerDistribution
GENERATOR - Static variable in class broadwick.statistics.distributions.Normal
generator - Variable in class broadwick.statistics.distributions.TruncatedNormalDistribution
GENERATOR - Static variable in class broadwick.stochastic.algorithms.AbstractTauLeapingBase
GENERATOR - Static variable in class broadwick.stochastic.algorithms.GillespieSimple
getAlias() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the alias property.
getAlias() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the alias property.
getAlias() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the alias property.
getAlias() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the alias property.
getAlias() - Method in class broadwick.config.generated.DataFiles.PopulationFile: Gets the value of the alias property.
getAlias() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the alias property.
getAllModelConfigurations() - Method in class broadwick.Broadwick: Get a collection of XML elements one for each section.
getAnimal(String) - Method in class broadwick.data.Lookup: Get an animal from the list of animals in the system.
getAnimalLocationIdAtDate(String, int) - Method in class broadwick.data.Lookup: Get an animals location at a specified date.
getAnimals() - Method in class broadwick.data.Lookup: Get all the animals that have been read from the file(s) specified in the configuration file.
getAnimals(int) - Method in class broadwick.data.Lookup: Get all the animals that have been read from the file(s) specified in the configuration file whose date of birth is before or on a given date and whose date of death (it there is any) is on or after the same date.
getAttributeByName(String) - Method in class broadwick.graph.Edge: Obtain an attribute of this edge by the attributes name.
getAttributeByName(String) - Method in class broadwick.graph.Vertex: Obtain an attribute of this vertex by the attributes name.
getBatchMovementFile() - Method in class broadwick.config.generated.DataFiles: Gets the value of the batchMovementFile property.
getBatchSizeColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the batchSizeColumn property.
getBinContents() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get a collection of the values held in the histogram.
getBinomial(int, double) - Method in class broadwick.rng.RNG: Generates a random value from the binomial distribution with the given N and p.
getBins() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get the bins in the histogram.
getBoolean() - Method in class broadwick.rng.RNG: Get a boolean (true/false) value.
getCDF() - Method in class broadwick.stochastic.TransitionKernel: Get the cumulativeDistFn for this transition kernel.
getClassname() - Method in class broadwick.config.generated.Models.Model: Gets the value of the classname property.
getClosingParenthesis(String) - Method in class broadwick.phylo.NewickTreeParser: Get the index of the closing parenthesis in a string that starts with an opening parenthesis.
getColumn() - Method in class broadwick.config.generated.CustomTags.CustomTag: Gets the value of the column property.
getConfigurationFileName() - Method in class broadwick.CliOptions: Get the name of the configuration file specified on the command line.
getConnection() - Method in interface broadwick.data.DatabaseImpl: Get a connection to the database.
getConnection() - Method in class broadwick.data.H2Database
getConsole() - Method in class broadwick.config.generated.Logs: Gets the value of the console property.
getCustomTag() - Method in class broadwick.config.generated.CustomTags: Gets the value of the customTag property.
getCustomTags() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the customTags property.
getCustomTags() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the customTags property.
getCustomTags() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the customTags property.
getCustomTags() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the customTags property.
getCustomTags() - Method in class broadwick.config.generated.DataFiles.PopulationFile: Gets the value of the customTags property.
getCustomTags() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the customTags property.
getData() - Method in class broadwick.config.generated.Project: Gets the value of the data property.
getData(Integer) - Method in class broadwick.statistics.distributions.IntegerDistribution: Deprecated.
use getFrequency() instead
getDatabases() - Method in class broadwick.config.generated.Project.Data: Gets the value of the databases property.
getDatafiles() - Method in class broadwick.config.generated.Project.Data: Gets the value of the datafiles property.
getDate(DateTime) - Static method in class broadwick.BroadwickConstants: Convert a date object to an integer (number of days from a fixed start date, here 1/1/1900).
getDate(String, String) - Static method in class broadwick.BroadwickConstants: Convert a date object to an integer (number of days from a fixed start date, here 1/1/1900).
getDateFormat() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the dateFormat property.
getDateFormat() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the dateFormat property.
getDateFormat() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the dateFormat property.
getDateFormat() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the dateFormat property.
getDateFormat() - Method in class broadwick.config.generated.DataFiles.PopulationFile: Gets the value of the dateFormat property.
getDateFormat() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the dateFormat property.
getDateOfBirthColumn() - Method in class broadwick.config.generated.LifeHistoryType: Gets the value of the dateOfBirthColumn property.
getDateOfDeathColumn() - Method in class broadwick.config.generated.LifeHistoryType: Gets the value of the dateOfDeathColumn property.
getDefaultObserver() - Method in class broadwick.stochastic.StochasticSimulator: Get the default observer for the stochastic process.
getDepartureDateColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the departureDateColumn property.
getDepartureDateColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the departureDateColumn property.
getDepartureLocationIdColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the departureLocationIdColumn property.
getDepartureLocationIdColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the departureLocationIdColumn property.
getDependentVariables() - Method in class broadwick.odesolver.OdeSolver: Get the dependent variables.
getDependetVariablesAsCsv() - Method in class broadwick.odesolver.OdeSolver: Get a csv representation of the current state of the dependent variables.
getDepth(V) - Method in class broadwick.graph.Tree: Returns the (unweighted) distance of vertex from the root of this tree.
getDest(E) - Method in class broadwick.graph.DirectedGraph
getDest(E) - Method in interface broadwick.graph.Graph: If directed_edge is a directed edge in this graph, returns the destination; otherwise returns null.
getDest(E) - Method in class broadwick.graph.Tree
getDest(E) - Method in class broadwick.graph.UndirectedGraph
getDestinationDateColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the destinationDateColumn property.
getDestinationDateColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the destinationDateColumn property.
getDestinationLocationIdColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the destinationLocationIdColumn property.
getDestinationLocationIdColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the destinationLocationIdColumn property.
getDeviation() - Method in class broadwick.config.generated.GaussianPrior: Gets the value of the deviation property.
getDialect() - Method in interface broadwick.data.DatabaseImpl: Obtain the database dialect e.g.
getDialect() - Method in class broadwick.data.H2Database
getDirectedMovementFile() - Method in class broadwick.config.generated.DataFiles: Gets the value of the directedMovementFile property.
getDouble() - Method in class broadwick.rng.RNG: Generates a uniformly distributed random value from the open interval ( 0.0, 1.0) (i.e., endpoints excluded).
getDouble(double, double) - Method in class broadwick.rng.RNG: Generates a uniformly distributed random value from the open interval ( lower, upper) (i.e., endpoints excluded).
getEastingColumn() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the eastingColumn property.
getEdge(String) - Method in class broadwick.graph.DirectedGraph
getEdge(String) - Method in interface broadwick.graph.Graph: Returns a view the edges in this graph with the given id.
getEdge(String) - Method in class broadwick.graph.Tree
getEdge(String) - Method in class broadwick.graph.UndirectedGraph
getEdgeAttributes() - Method in interface broadwick.graph.Graph: Get the attributes for the edges in the graph.
getEdges() - Method in class broadwick.graph.DirectedGraph
getEdges() - Method in interface broadwick.graph.Graph: Returns a view of all edges in this graph.
getEdges() - Method in class broadwick.graph.Tree
getEdges() - Method in class broadwick.graph.UndirectedGraph
getEdgesInPath(V, V) - Method in class broadwick.graph.algorithms.ShortestPath: Returns a List of the edges on the shortest path from source to target, in order of their occurrence on this path.
getEdgeType() - Method in class broadwick.graph.DirectedGraph
getEdgeType() - Method in interface broadwick.graph.Graph: Get the type of edge (directed/undirected employed in the graph.
getEdgeType() - Method in class broadwick.graph.Tree
getEdgeType() - Method in class broadwick.graph.UndirectedGraph
getEndpoints(E) - Method in class broadwick.graph.DirectedGraph
getEndpoints(E) - Method in interface broadwick.graph.Graph: Returns the endpoints of edge as a Pair.
getEndpoints(E) - Method in class broadwick.graph.Tree
getEndpoints(E) - Method in class broadwick.graph.UndirectedGraph
getExpectedValue() - Method in class broadwick.montecarlo.MonteCarloDefaultResults
getExpectedValue() - Method in interface broadwick.montecarlo.MonteCarloResults: Get the score for the Monte Carlo simulation.
getExpectedValue() - Method in class broadwick.montecarlo.Poison
getFile() - Method in class broadwick.config.generated.Logs: Gets the value of the file property.
getFileExtension(String) - Static method in class broadwick.io.FileUtils: Get the extension of a file, given the name of the file.
getFrequency(Integer) - Method in class broadwick.statistics.distributions.IntegerDistribution: Get the size of the histogram at the given bin.
getFullMovementFile() - Method in class broadwick.config.generated.DataFiles: Gets the value of the fullMovementFile property.
getGaussian(double, double) - Method in class broadwick.rng.RNG: Generates a random value from the Normal (or Gaussian) distribution with the given mean and standard deviation.
getGaussianPriorAndUniformPrior() - Method in class broadwick.config.generated.Models.Model.Priors: Gets the value of the gaussianPriorAndUniformPrior property.
getGeometricMean() - Method in class broadwick.statistics.Samples: Obtain the geometric mean of the set of observables in the accumulator.
getGroupIdColumn() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the groupIdColumn property.
getHarmonicMean() - Method in class broadwick.statistics.Samples: Obtain the harmonic mean of the set of observables in the accumulator.
getHeight() - Method in class broadwick.graph.Tree: Returns the maximum depth in this tree.
getHint() - Method in class broadwick.config.generated.Parameter: Gets the value of the hint property.
getHint() - Method in class broadwick.config.generated.Prior: Gets the value of the hint property.
getId() - Method in class broadwick.config.generated.Models.Model: Gets the value of the id property.
getId() - Method in class broadwick.config.generated.Parameter: Gets the value of the id property.
getId() - Method in class broadwick.config.generated.Prior: Gets the value of the id property.
getIdColumn() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the idColumn property.
getIdColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the idColumn property.
getIdColumn() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the idColumn property.
getIdColumn() - Method in class broadwick.config.generated.LifeHistoryType: Gets the value of the idColumn property.
getImplementationTimeStamp() - Static method in class broadwick.BroadwickVersion: Get the build time in the Manifest.MF of the jar.
getImplementationTimeStamp(Manifest) - Static method in class broadwick.BroadwickVersion: Get the build timestamp from the supplied Manifest.mf file.
getImplementationVersion() - Static method in class broadwick.BroadwickVersion: Get the implementation number defined in the Manifest.MF of the jar.
getImplementationVersion(Manifest) - Static method in class broadwick.BroadwickVersion: Get the build version number from the supplied Manifest.mf file..
getInEdges(V) - Method in class broadwick.graph.DirectedGraph
getInEdges(V) - Method in interface broadwick.graph.Graph: Returns a Collection view of the incoming edges incident to vertex in this graph.
getInEdges(V) - Method in class broadwick.graph.Tree
getInEdges(V) - Method in class broadwick.graph.UndirectedGraph
getInitialStep() - Method in class broadwick.montecarlo.markovchain.MarkovChain
getInitialStep() - Method in interface broadwick.montecarlo.markovchain.MarkovStepGenerator: Get the initial Step of the path.
getInitialVal() - Method in class broadwick.config.generated.Prior: Gets the value of the initialVal property.
getInitialValues() - Method in interface broadwick.odesolver.Ode: Get the initial values of each dependent variable.
getInteger(int, int) - Method in class broadwick.rng.RNG: Generates a uniformly distributed random integer between lower and upper (endpoints included).
getIntercept() - Method in class broadwick.statistics.regression.SimpleLinearRegression: Returns the intercept of the estimated regression line.
getInterceptStdErr() - Method in class broadwick.statistics.regression.SimpleLinearRegression: Returns the standard error of the intercept estimate, usually denoted s(b0).
getLevel() - Method in class broadwick.config.generated.Logs.Console: Gets the value of the level property.
getLevel() - Method in class broadwick.config.generated.Logs.File: Gets the value of the level property.
getLifeHistory() - Method in class broadwick.config.generated.DataFiles.PopulationFile: Gets the value of the lifeHistory property.
getLocation(String) - Method in class broadwick.data.Lookup: Get a location from the list of locations in the system.
getLocationColumn() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the locationColumn property.
getLocationIdColumn() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the locationIdColumn property.
getLocationIdColumn() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the locationIdColumn property.
getLocationIdColumn() - Method in class broadwick.config.generated.PopulationType: Gets the value of the locationIdColumn property.
getLocationOfBirthColumn() - Method in class broadwick.config.generated.LifeHistoryType: Gets the value of the locationOfBirthColumn property.
getLocationOfDeathColumn() - Method in class broadwick.config.generated.LifeHistoryType: Gets the value of the locationOfDeathColumn property.
getLocations() - Method in class broadwick.data.Lookup: Get all the movements that have been read from the file(s) specified in the configuration file.
getLocationsFile() - Method in class broadwick.config.generated.DataFiles: Gets the value of the locationsFile property.
getLogs() - Method in class broadwick.config.generated.Project: Gets the value of the logs property.
getManifest() - Static method in class broadwick.BroadwickVersion: Get the object corresponding to the Manifest.mf file.
getMarketDateColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the marketDateColumn property.
getMarketDateColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the marketDateColumn property.
getMarketIdColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the marketIdColumn property.
getMarketIdColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the marketIdColumn property.
getMax() - Method in class broadwick.config.generated.UniformPrior: Gets the value of the max property.
getMean() - Method in class broadwick.config.generated.GaussianPrior: Gets the value of the mean property.
getMean() - Method in interface broadwick.statistics.distributions.DiscreteDistribution: Get the numerical value of the mean of this distribution.
getMean() - Method in class broadwick.statistics.distributions.HypergeometricDistribution: Get the numerical value of the mean of this distribution.
getMean() - Method in class broadwick.statistics.Samples: Obtain the mean of the set of observables in the accumulator.
getMin() - Method in class broadwick.config.generated.UniformPrior: Gets the value of the min property.
getModel() - Method in class broadwick.config.generated.Models: Gets the value of the model property.
getModels() - Method in class broadwick.config.generated.Project: Gets the value of the models property.
getModelsConfiguration(String, NodeList) - Method in class broadwick.Broadwick: Get the XML string of the model with the given id from a list of configured models.
getMovementDateColumn() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the movementDateColumn property.
getMovementDirectionColumn() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the movementDirectionColumn property.
getMovements() - Method in class broadwick.data.Lookup: Get all the movements that have been read from the file(s) specified in the configuration file.
getMovements(int, int) - Method in class broadwick.data.Lookup: Get all the movements that have been read from the file(s) specified in the configuration file filtered on a date range.
getMovementsForAnimal(String) - Method in class broadwick.data.Lookup: Get all the recorded movements for a given animal.
getN() - Method in class broadwick.statistics.distributions.MultinomialDistribution: Returns the parameter N of this object.
getN() - Method in class broadwick.statistics.regression.SimpleLinearRegression: Returns the number of observations that have been added to the model.
getName() - Method in class broadwick.config.generated.CustomTags.CustomTag: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.Databases: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.DataFiles.PopulationFile: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the name property.
getName() - Method in class broadwick.config.generated.Logs.File: Gets the value of the name property.
getName() - Method in class broadwick.stochastic.algorithms.GillespieSimple
getName() - Method in class broadwick.stochastic.algorithms.TauLeaping
getName() - Method in class broadwick.stochastic.algorithms.TauLeapingFixedStep
getName() - Method in class broadwick.stochastic.StochasticSimulator: Gets the name of the algorithm.
getNegativeResultColumn() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the negativeResultColumn property.
getNextEventDataAndRemove() - Method in class broadwick.odesolver.OdeSolver.ThetaQueue: Get the next observer and the collection of events they are subscribed to and remove it from the theta queue.
getNextEventDataAndRemove() - Method in class broadwick.stochastic.StochasticSimulator.ThetaQueue: Get the next observer and the collection of events they are subscribed to and remove it from the theta queue.
getNextThetaEventTime() - Method in class broadwick.odesolver.OdeSolver: Theta defines a moment, where the simulator has to invoke theta of a observers.
getNextThetaEventTime() - Method in class broadwick.stochastic.StochasticSimulator: Theta defines a moment, where the simulator has to invoke theta of a observers.
getNorthingColumn() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the northingColumn property.
getNullLocation() - Static method in class broadwick.data.Location: Get the NULL location, defined as the one with no id, coordinates or occupants.
getNumAnimals() - Method in class broadwick.data.Lookup: Get the number of animals stored in the internal database.
getNumBins() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get the number of bins.
getNumLocations() - Method in class broadwick.data.Lookup: Get the number of locations stored in the internal database.
getNumMovements() - Method in class broadwick.data.Lookup: Get the number of movements stored in the internal database.
getNumMovements(int, int) - Method in class broadwick.data.Lookup: Get the number of movements stored in the internal database filtered on a date range.
getNumTests() - Method in class broadwick.data.Lookup: Get the number of tests stored in the internal database.
getOffMovements(int, int) - Method in class broadwick.data.Lookup: Get all the OFF movements that have been read from the file(s) specified in the configuration file filtered on a date range.
getOnMovements(int, int) - Method in class broadwick.data.Lookup: Get all the ON movements that have been read from the file(s) specified in the configuration file filtered on a date range.
getOpposite(V, E) - Method in class broadwick.graph.DirectedGraph
getOpposite(V, E) - Method in interface broadwick.graph.Graph: Returns the vertex at the other end of edge from vertex.
getOpposite(V, E) - Method in class broadwick.graph.Tree
getOpposite(V, E) - Method in class broadwick.graph.UndirectedGraph
getOutEdges(V) - Method in class broadwick.graph.DirectedGraph
getOutEdges(V) - Method in interface broadwick.graph.Graph: Returns a Collection view of the outgoing edges incident to vertex in this graph.
getOutEdges(V) - Method in class broadwick.graph.Tree
getOutEdges(V) - Method in class broadwick.graph.UndirectedGraph
getP() - Method in class broadwick.statistics.distributions.MultinomialDistribution: Returns the parameters (probabilities₁,...,probabilities_d) of this object.
getParameter() - Method in class broadwick.config.generated.Models.Model: Gets the value of the parameter property.
getParameterValue(String) - Method in class broadwick.model.Model: Get the value of a parameter for the model given the parameter name (as defined in the config file).
getParameterValueAsBoolean(String) - Method in class broadwick.model.Model: Get the value (as a boolean) of a parameter for the model given the parameter name (as defined in the config file).
getParameterValueAsDouble(String) - Method in class broadwick.model.Model: Get the value (as a double) of a parameter for the model given the parameter name (as defined in the config file).
getParameterValueAsInteger(String) - Method in class broadwick.model.Model: Get the value (as an integer) of a parameter for the model given the parameter name (as defined in the config file).
getPattern() - Method in class broadwick.config.generated.Logs.Console: Gets the value of the pattern property.
getPattern() - Method in class broadwick.config.generated.Logs.File: Gets the value of the pattern property.
getPoisson(double) - Method in class broadwick.rng.RNG: Generates a random value from the Poisson distribution with the given mean.
getPopulation() - Method in class broadwick.config.generated.DataFiles.PopulationFile: Gets the value of the population property.
getPopulationDateColumn() - Method in class broadwick.config.generated.PopulationType: Gets the value of the populationDateColumn property.
getPopulationFile() - Method in class broadwick.config.generated.DataFiles: Gets the value of the populationFile property.
getPopulationSizeColumn() - Method in class broadwick.config.generated.PopulationType: Gets the value of the populationSizeColumn property.
getPostiveResultColumn() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the postiveResultColumn property.
getPredecessor(V) - Method in class broadwick.graph.Tree: Get the vertex in this graph that is the source of the (single) edge that is incident on this vertex.
getPredecessorCount(V) - Method in class broadwick.graph.DirectedGraph
getPredecessorCount(V) - Method in interface broadwick.graph.Graph: Returns the number of predecessors that vertex has in this graph.
getPredecessorCount(V) - Method in class broadwick.graph.Tree
getPredecessorCount(V) - Method in class broadwick.graph.UndirectedGraph
getPredecessors(V) - Method in class broadwick.graph.DirectedGraph
getPredecessors(V) - Method in interface broadwick.graph.Graph: Returns a Collection view of the predecessors of vertex in this graph.
getPredecessors(V) - Method in class broadwick.graph.Tree
getPredecessors(V) - Method in class broadwick.graph.UndirectedGraph
getPriors() - Method in class broadwick.config.generated.Models.Model: Gets the value of the priors property.
getR() - Method in class broadwick.statistics.regression.SimpleLinearRegression: Returns Pearson's product moment correlation coefficient, usually denoted r.
getRandomBin() - Method in class broadwick.statistics.distributions.IntegerDistribution: Select a random bin from the cumulative distribution of the histograms contents.
getRandomBinFrequency() - Method in class broadwick.statistics.distributions.IntegerDistribution: Select a random bin from the cumulative distribution of the frequencies and return the frequency.
getResults() - Method in class broadwick.montecarlo.MonteCarlo: Get a copy of the results from the simulation.
getRoot() - Method in class broadwick.graph.Tree: Returns the root of this tree.
getRootMeanSquare() - Method in class broadwick.statistics.Samples: Obtain the root mean square of the set of observables in the accumulator.
getSamples() - Method in class broadwick.montecarlo.MonteCarloDefaultResults
getSamples() - Method in interface broadwick.montecarlo.MonteCarloResults: Get the results of the Monte Carlo simulations as a Samples object.
getSamples() - Method in class broadwick.montecarlo.Poison
getSeparator() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the separator property.
getSeparator() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the separator property.
getSeparator() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the separator property.
getSeparator() - Method in class broadwick.config.generated.DataFiles.LocationsFile: Gets the value of the separator property.
getSeparator() - Method in class broadwick.config.generated.DataFiles.PopulationFile: Gets the value of the separator property.
getSeparator() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the separator property.
getSize() - Method in class broadwick.statistics.Samples: Get the number of items added to the Accumulator.
getSlope() - Method in class broadwick.statistics.regression.SimpleLinearRegression: Returns the slope of the estimated regression line.
getSlopeStdErr() - Method in class broadwick.statistics.regression.SimpleLinearRegression: Returns the standard error of the slope estimate.
getSource(E) - Method in class broadwick.graph.DirectedGraph
getSource(E) - Method in interface broadwick.graph.Graph: If directed_edge is a directed edge in this graph, returns the source; otherwise returns null.
getSource(E) - Method in class broadwick.graph.Tree
getSource(E) - Method in class broadwick.graph.UndirectedGraph
getSpeciesColumn() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Gets the value of the speciesColumn property.
getSpeciesColumn() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Gets the value of the speciesColumn property.
getSpeciesColumn() - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Gets the value of the speciesColumn property.
getSpeciesColumn() - Method in class broadwick.config.generated.LifeHistoryType: Gets the value of the speciesColumn property.
getSpeciesColumn() - Method in class broadwick.config.generated.PopulationType: Gets the value of the speciesColumn property.
getStateName() - Method in interface broadwick.stochastic.SimulationState: Get the name of the state.
getStatus() - Method in interface broadwick.concurrent.Executor: Get the current status of the jobs in the executor.
getStatus() - Method in class broadwick.concurrent.LocalPoolExecutor
getStdDev() - Method in class broadwick.statistics.Samples: Obtain the standard deviation (error in the mean) of the set of observeables in the accumulator.
getSubTree(V) - Method in class broadwick.graph.Tree: Obtain the sub-tree with vertex as it's root.
getSuccessorCount(V) - Method in class broadwick.graph.DirectedGraph
getSuccessorCount(V) - Method in interface broadwick.graph.Graph: Returns the number of successors that vertex has in this graph.
getSuccessorCount(V) - Method in class broadwick.graph.Tree
getSuccessorCount(V) - Method in class broadwick.graph.UndirectedGraph
getSuccessors(V) - Method in class broadwick.graph.DirectedGraph
getSuccessors(V) - Method in interface broadwick.graph.Graph: Returns a Collection view of the successors of vertex in this graph.
getSuccessors(V) - Method in class broadwick.graph.Tree
getSuccessors(V) - Method in class broadwick.graph.UndirectedGraph
getSum() - Method in class broadwick.statistics.Samples: Get the sum of the values held in the accumulator.
getSumCounts() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get the sum of the counts in the histogram.
getSummary() - Method in class broadwick.statistics.Samples: Get a tab delimited string of the mean and standard deviation of the values in the accumulator.
getTestDateColumn() - Method in class broadwick.config.generated.DataFiles.TestsFile: Gets the value of the testDateColumn property.
getTests() - Method in class broadwick.data.Lookup: Get all the tests that have been read from the file(s) specified in the configuration file.
getTests(int, int) - Method in class broadwick.data.Lookup: Get all the tests that have been read from the file(s) specified in the configuration file.
getTestsFile() - Method in class broadwick.config.generated.DataFiles: Gets the value of the testsFile property.
getTransitionEvents() - Method in class broadwick.stochastic.TransitionKernel: Get the collection of events stored in the transition kernel.
getTransitionProbability(SimulationEvent) - Method in class broadwick.stochastic.TransitionKernel: Get the probability of an event occurring.
getType() - Method in class broadwick.config.generated.CustomTags.CustomTag: Gets the value of the type property.
getUniformPrior(String) - Method in class broadwick.model.Model: Get the prior of a paramter for the model given the parameter name (as defined in the config file).
getValidatedProject() - Method in class broadwick.config.ConfigValidator: If the project has been validated, i.e.
getValidationErrors() - Method in class broadwick.config.ConfigValidationErrors: Get the validation errors.
getValue() - Method in class broadwick.config.generated.Parameter: Gets the value of the value property.
getVariance() - Method in interface broadwick.statistics.distributions.DiscreteDistribution: Get the numerical value of the variance of this distribution.
getVariance() - Method in class broadwick.statistics.distributions.HypergeometricDistribution: Get the numerical value of the variance of this distribution.
getVariance() - Method in class broadwick.statistics.Samples: Default sample variance implementation based on the second moment \f$ M_n^{(2)} \f$ moment<2>, mean and count.
getVersionAndTimeStamp() - Static method in class broadwick.BroadwickVersion: Get the build version number and timestamp.
getVertex(String) - Method in class broadwick.graph.DirectedGraph
getVertex(String) - Method in interface broadwick.graph.Graph: Returns a view the vertex in this graph with a given id.Returns null if the edge does not exist.
getVertex(String) - Method in class broadwick.graph.Tree
getVertex(String) - Method in class broadwick.graph.UndirectedGraph
getVertexAttributes() - Method in interface broadwick.graph.Graph: Get the attributes for the vertics in the graph.
getVertexCount() - Method in class broadwick.graph.DirectedGraph
getVertexCount() - Method in interface broadwick.graph.Graph: Returns the number of vertices in this graph.
getVertexCount() - Method in class broadwick.graph.Tree
getVertexCount() - Method in class broadwick.graph.UndirectedGraph
getVertices() - Method in class broadwick.graph.DirectedGraph
getVertices() - Method in interface broadwick.graph.Graph: Returns a view of all vertices in this graph.
getVertices() - Method in class broadwick.graph.Tree
getVertices() - Method in class broadwick.graph.UndirectedGraph
GillespieSimple - Class in broadwick.stochastic.algorithms: Implementation of Gillespie's Direct method.
GillespieSimple(AmountManager, TransitionKernel) - Constructor for class broadwick.stochastic.algorithms.GillespieSimple: Implementation of Gillespie's Direct method.
GillespieSimple(AmountManager, TransitionKernel, boolean) - Constructor for class broadwick.stochastic.algorithms.GillespieSimple: Implementation of Gillespie's Direct method.
goOn(ApproxBayesianComp) - Method in interface broadwick.abc.AbcController: Returns whether or not to continue with the calculation.
goOn(ApproxBayesianComp) - Method in class broadwick.abc.AbcMaxNumStepController
goOn(MarkovChainMonteCarlo) - Method in interface broadwick.montecarlo.markovchain.controller.MarkovChainController: Returns whether or not to continue with the calculation.
goOn(MarkovChainMonteCarlo) - Method in class broadwick.montecarlo.markovchain.controller.MarkovChainMaxNumStepController
goOn(OdeSolver) - Method in class broadwick.odesolver.DefaultOdeController
goOn(OdeSolver) - Method in interface broadwick.odesolver.OdeController: Returns whether or not to continue with the stepwise solution of the ode.
goOn(StochasticSimulator) - Method in class broadwick.stochastic.DefaultController
goOn(StochasticSimulator) - Method in interface broadwick.stochastic.SimulationController: Returns whether or not to go on with the given simulation.
graph - Variable in class broadwick.graph.DirectedGraph
Graph<V extends Vertex,E extends Edge<V>> - Interface in broadwick.graph: A graph consisting of a set of vertices of type V set and a set of edges of type E.
graph - Variable in class broadwick.graph.UndirectedGraph
GraphMl - Class in broadwick.graph.writer: Simple class to write the nodes/edges of a network in graphML format.
GraphMl() - Constructor for class broadwick.graph.writer.GraphMl: hidden constructor for static class.
GraphViz - Class in broadwick.graph.writer: Simple class to write the nodes/edges of a network in graphviz (dot) format.
GraphViz() - Constructor for class broadwick.graph.writer.GraphViz: hidden constructor for static class.
GraphWriter - Interface in broadwick.graph.writer: Interface defining the writers.
group - Variable in class broadwick.data.Test
GROUP_ID - Static variable in class broadwick.data.readers.TestsFileReader
groupIdColumn - Variable in class broadwick.config.generated.DataFiles.TestsFile

H

H2Database - Class in broadwick.data: Implementation of a H2 database.
H2Database(String) - Constructor for class broadwick.data.H2Database: Create a new H2 database instance for a given database name.
H2Database(String, boolean) - Constructor for class broadwick.data.H2Database: Create a new H2 database instance for a given database name.
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.CustomTags.CustomTag
hashCode() - Method in class broadwick.config.generated.CustomTags.CustomTag
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.CustomTags
hashCode() - Method in class broadwick.config.generated.CustomTags
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Databases
hashCode() - Method in class broadwick.config.generated.Databases
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
hashCode() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
hashCode() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.DataFiles.FullMovementFile
hashCode() - Method in class broadwick.config.generated.DataFiles.FullMovementFile
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.DataFiles
hashCode() - Method in class broadwick.config.generated.DataFiles
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.DataFiles.LocationsFile
hashCode() - Method in class broadwick.config.generated.DataFiles.LocationsFile
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.DataFiles.PopulationFile
hashCode() - Method in class broadwick.config.generated.DataFiles.PopulationFile
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.DataFiles.TestsFile
hashCode() - Method in class broadwick.config.generated.DataFiles.TestsFile
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.GaussianPrior
hashCode() - Method in class broadwick.config.generated.GaussianPrior
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.LifeHistoryType
hashCode() - Method in class broadwick.config.generated.LifeHistoryType
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Logs.Console
hashCode() - Method in class broadwick.config.generated.Logs.Console
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Logs.File
hashCode() - Method in class broadwick.config.generated.Logs.File
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Logs
hashCode() - Method in class broadwick.config.generated.Logs
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Models
hashCode() - Method in class broadwick.config.generated.Models
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Models.Model
hashCode() - Method in class broadwick.config.generated.Models.Model
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Models.Model.Priors
hashCode() - Method in class broadwick.config.generated.Models.Model.Priors
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Parameter
hashCode() - Method in class broadwick.config.generated.Parameter
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.PopulationType
hashCode() - Method in class broadwick.config.generated.PopulationType
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Prior
hashCode() - Method in class broadwick.config.generated.Prior
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Project.Data
hashCode() - Method in class broadwick.config.generated.Project.Data
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.Project
hashCode() - Method in class broadwick.config.generated.Project
hashCode(HashCodeBuilder) - Method in class broadwick.config.generated.UniformPrior
hashCode() - Method in class broadwick.config.generated.UniformPrior
hashCode() - Method in class broadwick.phylo.PhyloNode
hasNext() - Method in class broadwick.graph.DepthFirstIterator
hasNext() - Method in class broadwick.io.FileInputIterator
hasParameter(String) - Method in class broadwick.model.Model: Determine whether or not a parameter exists in the config file.
hint - Variable in class broadwick.config.generated.Parameter
hint - Variable in class broadwick.config.generated.Prior
HypergeometricDistribution - Class in broadwick.statistics.distributions: The hypergeometric distribution applies to sampling without replacement from a finite population whose elements can be classified into two mutually exclusive categories like Pass/Fail.
HypergeometricDistribution(int, int, int) - Constructor for class broadwick.statistics.distributions.HypergeometricDistribution: A hypergeometric distribution gives the distribution of the number of successes in $n$ draws from a population of size $N$ containing $n_{succ}$ successes.

I

id - Variable in class broadwick.config.generated.Models.Model
id - Variable in class broadwick.config.generated.Parameter
id - Variable in class broadwick.config.generated.Prior
id - Variable in class broadwick.data.Animal
id - Variable in class broadwick.data.Location
id - Variable in class broadwick.data.Movement
ID - Static variable in class broadwick.data.readers.DirectedMovementsFileReader
ID - Static variable in class broadwick.data.readers.FullMovementsFileReader
ID - Static variable in class broadwick.data.readers.LocationsFileReader
ID - Static variable in class broadwick.data.readers.PopulationsFileReader
ID - Static variable in class broadwick.data.readers.TestsFileReader
id - Variable in class broadwick.data.Test
id - Variable in class broadwick.graph.Edge
id - Variable in class broadwick.graph.Vertex
idColumn - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
idColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
idColumn - Variable in class broadwick.config.generated.DataFiles.TestsFile
idColumn - Variable in class broadwick.config.generated.LifeHistoryType
IMPL_BUILD - Static variable in class broadwick.BroadwickVersion
IMPL_VERSION - Static variable in class broadwick.BroadwickVersion
inDegree(V) - Method in class broadwick.graph.DirectedGraph
inDegree(V) - Method in interface broadwick.graph.Graph: Returns the number of incoming edges incident to vertex.
inDegree(V) - Method in class broadwick.graph.Tree
inDegree(V) - Method in class broadwick.graph.UndirectedGraph
independentVariableEnd - Variable in class broadwick.odesolver.OdeSolver
independentVariableStart - Variable in class broadwick.odesolver.OdeSolver
init() - Method in class broadwick.model.Model: Initialise the model.
init(int) - Method in class broadwick.statistics.distributions.IntegerDistribution: Add a number of entries (keys) to the histogram (with zero value).
init() - Method in class broadwick.stochastic.StochasticSimulator: Initializes the algorithm.
initialState - Variable in class broadwick.stochastic.SimulationEvent
initialStep - Variable in class broadwick.montecarlo.markovchain.MarkovChain
initialVal - Variable in class broadwick.config.generated.Prior
insert() - Method in class broadwick.data.readers.BatchedMovementsFileReader
insert(Connection, String, String, String, String, Map<String, Integer>, Collection<Integer>) - Method in class broadwick.data.readers.DataFileReader: Perform the insertion into the database.
insert() - Method in class broadwick.data.readers.DataFileReader: Insert the data from the input file into the database.
insert() - Method in class broadwick.data.readers.DirectedMovementsFileReader: Insert the data from the input file into the database.
insert() - Method in class broadwick.data.readers.FullMovementsFileReader
insert() - Method in class broadwick.data.readers.LocationsFileReader
insert() - Method in class broadwick.data.readers.PopulationsFileReader
insert() - Method in class broadwick.data.readers.TestsFileReader
insertedColInfo - Variable in class broadwick.data.readers.BatchedMovementsFileReader
insertedColInfo - Variable in class broadwick.data.readers.DirectedMovementsFileReader
insertedColInfo - Variable in class broadwick.data.readers.FullMovementsFileReader
insertedColInfo - Variable in class broadwick.data.readers.LocationsFileReader
insertedColInfo - Variable in class broadwick.data.readers.PopulationsFileReader
insertedColInfo - Variable in class broadwick.data.readers.TestsFileReader
insertString - Variable in class broadwick.data.readers.BatchedMovementsFileReader
insertString - Variable in class broadwick.data.readers.DirectedMovementsFileReader
insertString - Variable in class broadwick.data.readers.FullMovementsFileReader
insertString - Variable in class broadwick.data.readers.LocationsFileReader
insertString - Variable in class broadwick.data.readers.PopulationsFileReader
insertString - Variable in class broadwick.data.readers.TestsFileReader
IntegerDistribution - Class in broadwick.statistics.distributions: A simple class for defining custom distributions.
IntegerDistribution() - Constructor for class broadwick.statistics.distributions.IntegerDistribution: Create an empty distribution.
IntegerDistribution(int) - Constructor for class broadwick.statistics.distributions.IntegerDistribution: Create the distribution with a specified number of bins.
intersection(Collection<T>, Collection<T>) - Static method in class broadwick.math.SetOperations: Get the intersection of two sets.
inverse() - Method in class broadwick.math.Matrix: Get the inverse of the matrix.
isDest(V, E) - Method in class broadwick.graph.DirectedGraph
isDest(V, E) - Method in interface broadwick.graph.Graph: Returns true if vertex is the destination of edge.
isDest(V, E) - Method in class broadwick.graph.Tree
isDest(V, E) - Method in class broadwick.graph.UndirectedGraph
isOverwrite() - Method in class broadwick.config.generated.Logs.File: Gets the value of the overwrite property.
isPredecessor(V, V) - Method in class broadwick.graph.DirectedGraph
isPredecessor(V, V) - Method in interface broadwick.graph.Graph: Returns true if v1 is a predecessor of v2 in this graph.
isPredecessor(V, V) - Method in class broadwick.graph.Tree
isPredecessor(V, V) - Method in class broadwick.graph.UndirectedGraph
isSource(V, E) - Method in class broadwick.graph.DirectedGraph
isSource(V, E) - Method in interface broadwick.graph.Graph: Returns true if vertex is the source of edge.
isSource(V, E) - Method in class broadwick.graph.Tree
isSource(V, E) - Method in class broadwick.graph.UndirectedGraph
isSubset(Set<T>, Set<T>) - Static method in class broadwick.math.SetOperations: Is setA a subset of setB.
isSuccessor(V, V) - Method in class broadwick.graph.DirectedGraph
isSuccessor(V, V) - Method in interface broadwick.graph.Graph: Returns true if v1 is a successor of v2 in this graph.
isSuccessor(V, V) - Method in class broadwick.graph.Tree
isSuccessor(V, V) - Method in class broadwick.graph.UndirectedGraph
isSuperset(Set<T>, Set<T>) - Static method in class broadwick.math.SetOperations: Is setA a superset of setB.
isThetaEventInCurrentStep(double) - Method in class broadwick.stochastic.algorithms.AbstractTauLeapingBase: Determine of there is a theta event in the current time step, taking into account possible reverse time jumps.
isThetaEventInCurrentStep(double) - Method in class broadwick.stochastic.algorithms.GillespieSimple: Determine of there is a theta event in the current time step, taking into account possible reverse time jumps.
iterator() - Method in class broadwick.io.FileInput: Obtain an iterator for this input file.

J

job - Variable in class broadwick.concurrent.LocalPoolExecutor
join(MonteCarloResults) - Method in class broadwick.montecarlo.MonteCarloDefaultResults
join(MonteCarloResults) - Method in interface broadwick.montecarlo.MonteCarloResults: Join another Monte Carlo results object to this one.
join(MonteCarloResults) - Method in class broadwick.montecarlo.Poison
joinedResults - Variable in class broadwick.montecarlo.Consumer
jooq - Variable in class broadwick.data.Lookup
jungGraph - Variable in class broadwick.graph.algorithms.ShortestPath

K

kernel - Variable in class broadwick.stochastic.TransitionKernel

L

length() - Method in class broadwick.math.Vector: Obtain the length, i.e.
level - Variable in class broadwick.config.generated.Logs.Console
level - Variable in class broadwick.config.generated.Logs.File
LIFE_HISTORIES_TABLE_NAME - Static variable in class broadwick.data.readers.PopulationsFileReader
lifeHistory - Variable in class broadwick.config.generated.DataFiles.PopulationFile
LifeHistoryType - Class in broadwick.config.generated: Java class for LifeHistoryType complex type.
LifeHistoryType() - Constructor for class broadwick.config.generated.LifeHistoryType
LINEWIDTH - Static variable in class broadwick.CliOptions
lnFactorial(int) - Static method in class broadwick.math.Factorial: Returns the value of the natural logarithm of factorial n.
LocalPoolExecutor - Class in broadwick.concurrent: This Executor controls the execution of several threads using a fixed thread pool.
LocalPoolExecutor(int, int, Callable<?>) - Constructor for class broadwick.concurrent.LocalPoolExecutor: Create the Callable executor that will run a supplied number of instances of a supplied callable, canceling the execution if a thread throws an exception.
LocalPoolExecutor(int, List<Callable<?>>) - Constructor for class broadwick.concurrent.LocalPoolExecutor: Create the Callable executor that will run each callable in a collection, canceling the execution if a thread throws an exception.
Location - Class in broadwick.data: Utility class for location data.
Location(String, Double, Double, Map<String, Integer>) - Constructor for class broadwick.data.Location: Create a new location from a location id and coordinates.
LOCATION - Static variable in class broadwick.data.readers.PopulationsFileReader
location - Variable in class broadwick.data.Test
LOCATION_ID - Static variable in class broadwick.data.readers.DirectedMovementsFileReader
LOCATION_ID - Static variable in class broadwick.data.readers.TestsFileReader
LOCATION_OF_BIRTH - Static variable in class broadwick.data.readers.PopulationsFileReader
LOCATION_OF_DEATH - Static variable in class broadwick.data.readers.PopulationsFileReader
locationColumn - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
locationIdColumn - Variable in class broadwick.config.generated.DataFiles.LocationsFile
locationIdColumn - Variable in class broadwick.config.generated.DataFiles.TestsFile
locationIdColumn - Variable in class broadwick.config.generated.PopulationType
locationOfBirth - Variable in class broadwick.data.Animal
locationOfBirthColumn - Variable in class broadwick.config.generated.LifeHistoryType
locationOfDeath - Variable in class broadwick.data.Animal
locationOfDeathColumn - Variable in class broadwick.config.generated.LifeHistoryType
locationsCache - Variable in class broadwick.data.Lookup
locationsFile - Variable in class broadwick.config.generated.DataFiles
LocationsFile() - Constructor for class broadwick.config.generated.DataFiles.LocationsFile
LocationsFileReader - Class in broadwick.data.readers: Reader for the files describing the locations for the simulation.
LocationsFileReader(DataFiles.LocationsFile, DatabaseImpl) - Constructor for class broadwick.data.readers.LocationsFileReader: Create the locations file reader.
log - Variable in class broadwick.Broadwick
logDbStatistics() - Method in class broadwick.data.DataReader: Save a message giving the numbers of elements in the database.
logFormatThreadMsg - Variable in class broadwick.LoggingFacade
loggerContext - Variable in class broadwick.LoggingFacade
LoggingFacade - Class in broadwick: Facade class to the underlying logger to allow the loggers to be configured programmatically.
LoggingFacade() - Constructor for class broadwick.LoggingFacade: Create the logging facade, by default adding a console logger to output logging info to the screen (console).
Logs - Class in broadwick.config.generated: Java class for Logs complex type.
Logs() - Constructor for class broadwick.config.generated.Logs
logs - Variable in class broadwick.config.generated.Project
Logs.Console - Class in broadwick.config.generated: Java class for anonymous complex type.
Logs.File - Class in broadwick.config.generated: Java class for anonymous complex type.
lookup - Variable in class broadwick.data.DataReader
Lookup - Class in broadwick.data: This class works as an interface to the databases holding the movements, locations and animal data read from the configuration file.
Lookup(DatabaseImpl) - Constructor for class broadwick.data.Lookup: Create the lookup object for accessing data in the internal databases.
lookup - Variable in class broadwick.model.Model
lower - Variable in class broadwick.statistics.distributions.TruncatedNormalDistribution
lowerBounds - Variable in class broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution

M

main(String[]) - Static method in class broadwick.Broadwick: Invocation point.
MARKET_DATE - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
MARKET_DATE - Static variable in class broadwick.data.readers.FullMovementsFileReader
MARKET_ID - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
MARKET_ID - Static variable in class broadwick.data.readers.FullMovementsFileReader
marketDate - Variable in class broadwick.data.Movement
marketDateColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
marketDateColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
marketId - Variable in class broadwick.data.Movement
marketIdColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
marketIdColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
MarkovChain - Class in broadwick.montecarlo.markovchain: An implementation of a Markov Chain which stores the history.
MarkovChain(MonteCarloStep) - Constructor for class broadwick.montecarlo.markovchain.MarkovChain: Create a new Markov chain with an initial step.
MarkovChain(MonteCarloStep, MarkovProposalFunction) - Constructor for class broadwick.montecarlo.markovchain.MarkovChain: Create a new Markov Chain with an initial step and proposal function.
MarkovChainController - Interface in broadwick.montecarlo.markovchain.controller: Controller class for running monte carlo calculations.
MarkovChainMaxNumStepController - Class in broadwick.montecarlo.markovchain.controller: Create a default controller that run 1000 steps.
MarkovChainMaxNumStepController() - Constructor for class broadwick.montecarlo.markovchain.controller.MarkovChainMaxNumStepController: Create a Monte Carlo controller object that stops the run after a specified number of steps (a fixed path length).
MarkovChainMaxNumStepController(int) - Constructor for class broadwick.montecarlo.markovchain.controller.MarkovChainMaxNumStepController: Create a Monte Carlo controller object that stops the run after a specified number of steps (a fixed path length).
MarkovChainMonteCarlo - Class in broadwick.montecarlo.markovchain: Monte Carlo class that is responsible for constructing Monte Carlo chains and the simulations thereon.
MarkovChainMonteCarlo(MonteCarloScenario, int, MonteCarloResults, MarkovStepGenerator) - Constructor for class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo: Create a Monte Carlo instance.
MarkovChainMonteCarlo(MonteCarloScenario, int, MonteCarloResults, MarkovChainController, MarkovStepGenerator) - Constructor for class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo: Create a Monte Carlo instance.
MarkovChainObserver - Class in broadwick.montecarlo.markovchain.observer: Implementing classes are used to take measurements during a Monte Carlo run.
MarkovChainObserver(MarkovChainMonteCarlo) - Constructor for class broadwick.montecarlo.markovchain.observer.MarkovChainObserver: Creates an observer dedicated to one Monte Carlo process.
MarkovNormalProposal - Class in broadwick.montecarlo.markovchain.proposal: A proposal class that samples each new parameter in the steps coordinate from a normal distribution.
MarkovNormalProposal() - Constructor for class broadwick.montecarlo.markovchain.proposal.MarkovNormalProposal
MarkovProposalFunction - Interface in broadwick.montecarlo.markovchain.proposal: A Markov proposal distribution generates a new step in a Markov Chain (i.e.
MarkovStepGenerator - Interface in broadwick.montecarlo.markovchain: A Path consists of several steps generated at random.
Matrix - Class in broadwick.math: Implementation of real valued Matrix.
Matrix(Array2DRowRealMatrix) - Constructor for class broadwick.math.Matrix: Create a matrix from the internal representation of the matrix (copy construtor).
Matrix(double[][]) - Constructor for class broadwick.math.Matrix: Create a matrix using the data in an array (copy constructor).
Matrix(int, int) - Constructor for class broadwick.math.Matrix: Create a matrix with the given dimensions.
max - Variable in class broadwick.config.generated.UniformPrior
max(long[]) - Static method in class broadwick.utils.ArrayUtils: Get the maximum element in an array of longs.
maxSteps - Variable in class broadwick.montecarlo.markovchain.controller.MarkovChainMaxNumStepController
maxTime - Variable in class broadwick.stochastic.DefaultController
mcController - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
mean - Variable in class broadwick.config.generated.GaussianPrior
mean - Variable in class broadwick.statistics.distributions.Normal
mean - Variable in class broadwick.statistics.distributions.TruncatedNormalDistribution
means - Variable in class broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution
MetropolisHastings - Class in broadwick.montecarlo.acceptor: A Metropolis-Hastings acceptor.
MetropolisHastings(int) - Constructor for class broadwick.montecarlo.acceptor.MetropolisHastings: Create a MetropolisHastings acceptor with a given random seed.
min - Variable in class broadwick.config.generated.UniformPrior
mnd - Variable in class broadwick.statistics.distributions.MultivariateNormalDistribution
model - Variable in class broadwick.abc.ApproxBayesianComp
model - Variable in class broadwick.config.generated.Models
Model() - Constructor for class broadwick.config.generated.Models.Model
Model - Class in broadwick.model: This interface declares a model for the Broadwick framework.
Model() - Constructor for class broadwick.model.Model
model - Variable in class broadwick.model.Model
model - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
ModelParameterException - Exception in broadwick.model: This class defines a checked exception in dealing with model parameters.
ModelParameterException() - Constructor for exception broadwick.model.ModelParameterException: Constructs a ModelParameterException with null as its error message string.
ModelParameterException(String) - Constructor for exception broadwick.model.ModelParameterException: Constructs a ModelParameterException, saving a reference to the error message string s for later retrieval by the getMessage method.
Models - Class in broadwick.config.generated: Java class for Models complex type.
Models() - Constructor for class broadwick.config.generated.Models
models - Variable in class broadwick.config.generated.Project
Models.Model - Class in broadwick.config.generated: Java class for anonymous complex type.
Models.Model.Priors - Class in broadwick.config.generated: Java class for anonymous complex type.
monteCarlo - Variable in class broadwick.montecarlo.markovchain.observer.MarkovChainObserver
MonteCarlo - Class in broadwick.montecarlo: An implementation of the Monte Carlo method, it runs many MonteCarloSimulations and gathers the statistics of their outputs.
MonteCarlo(MonteCarloScenario, int) - Constructor for class broadwick.montecarlo.MonteCarlo: Create a Monte Carlo object that is capable of running numSimulation MonteCarloScenarios.
MonteCarloAcceptor - Interface in broadwick.montecarlo.acceptor: MonteCarloAcceptor for a Monte Carlo step.
MonteCarloDefaultResults - Class in broadwick.montecarlo: A default implementation for the MonteCarloResults interface.
MonteCarloDefaultResults() - Constructor for class broadwick.montecarlo.MonteCarloDefaultResults: Create a default implementation of the MonteCarloResults class.
MonteCarloResults - Interface in broadwick.montecarlo: This interface encapsulates the results from a Monte Carlo run.
MonteCarloScenario - Class in broadwick.montecarlo: A simple model class thats runs a model and creates named quantities, i.e.
MonteCarloScenario() - Constructor for class broadwick.montecarlo.MonteCarloScenario
MonteCarloStep - Class in broadwick.montecarlo: A representation of the current step in a Markov Chain.
MonteCarloStep(MonteCarloStep) - Constructor for class broadwick.montecarlo.MonteCarloStep: Copy constructor.
MonteCarloStep(Map<String, Double>) - Constructor for class broadwick.montecarlo.MonteCarloStep: Create a single step in a Markov Chain.
Movement - Class in broadwick.data: Utility class for movement data.
Movement() - Constructor for class broadwick.data.Movement
MOVEMENT_DATE - Static variable in class broadwick.data.readers.DirectedMovementsFileReader
MOVEMENT_DIRECTION - Static variable in class broadwick.data.readers.DirectedMovementsFileReader
movementDateColumn - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
movementDirectionColumn - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
movementsCache - Variable in class broadwick.data.Lookup
MovementsComparator - Class in broadwick.data: Implement a comparator for movements so that movements can be stored in ascending date order with OFF movements appearing before ON movements in the movements cache.
MovementsComparator() - Constructor for class broadwick.data.MovementsComparator
MultinomialDistribution - Class in broadwick.statistics.distributions: Defines the Multinomial distribution with parameters numSamples and probabilities₁, ...,probabilities_d.
MultinomialDistribution(int, double[]) - Constructor for class broadwick.statistics.distributions.MultinomialDistribution: Creates a MultinomialDist object with parameters numSamples and (probabilities₁,...,probabilities_d) such that ∑_i=1^dprobabilities_i = 1.
multiply(Matrix) - Method in class broadwick.math.Matrix: Returns the result of postmultiplying this by m.
multiply(double) - Method in class broadwick.math.Matrix: Returns the result of postmultiplying this by a scalar.
multiply(Vector) - Method in class broadwick.math.Matrix: Returns the result of multiplying this by the vector v.
multiply(Vector) - Method in class broadwick.math.Vector: Calculate the dot product of this vector with v.
MultivariateNormalDistribution - Class in broadwick.statistics.distributions: Sample from a Multivariate Normal (Gaussian) Distribution, a generalization of the one-dimensional (univariate) normal distribution to higher dimensions.
MultivariateNormalDistribution(double[], double[][]) - Constructor for class broadwick.statistics.distributions.MultivariateNormalDistribution: Create a normal distribution with a given mean and standard deviation.

N

n - Variable in class broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution
name - Variable in class broadwick.config.generated.CustomTags.CustomTag
name - Variable in class broadwick.config.generated.Databases
name - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
name - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
name - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
name - Variable in class broadwick.config.generated.DataFiles.LocationsFile
name - Variable in class broadwick.config.generated.DataFiles.PopulationFile
name - Variable in class broadwick.config.generated.DataFiles.TestsFile
name - Variable in class broadwick.config.generated.Logs.File
name - Variable in class broadwick.graph.EdgeAttribute
name - Variable in class broadwick.graph.VertexAttribute
name - Variable in class broadwick.rng.RNG
NEGATIVE_RESULT - Static variable in class broadwick.data.readers.TestsFileReader
negativeResult - Variable in class broadwick.data.Test
negativeResultColumn - Variable in class broadwick.config.generated.DataFiles.TestsFile
newickString - Variable in class broadwick.phylo.NewickTreeParser
NewickTreeParser - Class in broadwick.phylo: Parser for a Newick tree.
NewickTreeParser(String) - Constructor for class broadwick.phylo.NewickTreeParser: Create the parser.
NewickTreeParser() - Constructor for class broadwick.phylo.NewickTreeParser: Create the parser.
NEWLINE - Static variable in class broadwick.config.ConfigValidationErrors
next() - Method in class broadwick.graph.DepthFirstIterator
next() - Method in class broadwick.io.FileInputIterator
nextThetaEventTime - Variable in class broadwick.odesolver.OdeSolver.ThetaQueue
nextThetaEventTime - Variable in class broadwick.stochastic.StochasticSimulator.ThetaQueue
Normal - Class in broadwick.statistics.distributions: Sample fro a Normal (Gaussian) Distribution.
Normal() - Constructor for class broadwick.statistics.distributions.Normal: Create a normal distribution of zero mean and unit standard deviation.
Normal(double, double) - Constructor for class broadwick.statistics.distributions.Normal: Create a normal distribution with a given mean and standard deviation.
normaliseBins(int) - Method in class broadwick.statistics.distributions.IntegerDistribution: Normalise the frequency distribution.
northing - Variable in class broadwick.data.Location
NORTHING - Static variable in class broadwick.data.readers.LocationsFileReader
northingColumn - Variable in class broadwick.config.generated.DataFiles.LocationsFile
nullLocation - Static variable in class broadwick.data.Location
NullOutputStream - Class in broadwick.io: A Null output stream similar to > /dev/null.
NullOutputStream() - Constructor for class broadwick.io.NullOutputStream: Creates a new null output stream to write data to the null output stream.
numAcceptedSteps - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
numCols - Variable in class broadwick.math.Matrix
numErrors - Variable in class broadwick.config.ConfigValidationErrors
numRows - Variable in class broadwick.math.Matrix
numRuns - Variable in class broadwick.concurrent.LocalPoolExecutor
numSamples - Variable in class broadwick.statistics.distributions.MultinomialDistribution
numSamplesTaken - Variable in class broadwick.abc.ApproxBayesianComp
numSimulations - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
numSimulations - Variable in class broadwick.montecarlo.MonteCarlo
numSimulations - Variable in class broadwick.montecarlo.Producer
numSimulationsFound - Variable in class broadwick.montecarlo.Consumer
numStepsTaken - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo

O

ObjectFactory - Class in broadwick.config.generated: This object contains factory methods for each Java content interface and Java element interface generated in the broadwick.config.generated package.
ObjectFactory() - Constructor for class broadwick.config.generated.ObjectFactory: Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: broadwick.config.generated
observedData - Variable in class broadwick.abc.ApproxBayesianComp
observeEvent(SimulationEvent, double, int) - Method in class broadwick.stochastic.Observer: Gets called before an event is triggered.
Observer - Class in broadwick.odesolver: Implementing classes are used to observe certain aspects of the solver.
Observer(OdeSolver) - Constructor for class broadwick.odesolver.Observer: Creates an observer dedicated to an ODE solver.
Observer - Class in broadwick.stochastic: Implementing classes are used to observe certain aspects of simulations (stochastic processes).
Observer(StochasticSimulator) - Constructor for class broadwick.stochastic.Observer: Creates an observer dedicated to one process.
observers - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
observers - Variable in class broadwick.odesolver.OdeSolver
observers - Variable in class broadwick.stochastic.StochasticSimulator
Ode - Interface in broadwick.odesolver: Interface defining a First Order Ordinary Differential Equation.
ode - Variable in class broadwick.odesolver.OdeSolver
OdeController - Interface in broadwick.odesolver: An OdeController (and its implementing classes) are responsible for controlling the ODE solver in the sense that the solver checks with the controller object whether to go on or not.
OdeSolver - Class in broadwick.odesolver: A base class for all ODE solvers.
OdeSolver(Ode, double, double, double) - Constructor for class broadwick.odesolver.OdeSolver: Create the solver object with initial consitions.
OdeSolver.ThetaQueue - Class in broadwick.odesolver: Manages the registered theta events.
ok - Variable in class broadwick.concurrent.LocalPoolExecutor
open(String) - Method in interface broadwick.data.DatabaseImpl: Open the database for connection.
open(String) - Method in class broadwick.data.H2Database
options - Variable in class broadwick.CliOptions
outDegree(V) - Method in class broadwick.graph.DirectedGraph
outDegree(V) - Method in interface broadwick.graph.Graph: Returns the number of outgoing edges incident to vertex.
outDegree(V) - Method in class broadwick.graph.Tree
outDegree(V) - Method in class broadwick.graph.UndirectedGraph
overwrite - Variable in class broadwick.config.generated.Logs.File

P

Pair<A,B> - Class in broadwick.utils: HashMap compatible Pair class (i.e.
Pair(A, B) - Constructor for class broadwick.utils.Pair: Create the pair object with the given coordinates.
parameter - Variable in class broadwick.config.generated.Models.Model
Parameter - Class in broadwick.config.generated: Java class for Parameter complex type.
Parameter() - Constructor for class broadwick.config.generated.Parameter
parameters - Variable in class broadwick.abc.AbcNamedQuantity
parameters - Variable in class broadwick.model.Model
parse(String) - Method in class broadwick.phylo.NewickTreeParser: Parse a given string that MUST be a valid Newick format.
parse() - Method in class broadwick.phylo.NewickTreeParser: Parse a string from a Newick file.
parseNode(String, Tree<PhyloNode, Edge<PhyloNode>>, PhyloNode) - Method in class broadwick.phylo.NewickTreeParser: Parse a string containing information on a node in Newick format and attach it to a given tree.
parseString(String, PhyloNode, Tree<PhyloNode, Edge<PhyloNode>>) - Method in class broadwick.phylo.NewickTreeParser: Parse a string in Newick format (where the root node has been removed) recursively.
path - Variable in class broadwick.io.FileInput
pathGenerator - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
pattern - Variable in class broadwick.config.generated.Logs.Console
pattern - Variable in class broadwick.config.generated.Logs.File
performEvent(SimulationEvent, int) - Method in interface broadwick.stochastic.AmountManager: Reflects a (multiple) firing of a reaction by adjusting the populations of the states.
performStep() - Method in class broadwick.stochastic.algorithms.GillespieSimple
performStep() - Method in class broadwick.stochastic.algorithms.TauLeaping
performStep() - Method in class broadwick.stochastic.algorithms.TauLeapingFixedStep
performStep() - Method in class broadwick.stochastic.StochasticSimulator: Performs one simulation step.
PhyloNode - Class in broadwick.phylo: A node object for phylogenetic trees.
PhyloNode(String, double) - Constructor for class broadwick.phylo.PhyloNode: Create an instance of the node.
Poison - Class in broadwick.montecarlo: Poison object that causes the consumer of the MonteCarlo results to stop looking for objects on the queue.
Poison() - Constructor for class broadwick.montecarlo.Poison
poolSize - Variable in class broadwick.concurrent.LocalPoolExecutor
population - Variable in class broadwick.config.generated.DataFiles.PopulationFile
POPULATION - Static variable in class broadwick.data.readers.PopulationsFileReader
populationDateColumn - Variable in class broadwick.config.generated.PopulationType
populationFile - Variable in class broadwick.config.generated.DataFiles
PopulationFile() - Constructor for class broadwick.config.generated.DataFiles.PopulationFile
populationFile - Variable in class broadwick.data.readers.PopulationsFileReader
populations - Variable in class broadwick.data.Location
POPULATIONS_TABLE_NAME - Static variable in class broadwick.data.readers.PopulationsFileReader
PopulationsFileReader - Class in broadwick.data.readers: Read a file containing the population data.
PopulationsFileReader(DataFiles.PopulationFile, DatabaseImpl) - Constructor for class broadwick.data.readers.PopulationsFileReader: Create the populations file reader.
populationSizeColumn - Variable in class broadwick.config.generated.PopulationType
PopulationType - Class in broadwick.config.generated: Java class for PopulationType complex type.
PopulationType() - Constructor for class broadwick.config.generated.PopulationType
POSITIVE_RESULT - Static variable in class broadwick.data.readers.TestsFileReader
positiveResult - Variable in class broadwick.data.Test
posteriors - Variable in class broadwick.abc.ApproxBayesianComp
postiveResultColumn - Variable in class broadwick.config.generated.DataFiles.TestsFile
predict(double) - Method in class broadwick.statistics.regression.SimpleLinearRegression: Returns the "predicted" y value associated with the supplied x value, based on the data that has been added to the model when this method is activated.
preMultiply(Vector) - Method in class broadwick.math.Matrix: Returns the (row) vector result of premultiplying this by the vector v.
Prior - Class in broadwick.config.generated: Java class for Prior complex type.
Prior() - Constructor for class broadwick.config.generated.Prior
priors - Variable in class broadwick.abc.ApproxBayesianComp
priors - Variable in class broadwick.config.generated.Models.Model
Priors() - Constructor for class broadwick.config.generated.Models.Model.Priors
priors - Variable in class broadwick.model.Model
prob(int[]) - Method in class broadwick.statistics.distributions.MultinomialDistribution: Returns the probability mass function p(x₁, x₂,…, x_d), which should be a real number in [0, 1].
probabilities - Variable in class broadwick.statistics.distributions.MultinomialDistribution
process - Variable in class broadwick.stochastic.Observer
Producer - Class in broadwick.montecarlo: This class runs a single simulation of the model to 'produce' results (hence the name).
Producer(ArrayBlockingQueue<MonteCarloResults>, MonteCarloScenario, int) - Constructor for class broadwick.montecarlo.Producer: Create the producer object.
product - Variable in class broadwick.statistics.Samples
project - Variable in class broadwick.Broadwick
project - Variable in class broadwick.config.ConfigValidator
Project - Class in broadwick.config.generated: Java class for anonymous complex type.
Project() - Constructor for class broadwick.config.generated.Project
Project.Data - Class in broadwick.config.generated: Java class for anonymous complex type.
pushTheta(double, Observer, Object) - Method in class broadwick.odesolver.OdeSolver.ThetaQueue: Add a new theta event to the registry, including the time, collection of observers and collection of events.
pushTheta(double, Observer, Object) - Method in class broadwick.stochastic.StochasticSimulator.ThetaQueue: Add a new theta event to the registry, including the time, collection of observers and collection of events.

Q

queue - Variable in class broadwick.montecarlo.Consumer
queue - Variable in class broadwick.montecarlo.Producer

R

read() - Method in class broadwick.io.FileInput: Read the contents of the file into a single string object.
readAllBatchedMovementSections(List<DataFiles.BatchMovementFile>, String) - Method in class broadwick.data.DataReader: Read the batched movements sections of the configuration file.
readAllDirectedMovementSections(List<DataFiles.DirectedMovementFile>, String) - Method in class broadwick.data.DataReader: Read the directed movements sections of the configuration file.
readAllFullMovementSections(List<DataFiles.FullMovementFile>, String) - Method in class broadwick.data.DataReader: Read the full movements sections of the configuration file.
readAllLocationSections(List<DataFiles.LocationsFile>, String) - Method in class broadwick.data.DataReader: Read the location sections of the configuration file.
readAllPopulationSections(List<DataFiles.PopulationFile>, String) - Method in class broadwick.data.DataReader: Read the populations sections of the configuration file.
readAllTestSections(List<DataFiles.TestsFile>, String) - Method in class broadwick.data.DataReader: Read the test sections of the configuration file.
readConfigFile(LoggingFacade, String) - Method in class broadwick.Broadwick: Read the configuration file from the configuration file.
readDataFiles(DataFiles) - Method in class broadwick.data.DataReader: Read the datafiles, each section type of the element (e.g.
readDataSection() - Method in class broadwick.data.DataReader: Read the data section from the configuration file.
reader - Variable in class broadwick.io.FileInput
reader - Variable in class broadwick.io.FileInputIterator
readLifeHistory() - Method in class broadwick.data.readers.PopulationsFileReader: Read the life history declarations of a population file section in the configuration file, if there are errors, they are noted and and exception is thrown with ALL the errors at the end of the method.
readLine() - Method in class broadwick.io.FileInput: Read a line from the input file, split it according to the seperator specified in the constructor and get a list of tokens from the line.
readNextLine() - Method in class broadwick.io.FileInput: Get the next (non-comment) line from the file.
readPopulation() - Method in class broadwick.data.readers.PopulationsFileReader: Read the populations declarations of a population file section in the configuration file, if there are errors, they are noted and and exception is thrown with ALL the errors at the end of the method.
registerModels(Project, Lookup) - Method in class broadwick.Broadwick: Create and register the models internally.
registerNewTheta(Observer, double, Object) - Method in class broadwick.odesolver.OdeSolver: Register a new theta event that is triggered at a given time.
registerNewTheta(Observer, double, Object) - Method in class broadwick.stochastic.StochasticSimulator: Register a new theta event that is triggered at a given time.
regression - Variable in class broadwick.statistics.regression.SimpleLinearRegression
reinitialize() - Method in class broadwick.stochastic.algorithms.GillespieSimple
reinitialize() - Method in class broadwick.stochastic.algorithms.TauLeaping
reinitialize() - Method in class broadwick.stochastic.algorithms.TauLeapingFixedStep
reinitialize() - Method in class broadwick.stochastic.StochasticSimulator: Reset propensities when a event has been executed.
rejectionSample() - Method in class broadwick.statistics.distributions.TruncatedNormalDistribution
remove() - Method in class broadwick.graph.DepthFirstIterator
remove() - Method in class broadwick.io.FileInputIterator
removeData(double, double) - Method in class broadwick.statistics.regression.SimpleLinearRegression: Removes the observation (x,y) from the regression data set, mirroring the addData method.
removeEdge(E) - Method in class broadwick.graph.DirectedGraph
removeEdge(E) - Method in interface broadwick.graph.Graph: Removes edge from this graph.
removeEdge(E) - Method in class broadwick.graph.Tree
removeEdge(E) - Method in class broadwick.graph.UndirectedGraph
removeVertex(V) - Method in class broadwick.graph.DirectedGraph
removeVertex(V) - Method in interface broadwick.graph.Graph: Remove the passed node, and, in the case of a tree, all nodes that are descendants of the passed node.
removeVertex(V) - Method in class broadwick.graph.Tree
removeVertex(V) - Method in class broadwick.graph.UndirectedGraph
renameFileExtension(String, String) - Static method in class broadwick.io.FileUtils: Change the extension of a file name, e.g.
reset() - Method in class broadwick.montecarlo.MonteCarloDefaultResults
reset() - Method in interface broadwick.montecarlo.MonteCarloResults: Clear the results of the MonteCarloResults object.
reset() - Method in class broadwick.montecarlo.Poison
reset(int) - Method in class broadwick.statistics.distributions.IntegerDistribution: Resets the value in each bin.
reset() - Method in class broadwick.statistics.distributions.IntegerDistribution: Resets the value in each bin.
resetAmount() - Method in interface broadwick.stochastic.AmountManager: Resets the amount of each species to the initial amount retrieved by the networks AnnotationManager.
resultsConsumer - Variable in class broadwick.montecarlo.MonteCarlo
reverseTime - Variable in class broadwick.stochastic.StochasticSimulator
RNG - Class in broadwick.rng: Random number generator singleton class This class is not thread safe.
RNG() - Constructor for class broadwick.rng.RNG: Create a random number generator using the default JDK-provied PRNG.
RNG(RNG.Generator) - Constructor for class broadwick.rng.RNG: Create a random number generator from a given generator using the current time as a seed.
RNG.Generator - Enum in broadwick.rng: Random number generator type.
RngException - Exception in broadwick.rng: A RuntimeException for random number generators.
RngException() - Constructor for exception broadwick.rng.RngException: Constructs a new RNG exception with null as its detail message.
RngException(String) - Constructor for exception broadwick.rng.RngException: Constructs a new RNG exception with the specified detail message.
rollback() - Method in interface broadwick.stochastic.AmountManager: Restore the amount array from the recently saved one.
rootLogger - Variable in class broadwick.LoggingFacade
rows() - Method in class broadwick.math.Matrix: Get the number of rows in the matrix.
run(AbcNamedQuantity) - Method in interface broadwick.abc.AbcModel: Run the model to generate data.
run() - Method in class broadwick.abc.ApproxBayesianComp: Run the ABC algorithm.
run() - Method in class broadwick.Broadwick: Run the Broadwick framework.
run() - Method in interface broadwick.concurrent.Executor: Run the required number of jobs, checking for thrown exceptions once each task has completed.
run() - Method in class broadwick.concurrent.LocalPoolExecutor
run() - Method in class broadwick.model.Model: Run the model.
run() - Method in class broadwick.montecarlo.Consumer
run() - Method in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo: Run the MonteCarlo Simulation.
run() - Method in class broadwick.montecarlo.MonteCarlo: Run the Monte Carlo simulations.
run(int) - Method in class broadwick.montecarlo.MonteCarloScenario: Compute the value of the Monte Carlo model/simulation at the given set of coordinates.
run() - Method in class broadwick.montecarlo.Producer
run() - Method in class broadwick.odesolver.OdeSolver: Solve the system of ODEs.
run() - Method in class broadwick.odesolver.RungeKutta4
run(double) - Method in class broadwick.stochastic.StochasticSimulator: Starts the simulation up to a given time.
run() - Method in class broadwick.stochastic.StochasticSimulator: Start the simulation with the given SimulationController.
runCustomQuery(String) - Method in class broadwick.data.Lookup: Run a custom query against the database.
RungeKutta4 - Class in broadwick.odesolver: A fourth order Runge Kutta solver for systems of ODEs.
RungeKutta4(Ode, double, double, double) - Constructor for class broadwick.odesolver.RungeKutta4: Create the solver for a give ode object and initial consitions.

S

sample() - Method in interface broadwick.abc.AbcPriorsSampler: Sample from the models Priors to obtain a set of model parameters.
sample() - Method in interface broadwick.statistics.distributions.ContinuousDistribution: Obtain a sample from the distribution.
sample() - Method in interface broadwick.statistics.distributions.ContinuousMultivariateDistribution: Obtain a sample from the distribution.
sample() - Method in interface broadwick.statistics.distributions.DiscreteDistribution: Generate a random value sampled from this distribution.
sample() - Method in class broadwick.statistics.distributions.HypergeometricDistribution
sample() - Method in class broadwick.statistics.distributions.MultivariateNormalDistribution
sample() - Method in class broadwick.statistics.distributions.Normal
sample() - Method in class broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution
sample() - Method in class broadwick.statistics.distributions.TruncatedNormalDistribution
samples - Variable in class broadwick.montecarlo.MonteCarloDefaultResults
Samples - Class in broadwick.statistics: This class collects data values and calculates their mean and variance.
Samples() - Constructor for class broadwick.statistics.Samples: Empty object where the internal values are initialised to 0.
Samples(double) - Constructor for class broadwick.statistics.Samples: Initialise the internal values of the accumulator with the argument given.
save(AbcNamedQuantity) - Method in class broadwick.abc.ApproxBayesianComp: Save the sample taken from the prior as it meets the criteria set for being a posterior sample.
save(String, Graph<? extends Vertex, ? extends Edge<Vertex>>) - Static method in class broadwick.graph.writer.EdgeList: Save the graph as in edge list format in the given file.
save(String, Graph<? extends Vertex, ? extends Edge<Vertex>>) - Static method in class broadwick.graph.writer.GraphMl: Save the graph as in graphML format in the given file.
save(String, Graph<? extends Vertex, ? extends Edge<Vertex>>) - Static method in class broadwick.graph.writer.GraphViz: Save the graph as in graphviz format in the given file.
save(String, Graph<? extends Vertex, ? extends Edge<Vertex>>) - Method in interface broadwick.graph.writer.GraphWriter: Write the XML document into file.
save() - Method in interface broadwick.stochastic.AmountManager: Makes a copy of the amount array.
saveToFile(String, String, boolean) - Static method in class broadwick.io.FileOutput: Save data in the form of a string to a named file.
saveToFile(String, String, boolean, Object...) - Static method in class broadwick.io.FileOutput: Save data in the form of a string to a named file.
scale(long[], double) - Static method in class broadwick.utils.ArrayUtils: Modify an array by multiplying each element by a constant scaling factor.
scaleBins(double) - Method in class broadwick.statistics.distributions.IntegerDistribution: Scale the values in the histogram by a given factor.
SCHEMA - Static variable in class broadwick.Constants
sd - Variable in class broadwick.statistics.distributions.TruncatedNormalDistribution
second - Variable in class broadwick.utils.Pair
SECTION_NAME - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
SECTION_NAME - Static variable in class broadwick.data.readers.DirectedMovementsFileReader
SECTION_NAME - Static variable in class broadwick.data.readers.FullMovementsFileReader
SECTION_NAME - Static variable in class broadwick.data.readers.LocationsFileReader
SECTION_NAME - Static variable in class broadwick.data.readers.PopulationsFileReader
SECTION_NAME - Static variable in class broadwick.data.readers.TestsFileReader
seed(int) - Method in class broadwick.rng.RNG: Seed the random number generator.
selectManyOf(T[], int) - Method in class broadwick.rng.RNG: Randomly pick N objects from an array of objects.
selectManyOf(Collection<T>, int) - Method in class broadwick.rng.RNG: Randomly pick N objects from an array of objects.
selectManyOf(Set<T>, int) - Method in class broadwick.rng.RNG: Randomly pick N objects from an array of objects.
selectOneOf(T[]) - Method in class broadwick.rng.RNG: Randomly pick an object from an array of objects.
selectOneOf(T[], double[]) - Method in class broadwick.rng.RNG: Randomly pick an object from an array of objects.
selectOneOf(Set<T>) - Method in class broadwick.rng.RNG
selectOneOf(Collection<T>) - Method in class broadwick.rng.RNG: Randomly pick an object from an array of objects.
separator - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
separator - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
separator - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
separator - Variable in class broadwick.config.generated.DataFiles.LocationsFile
separator - Variable in class broadwick.config.generated.DataFiles.PopulationFile
separator - Variable in class broadwick.config.generated.DataFiles.TestsFile
service - Variable in class broadwick.concurrent.LocalPoolExecutor
setAlias(String) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the alias property.
setAlias(String) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the alias property.
setAlias(String) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the alias property.
setAlias(String) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the alias property.
setAlias(String) - Method in class broadwick.config.generated.DataFiles.PopulationFile: Sets the value of the alias property.
setAlias(String) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the alias property.
setBatchSizeColumn(int) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the batchSizeColumn property.
setClassname(String) - Method in class broadwick.config.generated.Models.Model: Sets the value of the classname property.
setColumn(int) - Method in class broadwick.config.generated.CustomTags.CustomTag: Sets the value of the column property.
setConsole(Logs.Console) - Method in class broadwick.config.generated.Logs: Sets the value of the console property.
setCustomTags(CustomTags) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the customTags property.
setCustomTags(CustomTags) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the customTags property.
setCustomTags(CustomTags) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the customTags property.
setCustomTags(CustomTags) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the customTags property.
setCustomTags(CustomTags) - Method in class broadwick.config.generated.DataFiles.PopulationFile: Sets the value of the customTags property.
setCustomTags(CustomTags) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the customTags property.
setData(Project.Data) - Method in class broadwick.config.generated.Project: Sets the value of the data property.
setData(Integer) - Method in class broadwick.statistics.distributions.IntegerDistribution: Deprecated.
use getFrequency() instead
setData(Integer, Integer) - Method in class broadwick.statistics.distributions.IntegerDistribution: Deprecated.
use setFrequency() instead
setDatabases(Databases) - Method in class broadwick.config.generated.Project.Data: Sets the value of the databases property.
setDatafiles(DataFiles) - Method in class broadwick.config.generated.Project.Data: Sets the value of the datafiles property.
setDateFormat(String) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the dateFormat property.
setDateFormat(String) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the dateFormat property.
setDateFormat(String) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the dateFormat property.
setDateFormat(String) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the dateFormat property.
setDateFormat(String) - Method in class broadwick.config.generated.DataFiles.PopulationFile: Sets the value of the dateFormat property.
setDateFormat(String) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the dateFormat property.
setDateOfBirthColumn(int) - Method in class broadwick.config.generated.LifeHistoryType: Sets the value of the dateOfBirthColumn property.
setDateOfDeathColumn(int) - Method in class broadwick.config.generated.LifeHistoryType: Sets the value of the dateOfDeathColumn property.
setDepartureDateColumn(int) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the departureDateColumn property.
setDepartureDateColumn(int) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the departureDateColumn property.
setDepartureLocationIdColumn(int) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the departureLocationIdColumn property.
setDepartureLocationIdColumn(int) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the departureLocationIdColumn property.
setDestinationDateColumn(int) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the destinationDateColumn property.
setDestinationDateColumn(int) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the destinationDateColumn property.
setDestinationLocationIdColumn(int) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the destinationLocationIdColumn property.
setDestinationLocationIdColumn(int) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the destinationLocationIdColumn property.
setDeviation(double) - Method in class broadwick.config.generated.GaussianPrior: Sets the value of the deviation property.
setEastingColumn(Integer) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the eastingColumn property.
setEntry(int, int, double) - Method in class broadwick.math.Matrix: Set the matrix element at a given point.
setEntry(int, double) - Method in class broadwick.math.Vector: Set the value of the vector at a given index.
setFile(Logs.File) - Method in class broadwick.config.generated.Logs: Sets the value of the file property.
setFrequency(Integer) - Method in class broadwick.statistics.distributions.IntegerDistribution: Increment the size of a bin.
setFrequency(Integer, Integer) - Method in class broadwick.statistics.distributions.IntegerDistribution: Set the value of a bin.
setGroupIdColumn(Integer) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the groupIdColumn property.
setHint(String) - Method in class broadwick.config.generated.Parameter: Sets the value of the hint property.
setHint(String) - Method in class broadwick.config.generated.Prior: Sets the value of the hint property.
setId(String) - Method in class broadwick.config.generated.Models.Model: Sets the value of the id property.
setId(String) - Method in class broadwick.config.generated.Parameter: Sets the value of the id property.
setId(String) - Method in class broadwick.config.generated.Prior: Sets the value of the id property.
setIdColumn(int) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the idColumn property.
setIdColumn(int) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the idColumn property.
setIdColumn(Integer) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the idColumn property.
setIdColumn(int) - Method in class broadwick.config.generated.LifeHistoryType: Sets the value of the idColumn property.
setInitialVal(Double) - Method in class broadwick.config.generated.Prior: Sets the value of the initialVal property.
setLevel(String) - Method in class broadwick.config.generated.Logs.Console: Sets the value of the level property.
setLevel(String) - Method in class broadwick.config.generated.Logs.File: Sets the value of the level property.
setLifeHistory(LifeHistoryType) - Method in class broadwick.config.generated.DataFiles.PopulationFile: Sets the value of the lifeHistory property.
setLocationColumn(int) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the locationColumn property.
setLocationIdColumn(int) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the locationIdColumn property.
setLocationIdColumn(Integer) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the locationIdColumn property.
setLocationIdColumn(int) - Method in class broadwick.config.generated.PopulationType: Sets the value of the locationIdColumn property.
setLocationOfBirthColumn(int) - Method in class broadwick.config.generated.LifeHistoryType: Sets the value of the locationOfBirthColumn property.
setLocationOfDeathColumn(Integer) - Method in class broadwick.config.generated.LifeHistoryType: Sets the value of the locationOfDeathColumn property.
setLoggingLevel(String) - Method in class broadwick.LoggingFacade: Convert the string passed as argument to a Level.
setLogs(Logs) - Method in class broadwick.config.generated.Project: Sets the value of the logs property.
setMarketDateColumn(Integer) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the marketDateColumn property.
setMarketDateColumn(Integer) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the marketDateColumn property.
setMarketIdColumn(Integer) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the marketIdColumn property.
setMarketIdColumn(Integer) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the marketIdColumn property.
setMax(double) - Method in class broadwick.config.generated.UniformPrior: Sets the value of the max property.
setMean(double) - Method in class broadwick.config.generated.GaussianPrior: Sets the value of the mean property.
setMin(double) - Method in class broadwick.config.generated.UniformPrior: Sets the value of the min property.
setModelConfiguration(String) - Method in class broadwick.model.Model: Set the xml string for the element in the configuration file.
setModelDataLookup(Lookup) - Method in class broadwick.model.Model: Set the lookup object that allows access to the data files specified in the configuration file.
setModelParameters(List<Parameter>) - Method in class broadwick.model.Model: Set the list of parameters for the model.
setModelPriors(List<Prior>) - Method in class broadwick.model.Model: Set the list of priors for the model.
setModels(Models) - Method in class broadwick.config.generated.Project: Sets the value of the models property.
setMovementDateColumn(int) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the movementDateColumn property.
setMovementDirectionColumn(int) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the movementDirectionColumn property.
setName(String) - Method in class broadwick.config.generated.CustomTags.CustomTag: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.Databases: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.DataFiles.PopulationFile: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the name property.
setName(String) - Method in class broadwick.config.generated.Logs.File: Sets the value of the name property.
setNegativeResultColumn(int) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the negativeResultColumn property.
setNorthingColumn(Integer) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the northingColumn property.
SetOperations - Class in broadwick.math: Some basic set operations on the Java Set class.
SetOperations() - Constructor for class broadwick.math.SetOperations: Hidden utility constructor.
setOverwrite(Boolean) - Method in class broadwick.config.generated.Logs.File: Sets the value of the overwrite property.
setPattern(String) - Method in class broadwick.config.generated.Logs.Console: Sets the value of the pattern property.
setPattern(String) - Method in class broadwick.config.generated.Logs.File: Sets the value of the pattern property.
setPopulation(PopulationType) - Method in class broadwick.config.generated.DataFiles.PopulationFile: Sets the value of the population property.
setPopulationDateColumn(int) - Method in class broadwick.config.generated.PopulationType: Sets the value of the populationDateColumn property.
setPopulationSizeColumn(int) - Method in class broadwick.config.generated.PopulationType: Sets the value of the populationSizeColumn property.
setPostiveResultColumn(int) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the postiveResultColumn property.
setPriors(Models.Model.Priors) - Method in class broadwick.config.generated.Models.Model: Sets the value of the priors property.
setResultsConsumer(MonteCarloResults) - Method in class broadwick.montecarlo.MonteCarlo: Set the consumer object for this Monte Carlo simulation.
setRngSeed(int) - Method in class broadwick.stochastic.algorithms.GillespieSimple
setRngSeed(int) - Method in class broadwick.stochastic.algorithms.TauLeaping
setRngSeed(int) - Method in class broadwick.stochastic.algorithms.TauLeapingFixedStep
setRngSeed(int) - Method in class broadwick.stochastic.StochasticSimulator: Seed the RNG if required.
setSeparator(String) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the separator property.
setSeparator(String) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the separator property.
setSeparator(String) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the separator property.
setSeparator(String) - Method in class broadwick.config.generated.DataFiles.LocationsFile: Sets the value of the separator property.
setSeparator(String) - Method in class broadwick.config.generated.DataFiles.PopulationFile: Sets the value of the separator property.
setSeparator(String) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the separator property.
setSpeciesColumn(Integer) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile: Sets the value of the speciesColumn property.
setSpeciesColumn(int) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile: Sets the value of the speciesColumn property.
setSpeciesColumn(Integer) - Method in class broadwick.config.generated.DataFiles.FullMovementFile: Sets the value of the speciesColumn property.
setSpeciesColumn(Integer) - Method in class broadwick.config.generated.LifeHistoryType: Sets the value of the speciesColumn property.
setSpeciesColumn(Integer) - Method in class broadwick.config.generated.PopulationType: Sets the value of the speciesColumn property.
setTestDateColumn(int) - Method in class broadwick.config.generated.DataFiles.TestsFile: Sets the value of the testDateColumn property.
setTransitionProbabilities(Map<SimulationEvent, Double>) - Method in class broadwick.stochastic.TransitionKernel: Set the transition probabilities between states.
setType(String) - Method in class broadwick.config.generated.CustomTags.CustomTag: Sets the value of the type property.
setValue(String) - Method in class broadwick.config.generated.Parameter: Sets the value of the value property.
setXCoord(double) - Method in class broadwick.graph.Vertex: Set the x coordinate for the vertex.
setYCoord(double) - Method in class broadwick.graph.Vertex: Set the y coordinate for the vertex.
ShortestPath<V extends Vertex,E extends Edge<V>> - Class in broadwick.graph.algorithms: Calculates distances in a specified graph, using Dijkstra's single-source-shortest-path algorithm.
ShortestPath(Graph<V, E>) - Constructor for class broadwick.graph.algorithms.ShortestPath: Create a ShortestPath instance.
ShortestPath.EdgeWeightTransformer - Class in broadwick.graph.algorithms: Transformer class to transform the edge of a graph to a double (it's weight).
shutdown() - Method in class broadwick.concurrent.LocalPoolExecutor: Shutdown the ExecutionService, blocking until ALL the threads have finished before returning.
SimpleLinearRegression - Class in broadwick.statistics.regression: Estimates an ordinary least squares regression model with one independent variable.
SimpleLinearRegression() - Constructor for class broadwick.statistics.regression.SimpleLinearRegression: Create an empty SimpleLinearRegression instance.
simulation - Variable in class broadwick.montecarlo.MonteCarlo
simulation - Variable in class broadwick.montecarlo.Producer
SimulationController - Interface in broadwick.stochastic: A SimulationController (and its implementing classes) are responsible for controlling the simulation in the sense that the StochasticSimulator checks with the controller object whether to go on or not.
SimulationEvent - Class in broadwick.stochastic: A class containing all the details of an event in the stochastic ODE model.
SimulationEvent(SimulationState, SimulationState) - Constructor for class broadwick.stochastic.SimulationEvent: Construct a new event from the initial state in one bin to a final state in another bin.
SimulationException - Exception in broadwick.stochastic: A RuntimeException for stochastic solvers.
SimulationException() - Constructor for exception broadwick.stochastic.SimulationException: Constructs a new math exception with null as its detail message.
SimulationException(String) - Constructor for exception broadwick.stochastic.SimulationException: Constructs a new exception with the specified detail message.
SimulationState - Interface in broadwick.stochastic: Interface for simulations states.
size() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get the size (the number of bins) in the histogram.
solver - Variable in class broadwick.odesolver.Observer
source - Variable in class broadwick.graph.Edge
SPACE - Static variable in class broadwick.CliOptions
species - Variable in class broadwick.data.Animal
species - Variable in class broadwick.data.Movement
SPECIES - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
SPECIES - Static variable in class broadwick.data.readers.DirectedMovementsFileReader
SPECIES - Static variable in class broadwick.data.readers.FullMovementsFileReader
SPECIES - Static variable in class broadwick.data.readers.PopulationsFileReader
speciesColumn - Variable in class broadwick.config.generated.DataFiles.BatchMovementFile
speciesColumn - Variable in class broadwick.config.generated.DataFiles.DirectedMovementFile
speciesColumn - Variable in class broadwick.config.generated.DataFiles.FullMovementFile
speciesColumn - Variable in class broadwick.config.generated.LifeHistoryType
speciesColumn - Variable in class broadwick.config.generated.PopulationType
started() - Method in class broadwick.montecarlo.markovchain.observer.MarkovChainObserver: Gets called when the simulation has started after the initialization and before the termination condition is checked the first time.
started() - Method in class broadwick.odesolver.Observer: Gets called when the ODE solver has started after the initialization and before the termination condition is checked the first time.
started() - Method in class broadwick.stochastic.Observer: Gets called when the simulation has started after the initialization and before the termination condition is checked the first time.
startTime - Variable in class broadwick.stochastic.StochasticSimulator
Status() - Constructor for enum broadwick.concurrent.Executor.Status
status - Variable in class broadwick.concurrent.LocalPoolExecutor
Status() - Constructor for enum broadwick.config.ConfigValidationErrors.Status
stdDev - Variable in class broadwick.statistics.distributions.Normal
step() - Method in class broadwick.montecarlo.markovchain.observer.MarkovChainObserver: Gets called when the simulation has taken a step, whether or not the step is accepted or not or if the burn-in period has elapsed.
step - Variable in class broadwick.montecarlo.MonteCarloScenario
step() - Method in class broadwick.odesolver.Observer: Gets called after each termination check and before Simulator#performStep(fern.simulation.controller.SimulationController) is called.
step() - Method in class broadwick.stochastic.Observer: Gets called after each termination check and before Simulator#performStep(fern.simulation.controller.SimulationController) is called.
stepSize - Variable in class broadwick.odesolver.OdeSolver
StochasticSimulator - Class in broadwick.stochastic: Base class for stochastic simulators.
StochasticSimulator(AmountManager, TransitionKernel) - Constructor for class broadwick.stochastic.StochasticSimulator: Creates a new simulator using a given amount manager.
StochasticSimulator(AmountManager, TransitionKernel, boolean) - Constructor for class broadwick.stochastic.StochasticSimulator: Creates a new simulator.
StochasticSimulator.ThetaQueue - Class in broadwick.stochastic: Manages the registered theta events.
stopAllTasks(List<Future<?>>) - Method in class broadwick.concurrent.LocalPoolExecutor: Send a message to all the futures to cancel their execution.
subtract(Matrix) - Method in class broadwick.math.Matrix: Returns the result of subtracting m from this.
subtract(Vector) - Method in class broadwick.math.Vector: Subtract a vector from this one.
sum - Variable in class broadwick.statistics.Samples
sum(Double[]) - Static method in class broadwick.utils.ArrayUtils: Get the sum of an array of doubles.
sum(Integer[]) - Static method in class broadwick.utils.ArrayUtils: Get the sum of an array of integers.
sumInv - Variable in class broadwick.statistics.Samples
sumSqr - Variable in class broadwick.statistics.Samples
symDifference(Set<T>, Set<T>) - Static method in class broadwick.math.SetOperations: Get the elements of sets A,B that are not in their intersection.

T

TABLE_NAME - Static variable in class broadwick.data.readers.BatchedMovementsFileReader
TABLE_NAME - Static variable in class broadwick.data.readers.DirectedMovementsFileReader
TABLE_NAME - Static variable in class broadwick.data.readers.FullMovementsFileReader
TABLE_NAME - Static variable in class broadwick.data.readers.LocationsFileReader
TABLE_NAME - Static variable in class broadwick.data.readers.TestsFileReader
tableName - Static variable in class broadwick.data.readers.PopulationsFileReader
takeMeasurements() - Method in class broadwick.montecarlo.markovchain.observer.MarkovChainObserver: Gets called by the Monte Carlo process after the burnin period has elaspsed.
tau - Variable in class broadwick.stochastic.algorithms.TauLeapingFixedStep
TauLeaping - Class in broadwick.stochastic.algorithms: Implementation of the tau-leaping algorithm that makes an approximation to the stochastic ODE by picking a reasonable time-step and then performing all the reactions that occur in this step.
TauLeaping(AmountManager, TransitionKernel) - Constructor for class broadwick.stochastic.algorithms.TauLeaping: Create the tau-leaping object.
TauLeapingFixedStep - Class in broadwick.stochastic.algorithms: Implementation of the tau-leaping algorithm that makes an approximation to the stochastic ODE by picking a reasonable time-step and then performing all the reactions that occur in this step.
TauLeapingFixedStep(AmountManager, TransitionKernel, int) - Constructor for class broadwick.stochastic.algorithms.TauLeapingFixedStep: Create the tau-leaping object.
Test - Class in broadwick.data: Utility class for test data.
Test() - Constructor for class broadwick.data.Test
TEST_DATE - Static variable in class broadwick.data.readers.TestsFileReader
testDate - Variable in class broadwick.data.Test
testDateColumn - Variable in class broadwick.config.generated.DataFiles.TestsFile
testsCache - Variable in class broadwick.data.Lookup
testsFile - Variable in class broadwick.config.generated.DataFiles
TestsFile() - Constructor for class broadwick.config.generated.DataFiles.TestsFile
TestsFileReader - Class in broadwick.data.readers: Read a file containing the results of tests.
TestsFileReader(DataFiles.TestsFile, DatabaseImpl) - Constructor for class broadwick.data.readers.TestsFileReader: Create the tests file reader.
theta(double, Collection<Object>) - Method in class broadwick.odesolver.Observer: Gets called by the ODE solver when a certain moment in time is reached.
theta(double, Collection<Object>) - Method in class broadwick.stochastic.Observer: Gets called by simulators when a certain moment in time is reached.
thetaQueue - Variable in class broadwick.odesolver.OdeSolver
ThetaQueue() - Constructor for class broadwick.odesolver.OdeSolver.ThetaQueue: Construct an empty theta queue.
thetaQueue - Variable in class broadwick.stochastic.StochasticSimulator
ThetaQueue() - Constructor for class broadwick.stochastic.StochasticSimulator.ThetaQueue: Construct an empty theta queue.
thetas - Variable in class broadwick.odesolver.OdeSolver.ThetaQueue
thetas - Variable in class broadwick.stochastic.StochasticSimulator.ThetaQueue
thinningInterval - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
tMax - Variable in class broadwick.odesolver.DefaultOdeController
toArray() - Method in class broadwick.math.Matrix: Return an array representation of this matrix.
toArray() - Method in class broadwick.math.Vector: Return a copy of the vector as an array.
toArray() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get an array of the bin values.
toArrayListDouble(String) - Static method in class broadwick.utils.ArrayUtils: Create a new ArrayList from a comma separated list of ints encoded as string values.
toArrayListInteger(String) - Static method in class broadwick.utils.ArrayUtils: Create a new ArrayList from a comma separated list of integers encoded as string values.
toCollectionStrings(String) - Static method in class broadwick.utils.ArrayUtils: Split a string into a collection of strings, ignoring whitespace around each string.
toCsv() - Method in class broadwick.montecarlo.MonteCarloDefaultResults
toCsv() - Method in interface broadwick.montecarlo.MonteCarloResults: Get a CSV string of the Monte Carlo results stored in this class.
toCsv() - Method in class broadwick.montecarlo.Poison
toCsv() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get a string representation of the histogram in a csv format.
toDate(int) - Static method in class broadwick.BroadwickConstants: Convert an integer (number of days from a fixed start date, here 1/1/1900) to a DateTime object.
toDoubleArray(String[]) - Static method in class broadwick.utils.ArrayUtils: Given an array containing double values as string convert them to Doubles.
toDoubleArray(String) - Static method in class broadwick.utils.ArrayUtils: Given a comma separated string containing double values as strings convert them to an array of Doubles.
toIntegerArray(String[]) - Static method in class broadwick.utils.ArrayUtils: Given an array containing integer values as string convert them to integers.
toIntegerArray(String) - Static method in class broadwick.utils.ArrayUtils: Given a comma separated string containing integer values as strings convert them to an array of integers.
tokeniseLine(String) - Method in class broadwick.io.FileInput: Split a string (a line read from a file into tokens.
toLongArray() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get an array of the bin values.
toString() - Method in class broadwick.abc.AbcNamedQuantity
toString(ToStringBuilder) - Method in class broadwick.config.generated.CustomTags.CustomTag
toString() - Method in class broadwick.config.generated.CustomTags.CustomTag
toString(ToStringBuilder) - Method in class broadwick.config.generated.CustomTags
toString() - Method in class broadwick.config.generated.CustomTags
toString(ToStringBuilder) - Method in class broadwick.config.generated.Databases
toString() - Method in class broadwick.config.generated.Databases
toString(ToStringBuilder) - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
toString() - Method in class broadwick.config.generated.DataFiles.BatchMovementFile
toString(ToStringBuilder) - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
toString() - Method in class broadwick.config.generated.DataFiles.DirectedMovementFile
toString(ToStringBuilder) - Method in class broadwick.config.generated.DataFiles.FullMovementFile
toString() - Method in class broadwick.config.generated.DataFiles.FullMovementFile
toString(ToStringBuilder) - Method in class broadwick.config.generated.DataFiles.LocationsFile
toString() - Method in class broadwick.config.generated.DataFiles.LocationsFile
toString(ToStringBuilder) - Method in class broadwick.config.generated.DataFiles.PopulationFile
toString() - Method in class broadwick.config.generated.DataFiles.PopulationFile
toString(ToStringBuilder) - Method in class broadwick.config.generated.DataFiles.TestsFile
toString() - Method in class broadwick.config.generated.DataFiles.TestsFile
toString(ToStringBuilder) - Method in class broadwick.config.generated.DataFiles
toString() - Method in class broadwick.config.generated.DataFiles
toString(ToStringBuilder) - Method in class broadwick.config.generated.GaussianPrior
toString() - Method in class broadwick.config.generated.GaussianPrior
toString(ToStringBuilder) - Method in class broadwick.config.generated.LifeHistoryType
toString() - Method in class broadwick.config.generated.LifeHistoryType
toString(ToStringBuilder) - Method in class broadwick.config.generated.Logs.Console
toString() - Method in class broadwick.config.generated.Logs.Console
toString(ToStringBuilder) - Method in class broadwick.config.generated.Logs.File
toString() - Method in class broadwick.config.generated.Logs.File
toString(ToStringBuilder) - Method in class broadwick.config.generated.Logs
toString() - Method in class broadwick.config.generated.Logs
toString(ToStringBuilder) - Method in class broadwick.config.generated.Models.Model.Priors
toString() - Method in class broadwick.config.generated.Models.Model.Priors
toString(ToStringBuilder) - Method in class broadwick.config.generated.Models.Model
toString() - Method in class broadwick.config.generated.Models.Model
toString(ToStringBuilder) - Method in class broadwick.config.generated.Models
toString() - Method in class broadwick.config.generated.Models
toString(ToStringBuilder) - Method in class broadwick.config.generated.Parameter
toString() - Method in class broadwick.config.generated.Parameter
toString(ToStringBuilder) - Method in class broadwick.config.generated.PopulationType
toString() - Method in class broadwick.config.generated.PopulationType
toString(ToStringBuilder) - Method in class broadwick.config.generated.Prior
toString() - Method in class broadwick.config.generated.Prior
toString(ToStringBuilder) - Method in class broadwick.config.generated.Project.Data
toString() - Method in class broadwick.config.generated.Project.Data
toString(ToStringBuilder) - Method in class broadwick.config.generated.Project
toString() - Method in class broadwick.config.generated.Project
toString(ToStringBuilder) - Method in class broadwick.config.generated.UniformPrior
toString() - Method in class broadwick.config.generated.UniformPrior
toString() - Method in class broadwick.graph.Edge
toString(Graph<? extends Vertex, ? extends Edge<?>>) - Static method in class broadwick.graph.writer.EdgeList: Print the content of the graph.
toString(Graph<? extends Vertex, ? extends Edge<?>>, boolean) - Static method in class broadwick.graph.writer.GraphMl: Get the string representation of the network.
toString(Graph<? extends Vertex, ? extends Edge<?>>) - Static method in class broadwick.graph.writer.GraphMl: Get the string representation of the network.
toString(Graph<? extends Vertex, ? extends Edge<?>>) - Static method in class broadwick.graph.writer.GraphViz: Print the content of the graph.
toString(Graph<? extends Vertex, ? extends Edge<?>>) - Method in interface broadwick.graph.writer.GraphWriter: Print the content of the graph.
toString() - Method in class broadwick.math.Matrix
toString() - Method in class broadwick.math.Vector
toString() - Method in class broadwick.montecarlo.MonteCarloStep
toString() - Method in class broadwick.phylo.PhyloNode
toString() - Method in class broadwick.statistics.distributions.IntegerDistribution: Get a string representation of the histogram.
toString() - Method in class broadwick.statistics.distributions.MultinomialDistribution
toString() - Method in class broadwick.statistics.regression.SimpleLinearRegression
toString() - Method in class broadwick.stochastic.SimulationEvent
toString(Object[]) - Static method in class broadwick.utils.ArrayUtils: Create a csv string for an array of Objects.
toString(Object[], Format) - Static method in class broadwick.utils.ArrayUtils: Create a csv string for an array of Objects.
toString() - Method in class broadwick.utils.Pair: Generate a string describing this pair object.
toStringArray(String, Pattern) - Static method in class broadwick.utils.ArrayUtils: Split a string into an array strings,ignoring whitespace around each string.
toStringArray(String, char) - Static method in class broadwick.utils.ArrayUtils: Split a string into an array strings,ignoring whitespace around each string.
toStringArray(String) - Static method in class broadwick.utils.ArrayUtils: Split a string into an array strings, ignoring whitespace around each string.
total - Variable in class broadwick.statistics.Samples
toVerboseString() - Method in interface broadwick.stochastic.AmountManager: Get a detailed description of the states and their sizes (potentially for debugging).
transform(E) - Method in class broadwick.graph.algorithms.ShortestPath.EdgeWeightTransformer
transitionKernel - Variable in class broadwick.stochastic.StochasticSimulator
TransitionKernel - Class in broadwick.stochastic: Class that holds the transition kernel for a stochastic simulation.
TransitionKernel() - Constructor for class broadwick.stochastic.TransitionKernel: Create a transition kernel object to hold the transition probabilities between vents.
transpose() - Method in class broadwick.math.Matrix: Get the transpose of the matrix.
traverseTree(Tree<V, E>) - Method in class broadwick.graph.DepthFirstIterator: Perform a depth first traversal through the tree recording, in a linked list, the vertices visited in order.
Tree<V extends Vertex,E extends Edge<V>> - Class in broadwick.graph: A subtype of Graph which is a (directed, rooted) tree.
Tree() - Constructor for class broadwick.graph.Tree: Creates an instance of the tree.
tree - Variable in class broadwick.graph.Tree
TruncatedMultivariateNormalDistribution - Class in broadwick.statistics.distributions: Sample from a truncated Multivariate Normal (Gaussian) Distribution, i.e.
TruncatedMultivariateNormalDistribution(Vector, Matrix, Vector, Vector) - Constructor for class broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution: Create an instance of a multivariate distribution that is bounded.
TruncatedNormalDistribution - Class in broadwick.statistics.distributions: An implementation of the truncated normal distribution, i.e.
TruncatedNormalDistribution(double, double, double, double) - Constructor for class broadwick.statistics.distributions.TruncatedNormalDistribution: Create an instance of the normal distribution distribution truncated to given limits.
type - Variable in class broadwick.config.generated.CustomTags.CustomTag
type - Variable in class broadwick.graph.EdgeAttribute
type - Variable in class broadwick.graph.VertexAttribute

U

UndirectedGraph<V extends Vertex,E extends Edge<V>> - Class in broadwick.graph: A DirectedGraph, suitable for sparse graphs, that permits parallel edges..
UndirectedGraph() - Constructor for class broadwick.graph.UndirectedGraph: Creates an instance of the graph.
UniformPrior - Class in broadwick.config.generated: Java class for UniformPrior complex type.
UniformPrior() - Constructor for class broadwick.config.generated.UniformPrior
union(Set<T>, Set<T>) - Static method in class broadwick.math.SetOperations: Get the union of two sets.
unmarshallXmlString(String, Class<?>) - Static method in class broadwick.xml.XmlParser: This method unmarshalls (reads) the supplied XML string using JAXB using the supplied class object to create the JAXB context.
updateCreateTableCommand(String, Integer, String, Map<String, Integer>, StringBuilder, String, String, StringBuilder) - Method in class broadwick.data.readers.DataFileReader: Create or append to a string command in the form "CREATE TABLE IF NOT EXISTS [table] ([col1], [col2], ..., [coln]) values (?,?,...,?)" from the details read from the configuration file.
updateSectionDefiniton(String, int, Map<String, Integer>, StringBuilder, boolean, String) - Method in class broadwick.data.DataReader: Add a description of a configuration file section to an internal key value pair so that the correct column of a data file can be read.
updateStates(double) - Method in class broadwick.stochastic.algorithms.AbstractTauLeapingBase: Update all the reactions/transitions that have occurred in the tau step.
upper - Variable in class broadwick.statistics.distributions.TruncatedNormalDistribution
upperBounds - Variable in class broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution

V

valid - Variable in class broadwick.config.ConfigValidationErrors
validate() - Method in class broadwick.config.ConfigValidator: Validate the project.
validateCommandLineArguments() - Method in class broadwick.CliOptions: Perform validation the command line arguments.
validateModels() - Method in class broadwick.config.ConfigValidator: Validate the Models section of the configuration file.
validGenerators() - Static method in class broadwick.rng.RNG: Get a list of valid geometries for the lattice.
value - Variable in class broadwick.config.generated.Parameter
value - Variable in class broadwick.graph.EdgeAttribute
value - Variable in class broadwick.graph.VertexAttribute
valueOf(String) - Static method in enum broadwick.concurrent.Executor.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum broadwick.config.ConfigValidationErrors.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum broadwick.graph.EdgeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum broadwick.rng.RNG.Generator: Returns the enum constant of this type with the specified name.
values() - Static method in enum broadwick.concurrent.Executor.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum broadwick.config.ConfigValidationErrors.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum broadwick.graph.EdgeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum broadwick.rng.RNG.Generator: Returns an array containing the constants of this enum type, in the order they are declared.
Vector - Class in broadwick.math: Implementation of mathematical vector (not to be confused with the data structure).
Vector(int) - Constructor for class broadwick.math.Vector: Create a vector of a given dimension.
Vector(Vector) - Constructor for class broadwick.math.Vector: Copy constructor.
Vector(double[]) - Constructor for class broadwick.math.Vector: Copy constructor.
version - Static variable in class broadwick.BroadwickVersion
Vertex - Class in broadwick.graph: This class represents a generic vertex (node) in a graph.
Vertex(String) - Constructor for class broadwick.graph.Vertex: A generic vertex for a graph object.
VertexAttribute - Class in broadwick.graph: A generic node attribute.
VertexAttribute(String, Class, Object) - Constructor for class broadwick.graph.VertexAttribute: Create a node attribute object setting the value to be the default value.
vertexAttributes - Variable in class broadwick.graph.DirectedGraph
vertexAttributes - Variable in class broadwick.graph.Tree
vertexAttributes - Variable in class broadwick.graph.UndirectedGraph
vertexList - Variable in class broadwick.graph.DepthFirstIterator
vertexmaps - Variable in class broadwick.graph.DirectedGraph
vertexmaps - Variable in class broadwick.graph.Tree
vertexmaps - Variable in class broadwick.graph.UndirectedGraph

W

weight - Variable in class broadwick.graph.Edge
weightTransformer - Variable in class broadwick.graph.algorithms.ShortestPath
write(String) - Method in class broadwick.io.FileOutput: Write the string to the file stream.
write(String, Object...) - Method in class broadwick.io.FileOutput: Writes a formatted string to the file stream.
writer - Variable in class broadwick.montecarlo.markovchain.MarkovChainMonteCarlo

X

xCoord - Variable in class broadwick.graph.Vertex
XmlParser - Class in broadwick.xml: This simple class can be used to parse the XML string that the framework supplies to the model.
XmlParser() - Constructor for class broadwick.xml.XmlParser: Hiding utility class constructor.

Y

yCoord - Variable in class broadwick.graph.Vertex

Z

ZERO_DATE - Static variable in class broadwick.BroadwickConstants

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z