Hierarchy For All Packages

Package Hierarchies:

org.gcn.plinguacore.applications, org.gcn.plinguacore.parser, org.gcn.plinguacore.parser.input, org.gcn.plinguacore.parser.input.byteCounter, org.gcn.plinguacore.parser.input.messages, org.gcn.plinguacore.parser.input.plingua, org.gcn.plinguacore.parser.input.XML, org.gcn.plinguacore.parser.output, org.gcn.plinguacore.parser.output.binary, org.gcn.plinguacore.parser.output.XML, org.gcn.plinguacore.simulator, org.gcn.plinguacore.simulator.cellLike, org.gcn.plinguacore.simulator.cellLike.activeMembranes, org.gcn.plinguacore.simulator.cellLike.probabilistic, org.gcn.plinguacore.simulator.cellLike.stochastic, org.gcn.plinguacore.simulator.cellLike.transition, org.gcn.plinguacore.simulator.tissueLike, org.gcn.plinguacore.util, org.gcn.plinguacore.util.check, org.gcn.plinguacore.util.psystem, org.gcn.plinguacore.util.psystem.cellLike, org.gcn.plinguacore.util.psystem.cellLike.membrane, org.gcn.plinguacore.util.psystem.checkPsystem, org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem, org.gcn.plinguacore.util.psystem.factory, org.gcn.plinguacore.util.psystem.factory.cellLike, org.gcn.plinguacore.util.psystem.membrane, org.gcn.plinguacore.util.psystem.rule, org.gcn.plinguacore.util.psystem.rule.cellLike, org.gcn.plinguacore.util.psystem.rule.checkRule, org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule, org.gcn.plinguacore.util.psystem.rule.tissueLike, org.gcn.plinguacore.util.psystem.tissueLike, org.gcn.plinguacore.util.psystem.tissueLike.membrane

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.gcn.plinguacore.util.RandomArrayList<E> (implements java.util.Collection<E>)
  • org.gcn.plinguacore.parser.AbstractParserFactory
    • org.gcn.plinguacore.parser.input.InputParserFactory
    • org.gcn.plinguacore.parser.output.OutputParserFactory
  • org.gcn.plinguacore.util.psystem.factory.AbstractPsystemFactory (implements org.gcn.plinguacore.util.psystem.factory.IPsystemFactory)
    • org.gcn.plinguacore.util.psystem.factory.cellLike.AbstractCellLikePsystemFactory
      • org.gcn.plinguacore.simulator.cellLike.activeMembranes.CreationPsystemFactory
      • org.gcn.plinguacore.simulator.cellLike.activeMembranes.DivisionPsystemFactory
      • org.gcn.plinguacore.simulator.cellLike.transition.EvolutionCommunicationPsystemFactory
      • org.gcn.plinguacore.simulator.cellLike.transition.EvSymportAntiportPsystemFactory
        • org.gcn.plinguacore.simulator.cellLike.transition.SymportAntiportPsystemFactory
      • org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticPsystemFactory
        • org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticPsystemFactory
      • org.gcn.plinguacore.simulator.cellLike.transition.TransitionPsystemFactory
    • org.gcn.plinguacore.simulator.tissueLike.TissueLikePsystemFactory
  • org.gcn.plinguacore.util.psystem.rule.AbstractRule (implements org.gcn.plinguacore.util.psystem.rule.IRule, java.io.Serializable)
    • org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRule
      • org.gcn.plinguacore.util.psystem.rule.tissueLike.DoubleCommunicationTissueLikeRule (implements org.gcn.plinguacore.util.psystem.rule.IDoubleCommunicationRule)
  • org.gcn.plinguacore.simulator.AbstractSimulator (implements org.gcn.plinguacore.simulator.ISimulator)
    • org.gcn.plinguacore.simulator.AbstractSelectionExecutionSimulator
      • org.gcn.plinguacore.simulator.cellLike.CellLikeSimulator
        • org.gcn.plinguacore.simulator.cellLike.probabilistic.AbstractProbabilisticSimulator
          • org.gcn.plinguacore.simulator.cellLike.probabilistic.BinomialProbabilisticSimulator
          • org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticSimulator
        • org.gcn.plinguacore.simulator.cellLike.activeMembranes.ActiveMembranesSimulator
        • org.gcn.plinguacore.simulator.cellLike.transition.NonDeterministicTransitionSimulator
        • org.gcn.plinguacore.simulator.cellLike.transition.TransitionSimulator
      • org.gcn.plinguacore.simulator.tissueLike.TissueLikeSimulator
    • org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator
      • org.gcn.plinguacore.simulator.cellLike.stochastic.DeterministicWaitingTimesSimulator
      • org.gcn.plinguacore.simulator.cellLike.stochastic.DirectStochasticSimulator
      • org.gcn.plinguacore.simulator.cellLike.stochastic.EfficientStochasticSimulator
  • org.gcn.plinguacore.util.psystem.ActivationSets
  • org.gcn.plinguacore.util.psystem.AlphabetObject (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.gcn.plinguacore.applications.AppCompiler
  • org.gcn.plinguacore.applications.AppMain
  • org.gcn.plinguacore.applications.AppSimulator
  • org.gcn.plinguacore.util.check.BaseCheck<T>
    • org.gcn.plinguacore.util.psystem.checkPsystem.BaseCheckPsystem (implements org.gcn.plinguacore.util.psystem.checkPsystem.CheckPsystem)
  • org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembraneFactory
  • org.gcn.plinguacore.util.psystem.rule.cellLike.CellLikeRuleFactory (implements org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory)
  • org.gcn.plinguacore.util.psystem.rule.tissueLike.Communication
  • org.gcn.plinguacore.util.psystem.Configuration (implements java.lang.Cloneable, java.io.Serializable)
    • org.gcn.plinguacore.util.psystem.cellLike.CellLikeConfiguration
    • org.gcn.plinguacore.util.psystem.tissueLike.TissueLikeConfiguration
  • org.gcn.plinguacore.simulator.CreateSimulator
    • org.gcn.plinguacore.simulator.cellLike.activeMembranes.ActiveMembranesCreateSimulator
    • org.gcn.plinguacore.simulator.cellLike.probabilistic.ProbabilisticCreateSimulator
    • org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticCreateSimulator
    • org.gcn.plinguacore.simulator.tissueLike.TissueLikeCreateSimulator
    • org.gcn.plinguacore.simulator.cellLike.transition.TransitionCreateSimulator
  • org.gcn.plinguacore.util.check.DecoratorCheck<T>
    • org.gcn.plinguacore.util.psystem.checkPsystem.DecoratorCheckPsystem (implements org.gcn.plinguacore.util.psystem.checkPsystem.CheckPsystem)
      • org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.CompleteProbabilities (implements org.gcn.plinguacore.util.psystem.checkPsystem.CheckPsystem)
      • org.gcn.plinguacore.util.psystem.checkPsystem.specificCheckPsystem.ConsistentRules
  • org.gcn.plinguacore.util.psystem.rule.checkRule.DecoratorCheckRule
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCharges
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoConstant
      • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.Constant
        • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.Ratio
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCooperation
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCooperationWithDivision
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoCreation
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoDifferentMainLabels
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoDissolution
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoDivision
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoEmptyLeftMultiSet
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoEvolution
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoGeneStrings
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSet
      • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSetWithCreation
      • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSetWithDissolution
      • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftExternalMultiSetWithDivision
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftInnerMembranes
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoMultipleProduction
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoMultipleProductionWithDivision
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoPriority
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRepeatedLabels
      • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoLeftRepeatedLabels
      • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRightRepeatedLabels
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRightExternalMultiSet
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NoRightInnerMembranes
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.NotAllEmptyMultiSet
    • org.gcn.plinguacore.util.psystem.rule.checkRule.specificCheckRule.SymmetricCommunication
  • org.gcn.plinguacore.simulator.DecoratorSimulator (implements org.gcn.plinguacore.simulator.ISimulator)
    • org.gcn.plinguacore.simulator.AlternativeStepsSupportedSimulator
    • org.gcn.plinguacore.simulator.StepBackSupportedSimulator
  • org.gcn.plinguacore.simulator.ElementFileStream<ElementType> (implements java.io.Serializable)
  • org.gcn.plinguacore.util.GeneString
  • org.gcn.plinguacore.util.psystem.rule.HandRule (implements java.io.Serializable)
    • org.gcn.plinguacore.util.psystem.rule.LeftHandRule
    • org.gcn.plinguacore.util.psystem.rule.RightHandRule
  • org.gcn.plinguacore.util.HashMultiSet<E> (implements org.gcn.plinguacore.util.MultiSet<E>)
    • org.gcn.plinguacore.util.HashInfiniteMultiSet<E> (implements org.gcn.plinguacore.util.InfiniteMultiSet<E>)
  • org.gcn.plinguacore.util.IndexedPriorityQueue<E> (implements java.io.Serializable)
  • org.gcn.plinguacore.util.IndexedPriorityQueue.Node<T> (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.gcn.plinguacore.util.InmutableMultiSet<E> (implements org.gcn.plinguacore.util.MultiSet<E>)
  • org.gcn.plinguacore.parser.input.InputParser (implements org.gcn.plinguacore.parser.IParser)
    • org.gcn.plinguacore.parser.input.plingua.PlinguaInputParser
    • org.gcn.plinguacore.parser.input.XML.XMLCellLikeInputParser
  • org.gcn.plinguacore.parser.input.messages.InputParserAbstractMsg (implements org.gcn.plinguacore.parser.input.messages.InputParserMsg)
  • org.gcn.plinguacore.parser.input.messages.InputParserDecoratorMsg (implements org.gcn.plinguacore.parser.input.messages.InputParserMsg)
  • org.gcn.plinguacore.parser.input.messages.InputParserMsgFactory
  • java.io.InputStream (implements java.io.Closeable)
    • org.gcn.plinguacore.parser.input.byteCounter.InputStreamWrapper (implements org.gcn.plinguacore.parser.input.byteCounter.IByteCounter)
  • org.gcn.plinguacore.util.psystem.Label (implements java.lang.Cloneable, java.io.Serializable)
  • org.gcn.plinguacore.util.psystem.membrane.Membrane (implements java.io.Serializable)
    • org.gcn.plinguacore.util.psystem.membrane.ChangeableMembrane
      • org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeMembrane
        • org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeNoSkinMembrane
        • org.gcn.plinguacore.util.psystem.cellLike.membrane.CellLikeSkinMembrane (implements org.gcn.plinguacore.util.psystem.membrane.MembraneStructure)
      • org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembrane
        • org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeEnvironment
    • org.gcn.plinguacore.util.psystem.rule.InnerRuleMembrane
    • org.gcn.plinguacore.util.psystem.rule.OuterRuleMembrane
  • org.gcn.plinguacore.parser.input.messages.MsgInterval
  • org.gcn.plinguacore.parser.output.OutputParser (implements org.gcn.plinguacore.parser.IParser)
    • org.gcn.plinguacore.parser.output.binary.BinaryOutputParserFactory
    • org.gcn.plinguacore.parser.output.XML.XMLCellLikeOutputParser
  • org.gcn.plinguacore.util.Pair<E,T> (implements java.io.Serializable)
    • org.gcn.plinguacore.util.Triple<E,T,L>
  • cern.colt.PersistentObject (implements java.lang.Cloneable, java.io.Serializable)
    • cern.jet.random.engine.RandomEngine (implements cern.colt.function.DoubleFunction, cern.colt.function.IntFunction)
      • cern.jet.random.engine.MersenneTwister
        • org.gcn.plinguacore.util.RandomNumbersGenerator
  • org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserTokenManager (implements org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserConstants)
  • org.gcn.plinguacore.util.psystem.Psystem (implements java.io.Serializable)
    • org.gcn.plinguacore.util.psystem.cellLike.CellLikePsystem
    • org.gcn.plinguacore.util.psystem.tissueLike.TissueLikePsystem
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • java.io.StringReader
      • org.gcn.plinguacore.parser.input.byteCounter.StringReaderWrapper (implements org.gcn.plinguacore.parser.input.byteCounter.IByteCounter)
  • org.gcn.plinguacore.util.psystem.rule.RuleComparator (implements java.util.Comparator<T>)
  • org.gcn.plinguacore.util.psystem.rule.RulesSet (implements java.io.Serializable, java.util.Set<E>)
  • org.gcn.plinguacore.util.ShuffleIterator<E> (implements java.util.Iterator<E>)
  • org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticSimulator.Reaction (implements java.lang.Comparable<T>, java.io.Serializable)
  • org.gcn.plinguacore.simulator.cellLike.stochastic.StochasticTester
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Error
      • org.gcn.plinguacore.util.PlinguaPanicError
    • java.lang.Exception
      • org.gcn.plinguacore.parser.input.plingua.ParseException
        • org.gcn.plinguacore.parser.input.plingua.PlinguaSemanticsException
      • org.gcn.plinguacore.util.PlinguaCoreException
  • org.gcn.plinguacore.util.psystem.tissueLike.membrane.TissueLikeMembraneStructure (implements org.gcn.plinguacore.util.psystem.membrane.MembraneStructure)
  • org.gcn.plinguacore.util.psystem.rule.tissueLike.TissueLikeRuleFactory (implements org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory)
  • org.gcn.plinguacore.util.UnionIterator<E> (implements java.util.Iterator<E>)
  • org.gcn.plinguacore.util.UnionSet<E> (implements java.util.Set<E>)
  • org.gcn.plinguacore.parser.input.VerbosityConstants
  • org.gcn.plinguacore.util.XmlFileIDs

Interface Hierarchy

• org.gcn.plinguacore.util.psystem.rule.AbstractRuleFactory
• java.lang.Cloneable
  • org.gcn.plinguacore.util.psystem.membrane.MembraneStructure
• org.gcn.plinguacore.parser.input.byteCounter.IByteCounter
• org.gcn.plinguacore.util.psystem.factory.IModelsInfo
  • org.gcn.plinguacore.util.psystem.factory.IModelsClassProvider
• org.gcn.plinguacore.parser.input.messages.InputParserMsg
• org.gcn.plinguacore.parser.IParser
• org.gcn.plinguacore.parser.IParsersInfo
  • org.gcn.plinguacore.parser.IParsersClassProvider
• org.gcn.plinguacore.util.psystem.factory.IPsystemFactory
• org.gcn.plinguacore.util.psystem.rule.IRule
  • org.gcn.plinguacore.util.psystem.rule.IConstantRule
    • org.gcn.plinguacore.util.psystem.rule.IStochasticRule
  • org.gcn.plinguacore.util.psystem.rule.IDoubleCommunicationRule
  • org.gcn.plinguacore.util.psystem.rule.IPriorityRule
  • org.gcn.plinguacore.util.psystem.rule.IStochasticRule
• org.gcn.plinguacore.simulator.ISimulatorInfo
  • org.gcn.plinguacore.simulator.ISimulatorClassProvider
• java.lang.Iterable<T>
  • java.util.Collection<E>
    • org.gcn.plinguacore.util.InfiniteMultiSet<E>
    • org.gcn.plinguacore.util.MultiSet<E> (also extends java.io.Serializable)
      • org.gcn.plinguacore.util.InfiniteMultiSet<E>
  • org.gcn.plinguacore.util.InfiniteMultiSet<E>
  • org.gcn.plinguacore.util.MultiSet<E> (also extends java.util.Collection<E>, java.io.Serializable)
    • org.gcn.plinguacore.util.InfiniteMultiSet<E>
• org.gcn.plinguacore.parser.input.plingua.PlinguaJavaCcParserConstants
• java.io.Serializable
  • org.gcn.plinguacore.util.check.Check<T>
    • org.gcn.plinguacore.util.psystem.checkPsystem.CheckPsystem
  • org.gcn.plinguacore.util.psystem.checkPsystem.CheckPsystem
  • org.gcn.plinguacore.util.psystem.rule.checkRule.CheckRule
  • org.gcn.plinguacore.util.InfiniteMultiSet<E>
  • org.gcn.plinguacore.simulator.ISimulator
  • org.gcn.plinguacore.util.MultiSet<E> (also extends java.util.Collection<E>)
    • org.gcn.plinguacore.util.InfiniteMultiSet<E>