Hierarchy For All Packages

Package Hierarchies:

• org.colomoto.biolqm,
• org.colomoto.biolqm.helper.clingo,
• org.colomoto.biolqm.io,
• org.colomoto.biolqm.io.antlr,
• org.colomoto.biolqm.io.avatar,
• org.colomoto.biolqm.io.bnet,
• org.colomoto.biolqm.io.booleannet,
• org.colomoto.biolqm.io.boolsim,
• org.colomoto.biolqm.io.cnet,
• org.colomoto.biolqm.io.functions,
• org.colomoto.biolqm.io.ginml,
• org.colomoto.biolqm.io.gna,
• org.colomoto.biolqm.io.maboss,
• org.colomoto.biolqm.io.petrinet,
• org.colomoto.biolqm.io.pint,
• org.colomoto.biolqm.io.sbml,
• org.colomoto.biolqm.io.truthtable,
• org.colomoto.biolqm.modifier,
• org.colomoto.biolqm.modifier.booleanize,
• org.colomoto.biolqm.modifier.perturbation,
• org.colomoto.biolqm.modifier.reduction,
• org.colomoto.biolqm.modifier.reverse,
• org.colomoto.biolqm.modifier.subspace,
• org.colomoto.biolqm.tool,
• org.colomoto.biolqm.tool.attractor,
• org.colomoto.biolqm.tool.implicants,
• org.colomoto.biolqm.tool.inferinteraction,
• org.colomoto.biolqm.tool.simulation,
• org.colomoto.biolqm.tool.simulation.updater,
• org.colomoto.biolqm.tool.stablestate,
• org.colomoto.biolqm.tool.trapspaces,
• org.colomoto.common.task,
• org.colomoto.common.xml

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.colomoto.biolqm.tool.stablestate.StableStateList
        • org.colomoto.biolqm.tool.trapspaces.TrapSpaceList
  • org.colomoto.biolqm.io.AbstractFormat (implements org.colomoto.biolqm.io.LogicalModelFormat)
    • org.colomoto.biolqm.io.bnet.BNetFormat
    • org.colomoto.biolqm.io.functions.BooleanFunctionFormat
    • org.colomoto.biolqm.io.booleannet.BooleanNetFormat
    • org.colomoto.biolqm.io.boolsim.BoolSimFormat
    • org.colomoto.biolqm.io.cnet.CNetFormat
    • org.colomoto.biolqm.io.ginml.GINMLFormat
    • org.colomoto.biolqm.io.gna.GNAFormat
    • org.colomoto.biolqm.io.maboss.MaBoSSFormat
    • org.colomoto.biolqm.io.pint.PintFormat
    • org.colomoto.biolqm.io.petrinet.PNFormat
      • org.colomoto.biolqm.io.petrinet.APNNFormat
      • org.colomoto.biolqm.io.petrinet.INAFormat
      • org.colomoto.biolqm.io.petrinet.PNMLFormat
    • org.colomoto.biolqm.io.sbml.SBMLFormat
    • org.colomoto.biolqm.io.truthtable.TruthTableFormat
  • org.colomoto.biolqm.io.ginml.AbstractGINMLWriter
    • org.colomoto.biolqm.io.ginml.LogicalModel2GINML
  • org.colomoto.biolqm.modifier.AbstractModelModifierService (implements org.colomoto.biolqm.modifier.ModelModifierService)
    • org.colomoto.biolqm.modifier.booleanize.ModelBooleanizerService
    • org.colomoto.biolqm.modifier.reduction.ModelReductionService
    • org.colomoto.biolqm.modifier.reverse.ModelReverserService
    • org.colomoto.biolqm.modifier.perturbation.PerturbationService
    • org.colomoto.biolqm.modifier.subspace.SubSpaceService
  • org.colomoto.mddlib.operators.AbstractOperator (implements org.colomoto.mddlib.MDDOperator)
    • org.colomoto.mddlib.operators.AbstractFlexibleOperator
      • org.colomoto.biolqm.tool.stablestate.StableOperation
  • org.colomoto.biolqm.modifier.perturbation.AbstractPerturbation (implements org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation)
    • org.colomoto.biolqm.modifier.perturbation.FixedValuePerturbation
    • org.colomoto.biolqm.modifier.perturbation.InteractionPerturbation
    • org.colomoto.biolqm.modifier.perturbation.MultiplePerturbation<P>
    • org.colomoto.biolqm.modifier.perturbation.RangePerturbation
  • org.colomoto.biolqm.io.petrinet.AbstractPNEncoder
    • org.colomoto.biolqm.io.petrinet.PNEncoderAPNN
    • org.colomoto.biolqm.io.petrinet.PNEncoderINA
    • org.colomoto.biolqm.io.petrinet.PNEncoderPNML
  • org.colomoto.biolqm.tool.AbstractTool<R,S> (implements org.colomoto.biolqm.tool.LogicalModelTool<R,S>)
    • org.colomoto.biolqm.tool.attractor.AttractorTool
    • org.colomoto.biolqm.tool.stablestate.StableJBDD
    • org.colomoto.biolqm.tool.stablestate.StableStateTool
    • org.colomoto.biolqm.tool.trapspaces.TrapSpaceTool
  • org.colomoto.biolqm.io.avatar.AvatarClause
  • org.colomoto.biolqm.io.avatar.AvatarUtils
  • org.antlr.v4.runtime.BaseErrorListener (implements org.antlr.v4.runtime.ANTLRErrorListener)
    • org.colomoto.biolqm.io.antlr.ErrorListener
  • org.colomoto.biolqm.tool.simulation.updater.BaseUpdater (implements org.colomoto.biolqm.tool.simulation.LogicalModelUpdater)
    • org.colomoto.biolqm.tool.simulation.updater.AbstractDeterministicUpdater (implements org.colomoto.biolqm.tool.simulation.DeterministicUpdater)
      • org.colomoto.biolqm.tool.simulation.updater.BlockSequentialUpdater (implements org.colomoto.biolqm.tool.simulation.DeterministicUpdater)
      • org.colomoto.biolqm.tool.simulation.updater.SequentialUpdater (implements org.colomoto.biolqm.tool.simulation.DeterministicUpdater)
      • org.colomoto.biolqm.tool.simulation.updater.SynchronousUpdater (implements org.colomoto.biolqm.tool.simulation.DeterministicUpdater)
    • org.colomoto.biolqm.tool.simulation.updater.AbstractMultipleSuccessorUpdater (implements org.colomoto.biolqm.tool.simulation.MultipleSuccessorsUpdater)
      • org.colomoto.biolqm.tool.simulation.updater.AsynchronousUpdater
      • org.colomoto.biolqm.tool.simulation.updater.CompleteUpdater
      • org.colomoto.biolqm.tool.simulation.updater.PriorityUpdater
    • org.colomoto.biolqm.tool.simulation.updater.AbstractRandomUpdater (implements org.colomoto.biolqm.tool.simulation.RandomUpdater)
      • org.colomoto.biolqm.tool.simulation.updater.RandomUpdaterWithRates
  • org.colomoto.biolqm.io.antlr.BNetBaseListener (implements org.colomoto.biolqm.io.antlr.BNetListener)
  • org.colomoto.biolqm.io.bnet.BNetExport
  • org.colomoto.biolqm.io.bnet.BNetImport
  • org.colomoto.biolqm.io.antlr.BooleanFunctionBaseListener (implements org.colomoto.biolqm.io.antlr.BooleanFunctionListener)
  • org.colomoto.biolqm.io.functions.BooleanFunctionExport
  • org.colomoto.biolqm.io.functions.BooleanFunctionImport
  • org.colomoto.biolqm.modifier.booleanize.Booleanizer
  • org.colomoto.biolqm.io.antlr.BooleanNetBaseListener (implements org.colomoto.biolqm.io.antlr.BooleanNetListener)
  • org.colomoto.biolqm.io.booleannet.BooleanNetExport
  • org.colomoto.biolqm.io.booleannet.BooleanNetImport
  • org.colomoto.biolqm.io.antlr.BoolsimBaseListener (implements org.colomoto.biolqm.io.antlr.BoolsimListener)
  • org.colomoto.biolqm.io.boolsim.BoolSimExport
  • org.colomoto.biolqm.io.boolsim.BoolSimImport
  • org.colomoto.biolqm.helper.clingo.ClingoLauncher
  • org.colomoto.biolqm.helper.clingo.ClingoResult
  • org.colomoto.biolqm.io.cnet.CNetExport
  • org.colomoto.biolqm.ConnectivityMatrix
  • org.colomoto.biolqm.modifier.reduction.DuplicateRemover
  • org.colomoto.biolqm.io.antlr.ExpressionStack
  • org.colomoto.biolqm.ExtensionLoader
  • org.colomoto.biolqm.modifier.reduction.FixedComponentRemover
  • org.colomoto.biolqm.tool.implicants.Formula
  • org.colomoto.biolqm.io.gna.GNAExport
  • org.colomoto.biolqm.HelperTool
  • org.colomoto.biolqm.tool.implicants.ImplicantSearcher (implements java.lang.Iterable<T>)
  • org.colomoto.biolqm.tool.inferinteraction.InteractionSearcher
  • org.colomoto.biolqm.tool.stablestate.JBDDModel
  • org.colomoto.biolqm.LogicalModelComparator
  • org.colomoto.biolqm.LogicalModelImpl (implements org.colomoto.biolqm.LogicalModel)
    • org.colomoto.biolqm.StatefulLogicalModelImpl (implements org.colomoto.biolqm.StatefulLogicalModel)
  • org.colomoto.biolqm.LQMLauncher
  • org.colomoto.biolqm.LQMScriptLauncher
  • org.colomoto.biolqm.LQMServiceManager
  • org.colomoto.biolqm.io.maboss.MaBoSSEncoder
  • org.colomoto.biolqm.tool.implicants.MDD2PrimeImplicants
  • org.colomoto.biolqm.modifier.reduction.ModelReducer
  • org.colomoto.biolqm.modifier.reverse.ModelReverser (implements org.colomoto.biolqm.modifier.ModelModifier)
  • org.colomoto.biolqm.tool.simulation.MultipleSuccessorSimulation
  • org.colomoto.biolqm.NodeInfo
  • org.colomoto.biolqm.io.OutputStreamProvider
  • org.colomoto.biolqm.modifier.perturbation.PerturbationModifier (implements org.colomoto.biolqm.modifier.ModelModifier)
  • org.colomoto.biolqm.io.pint.PintExport
  • org.colomoto.biolqm.io.petrinet.PNConfig
  • org.colomoto.biolqm.tool.simulation.updater.PriorityClasses
  • org.colomoto.biolqm.tool.simulation.updater.RandomUpdaterWrapper (implements org.colomoto.biolqm.tool.simulation.RandomUpdater)
  • org.colomoto.biolqm.modifier.perturbation.RangeRestrictionOperation
  • org.antlr.v4.runtime.Recognizer<Symbol,ATNInterpreter>
    • org.antlr.v4.runtime.Lexer (implements org.antlr.v4.runtime.TokenSource)
      • org.colomoto.biolqm.io.antlr.BNetLexer
      • org.colomoto.biolqm.io.antlr.BooleanFunctionLexer
      • org.colomoto.biolqm.io.antlr.BooleanNetLexer
      • org.colomoto.biolqm.io.antlr.BoolsimLexer
    • org.antlr.v4.runtime.Parser
      • org.colomoto.biolqm.io.antlr.BNetParser
      • org.colomoto.biolqm.io.antlr.BooleanFunctionParser
      • org.colomoto.biolqm.io.antlr.BooleanNetParser
      • org.colomoto.biolqm.io.antlr.BoolsimParser
  • org.colomoto.biolqm.modifier.reduction.ReduceOperation
  • org.colomoto.biolqm.modifier.reduction.ReductionModifier (implements org.colomoto.biolqm.modifier.ModelModifier)
  • org.colomoto.biolqm.modifier.reduction.ReductionSettings
  • org.colomoto.biolqm.modifier.perturbation.RegulatorRemovalOperation
  • org.colomoto.biolqm.tool.implicants.RestrictedPathSearcher (implements java.lang.Iterable<T>)
  • org.colomoto.biolqm.modifier.reverse.ReverseOperation
  • org.antlr.v4.runtime.RuleContext (implements org.antlr.v4.runtime.tree.RuleNode)
    • org.antlr.v4.runtime.ParserRuleContext
      • org.colomoto.biolqm.io.antlr.BNetParser.AndContext
      • org.colomoto.biolqm.io.antlr.BNetParser.AssignContext
      • org.colomoto.biolqm.io.antlr.BNetParser.ExprContext
        • org.colomoto.biolqm.io.antlr.BNetParser.AndExprContext
        • org.colomoto.biolqm.io.antlr.BNetParser.OrExprContext
        • org.colomoto.biolqm.io.antlr.BNetParser.SimpleExprContext
      • org.colomoto.biolqm.io.antlr.BNetParser.HeaderContext
      • org.colomoto.biolqm.io.antlr.BNetParser.ModelContext
      • org.colomoto.biolqm.io.antlr.BNetParser.NotContext
      • org.colomoto.biolqm.io.antlr.BNetParser.OrContext
      • org.colomoto.biolqm.io.antlr.BNetParser.ValContext
      • org.colomoto.biolqm.io.antlr.BNetParser.VarContext
      • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AssignContext
      • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ExprContext
        • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.AndExprContext
        • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.OrExprContext
        • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.SimpleExprContext
      • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ModelContext
      • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.NotContext
      • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.ValContext
      • org.colomoto.biolqm.io.antlr.BooleanFunctionParser.VarContext
      • org.colomoto.biolqm.io.antlr.BooleanNetParser.AssignContext
      • org.colomoto.biolqm.io.antlr.BooleanNetParser.ExprContext
        • org.colomoto.biolqm.io.antlr.BooleanNetParser.AndExprContext
        • org.colomoto.biolqm.io.antlr.BooleanNetParser.OrExprContext
        • org.colomoto.biolqm.io.antlr.BooleanNetParser.SimpleExprContext
      • org.colomoto.biolqm.io.antlr.BooleanNetParser.ModelContext
      • org.colomoto.biolqm.io.antlr.BooleanNetParser.NotContext
      • org.colomoto.biolqm.io.antlr.BooleanNetParser.ValContext
      • org.colomoto.biolqm.io.antlr.BooleanNetParser.VarContext
      • org.colomoto.biolqm.io.antlr.BoolsimParser.AssignContext
      • org.colomoto.biolqm.io.antlr.BoolsimParser.ExprContext
        • org.colomoto.biolqm.io.antlr.BoolsimParser.AndExprContext
        • org.colomoto.biolqm.io.antlr.BoolsimParser.SimpleExprContext
      • org.colomoto.biolqm.io.antlr.BoolsimParser.ModelContext
      • org.colomoto.biolqm.io.antlr.BoolsimParser.NotContext
      • org.colomoto.biolqm.io.antlr.BoolsimParser.OpContext
      • org.colomoto.biolqm.io.antlr.BoolsimParser.VarContext
  • org.colomoto.biolqm.tool.attractor.SATAttractorFinder
  • org.colomoto.biolqm.io.sbml.SBMLQualBundle
  • org.colomoto.biolqm.io.sbml.SBMLqualExport
  • org.colomoto.biolqm.io.sbml.SBMLqualHelper
  • org.colomoto.biolqm.io.sbml.SBMLqualImport
  • org.colomoto.biolqm.tool.simulation.SingleSuccessorSimulation (implements java.lang.Iterable<T>)
  • org.colomoto.biolqm.tool.stablestate.StableASP (implements org.colomoto.biolqm.helper.clingo.ClingoResultHandler)
  • org.colomoto.biolqm.tool.stablestate.StructuralNodeOrderer (implements java.lang.Iterable<T>)
  • org.colomoto.biolqm.modifier.subspace.SubSpaceRestriction (implements org.colomoto.biolqm.modifier.ModelModifier)
  • org.colomoto.biolqm.tool.implicants.Term
  • java.lang.Thread (implements java.lang.Runnable)
    • org.colomoto.common.task.AbstractTask<T> (implements org.colomoto.common.task.Task<T>)
      • org.colomoto.biolqm.tool.stablestate.StableStateSearcher
      • org.colomoto.biolqm.tool.trapspaces.TrapSpaceIdentifier
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.io.IOException
        • org.colomoto.biolqm.io.avatar.AvatarLogicalModelException
  • org.colomoto.biolqm.tool.trapspaces.TrapSpace
  • org.colomoto.biolqm.tool.trapspaces.TrapSpaceSettings
  • org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverASP (implements org.colomoto.biolqm.helper.clingo.ClingoResultHandler, org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver)
  • org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolverBDD (implements org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver)
  • org.colomoto.biolqm.io.truthtable.TruthTableExport
  • org.colomoto.biolqm.io.truthtable.TruthTableImport
  • org.colomoto.common.xml.XMLWriter

Interface Hierarchy

• java.util.concurrent.Callable<V>
  • org.colomoto.common.task.Task<T>
• org.colomoto.biolqm.helper.clingo.ClingoResultHandler
• org.colomoto.biolqm.LogicalModel
  • org.colomoto.biolqm.StatefulLogicalModel
• org.colomoto.biolqm.io.LogicalModelFormat
• org.colomoto.biolqm.modifier.perturbation.LogicalModelPerturbation
• org.colomoto.biolqm.tool.simulation.LogicalModelUpdater
  • org.colomoto.biolqm.tool.simulation.DeterministicUpdater
  • org.colomoto.biolqm.tool.simulation.MultipleSuccessorsUpdater
  • org.colomoto.biolqm.tool.simulation.RandomUpdater
  • org.colomoto.biolqm.tool.simulation.SingleSuccessorUpdater
    • org.colomoto.biolqm.tool.simulation.DeterministicUpdater
    • org.colomoto.biolqm.tool.simulation.RandomUpdater
• org.colomoto.biolqm.modifier.ModelModifier
• org.colomoto.biolqm.NodeInfoHolder
• org.antlr.v4.runtime.tree.ParseTreeListener
  • org.colomoto.biolqm.io.antlr.BNetListener
  • org.colomoto.biolqm.io.antlr.BooleanFunctionListener
  • org.colomoto.biolqm.io.antlr.BooleanNetListener
  • org.colomoto.biolqm.io.antlr.BoolsimListener
• org.colomoto.biolqm.Service
  • org.colomoto.biolqm.tool.LogicalModelTool<R,S>
  • org.colomoto.biolqm.modifier.ModelModifierService
• org.colomoto.common.task.TaskListener
• org.colomoto.biolqm.tool.trapspaces.TrapSpaceSolver

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.colomoto.common.task.TaskStatus
    • org.colomoto.biolqm.io.LogicalModelFormat.MultivaluedSupport
    • org.colomoto.biolqm.io.antlr.Value
    • org.colomoto.biolqm.io.antlr.Operator
    • org.colomoto.biolqm.tool.simulation.SimulationStrategy
    • org.colomoto.biolqm.tool.stablestate.StableStateMethod