Hierarchy For All Packages

Package Hierarchies:

• broadwick,
• broadwick.abc,
• broadwick.concurrent,
• broadwick.config,
• broadwick.config.generated,
• broadwick.data,
• broadwick.data.readers,
• broadwick.graph,
• broadwick.graph.algorithms,
• broadwick.graph.writer,
• broadwick.grid,
• broadwick.io,
• broadwick.math,
• broadwick.model,
• broadwick.montecarlo,
• broadwick.montecarlo.acceptor,
• broadwick.montecarlo.markovchain,
• broadwick.montecarlo.markovchain.controller,
• broadwick.montecarlo.markovchain.observer,
• broadwick.montecarlo.markovchain.proposal,
• broadwick.odesolver,
• broadwick.phylo,
• broadwick.rng,
• broadwick.statistics,
• broadwick.statistics.distributions,
• broadwick.statistics.regression,
• broadwick.stochastic,
• broadwick.stochastic.algorithms,
• broadwick.utils,
• broadwick.xml

Class Hierarchy

• java.lang.Object
  • broadwick.abc.AbcAbsDistance (implements broadwick.abc.AbcDistance)
  • broadwick.abc.AbcMaxNumStepController (implements broadwick.abc.AbcController)
  • broadwick.abc.AbcNamedQuantity
  • broadwick.data.Animal (implements java.io.Serializable)
  • broadwick.abc.ApproxBayesianComp
  • broadwick.utils.ArrayUtils
  • broadwick.Broadwick
  • broadwick.BroadwickConstants
  • broadwick.BroadwickVersion
  • broadwick.CliOptions
  • broadwick.utils.CloneUtils
  • broadwick.config.ConfigValidationErrors
  • broadwick.config.ConfigValidator
  • broadwick.Constants
  • broadwick.montecarlo.Consumer (implements java.lang.Runnable)
  • broadwick.config.generated.CustomTags (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.CustomTags.CustomTag (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.Databases (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.data.readers.DataFileReader
    • broadwick.data.readers.BatchedMovementsFileReader
    • broadwick.data.readers.DirectedMovementsFileReader
    • broadwick.data.readers.FullMovementsFileReader
    • broadwick.data.readers.LocationsFileReader
    • broadwick.data.readers.PopulationsFileReader
    • broadwick.data.readers.TestsFileReader
  • broadwick.config.generated.DataFiles (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.DataFiles.BatchMovementFile (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.DataFiles.DirectedMovementFile (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.DataFiles.FullMovementFile (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.DataFiles.LocationsFile (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.DataFiles.PopulationFile (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.DataFiles.TestsFile (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.data.DataReader (implements java.lang.AutoCloseable)
  • broadwick.stochastic.DefaultController (implements broadwick.stochastic.SimulationController)
  • broadwick.odesolver.DefaultOdeController (implements broadwick.odesolver.OdeController)
  • broadwick.graph.DepthFirstIterator<V,E> (implements java.util.Iterator<E>)
  • broadwick.graph.DirectedGraph<V,E> (implements broadwick.graph.Graph<V,E>)
  • broadwick.graph.Edge<V> (implements java.io.Serializable)
  • broadwick.graph.EdgeAttribute (implements java.io.Serializable)
  • broadwick.graph.writer.EdgeList
  • broadwick.math.Factorial
  • broadwick.io.FileInput (implements java.lang.AutoCloseable)
  • broadwick.io.FileInputIterator (implements java.util.Iterator<E>)
  • broadwick.io.FileOutput (implements java.lang.AutoCloseable)
  • broadwick.io.FileUtils
  • broadwick.graph.writer.GraphMl
  • broadwick.graph.writer.GraphViz
  • broadwick.data.H2Database (implements broadwick.data.DatabaseImpl)
  • broadwick.statistics.distributions.HypergeometricDistribution (implements broadwick.statistics.distributions.DiscreteDistribution)
  • broadwick.statistics.distributions.IntegerDistribution (implements java.io.Serializable)
  • broadwick.config.generated.LifeHistoryType (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.concurrent.LocalPoolExecutor (implements broadwick.concurrent.Executor)
  • broadwick.data.Location
  • broadwick.LoggingFacade
  • broadwick.config.generated.Logs (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.Logs.Console (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.Logs.File (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.data.Lookup
  • broadwick.montecarlo.markovchain.MarkovChain (implements broadwick.montecarlo.markovchain.MarkovStepGenerator)
  • broadwick.montecarlo.markovchain.controller.MarkovChainMaxNumStepController (implements broadwick.montecarlo.markovchain.controller.MarkovChainController)
  • broadwick.montecarlo.markovchain.MarkovChainMonteCarlo
  • broadwick.montecarlo.markovchain.observer.MarkovChainObserver (implements java.lang.Comparable<T>)
  • broadwick.montecarlo.markovchain.proposal.MarkovNormalProposal (implements broadwick.montecarlo.markovchain.proposal.MarkovProposalFunction)
  • broadwick.math.Matrix
  • broadwick.montecarlo.acceptor.MetropolisHastings (implements broadwick.montecarlo.acceptor.MonteCarloAcceptor)
  • broadwick.model.Model
  • broadwick.config.generated.Models (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.Models.Model (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.montecarlo.MonteCarlo
  • broadwick.montecarlo.MonteCarloDefaultResults (implements broadwick.montecarlo.MonteCarloResults)
  • broadwick.montecarlo.MonteCarloScenario (implements java.io.Serializable)
  • broadwick.montecarlo.MonteCarloStep (implements java.io.Serializable)
  • broadwick.data.Movement (implements java.io.Serializable)
  • broadwick.data.MovementsComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • broadwick.statistics.distributions.MultinomialDistribution (implements java.io.Serializable)
  • broadwick.statistics.distributions.MultivariateNormalDistribution (implements broadwick.statistics.distributions.ContinuousMultivariateDistribution)
  • broadwick.phylo.NewickTreeParser
  • broadwick.statistics.distributions.Normal (implements broadwick.statistics.distributions.ContinuousDistribution)
  • broadwick.config.generated.ObjectFactory
  • broadwick.odesolver.Observer (implements java.lang.Comparable<T>)
  • broadwick.stochastic.Observer (implements java.lang.Comparable<T>)
  • broadwick.odesolver.OdeSolver
    • broadwick.odesolver.RungeKutta4
  • broadwick.odesolver.OdeSolver.ThetaQueue
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • java.io.FilterOutputStream
      • java.io.BufferedOutputStream
        • broadwick.io.NullOutputStream
  • broadwick.utils.Pair<A,B> (implements java.io.Serializable)
  • broadwick.config.generated.Parameter (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.montecarlo.Poison (implements broadwick.montecarlo.MonteCarloResults)
  • broadwick.config.generated.PopulationType (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.Prior (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
    • broadwick.config.generated.GaussianPrior (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
    • broadwick.config.generated.Models.Model.Priors (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
    • broadwick.config.generated.UniformPrior (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.montecarlo.Producer (implements java.lang.Runnable)
  • broadwick.config.generated.Project (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.config.generated.Project.Data (implements org.jvnet.jaxb2_commons.lang.Copyable, org.jvnet.jaxb2_commons.lang.CopyTo, org.jvnet.jaxb2_commons.lang.Equals, org.jvnet.jaxb2_commons.lang.HashCode, org.jvnet.jaxb2_commons.lang.ToString)
  • broadwick.rng.RNG (implements java.io.Serializable)
  • broadwick.statistics.Samples (implements java.io.Serializable)
  • broadwick.math.SetOperations
  • broadwick.graph.algorithms.ShortestPath<V,E>
  • broadwick.graph.algorithms.ShortestPath.EdgeWeightTransformer (implements org.apache.commons.collections15.Transformer<I,O>)
  • broadwick.statistics.regression.SimpleLinearRegression
  • broadwick.stochastic.SimulationEvent
  • broadwick.stochastic.StochasticSimulator
    • broadwick.stochastic.algorithms.AbstractTauLeapingBase
      • broadwick.stochastic.algorithms.TauLeaping
      • broadwick.stochastic.algorithms.TauLeapingFixedStep
    • broadwick.stochastic.algorithms.GillespieSimple
  • broadwick.stochastic.StochasticSimulator.ThetaQueue
  • broadwick.data.Test (implements java.io.Serializable)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • broadwick.BroadwickException
        • broadwick.io.BroadwickIOException
        • broadwick.model.ModelParameterException
        • broadwick.rng.RngException
        • broadwick.stochastic.SimulationException
  • broadwick.stochastic.TransitionKernel (implements java.lang.Cloneable)
  • broadwick.graph.Tree<V,E> (implements broadwick.graph.Graph<V,E>, java.io.Serializable)
  • broadwick.statistics.distributions.TruncatedMultivariateNormalDistribution (implements broadwick.statistics.distributions.ContinuousMultivariateDistribution)
  • broadwick.statistics.distributions.TruncatedNormalDistribution (implements broadwick.statistics.distributions.ContinuousDistribution)
  • broadwick.graph.UndirectedGraph<V,E> (implements broadwick.graph.Graph<V,E>)
  • broadwick.math.Vector
  • broadwick.graph.Vertex (implements java.io.Serializable)
    • broadwick.phylo.PhyloNode
  • broadwick.graph.VertexAttribute (implements java.io.Serializable)
  • broadwick.xml.XmlParser

Interface Hierarchy

• broadwick.abc.AbcController
• broadwick.abc.AbcDistance
• broadwick.abc.AbcModel
• broadwick.abc.AbcPriorsSampler
• broadwick.stochastic.AmountManager
• java.lang.AutoCloseable
  • broadwick.data.DatabaseImpl
• broadwick.statistics.distributions.ContinuousDistribution
• broadwick.statistics.distributions.ContinuousMultivariateDistribution
• broadwick.statistics.distributions.DiscreteDistribution
• broadwick.concurrent.Executor
• broadwick.graph.writer.GraphWriter
• broadwick.montecarlo.markovchain.controller.MarkovChainController
• broadwick.montecarlo.markovchain.proposal.MarkovProposalFunction
• broadwick.montecarlo.markovchain.MarkovStepGenerator
• broadwick.montecarlo.acceptor.MonteCarloAcceptor
• broadwick.montecarlo.MonteCarloResults
• broadwick.odesolver.Ode
• broadwick.odesolver.OdeController
• java.io.Serializable
  • broadwick.graph.Graph<V,E>
• broadwick.stochastic.SimulationController
• broadwick.stochastic.SimulationState

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • broadwick.concurrent.Executor.Status
    • broadwick.config.ConfigValidationErrors.Status
    • broadwick.graph.EdgeType
    • broadwick.rng.RNG.Generator