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## Hierarchy For All Packages

Package Hierarchies:
  <default>, biouml, biouml.model, biouml.model.dynamics, biouml.model.dynamics.resources, biouml.model.htmlgen, biouml.model.util, biouml.plugins, biouml.plugins.cellml, biouml.plugins.ginsim, biouml.plugins.gxl, biouml.plugins.jgraph, biouml.plugins.matlab, biouml.plugins.matlab.resources, biouml.plugins.sbml, biouml.plugins.sbml._test, biouml.plugins.sbml._test.semantic-test-suite, biouml.plugins.sbml._test.semantic-test-suite.algebraicRules, biouml.plugins.sbml._test.semantic-test-suite.algebraicRules.basic, biouml.plugins.sbml._test.semantic-test-suite.algebraicRules.fastReactionExample, biouml.plugins.sbml._test.semantic-test-suite.AUTOMATION, biouml.plugins.sbml._test.semantic-test-suite.AUTOMATION.wrappers, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1.BothBoundary, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1.Boundary, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1.Boundary2, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1.forward, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1.forward-from-zero, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1.NoEffect, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model1.StoichiometryIs2, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model2, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model2.base, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model2.boundaryA, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model2.boundaryAB, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model2.boundaryABC, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model2.boundaryC, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model2.stoichiometryA2, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model3, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model3.base, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model3.boundaryD, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model3.boundaryS4, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model3.stoichiometry2S4, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model3.stoichiometryD2, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model4, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model4.base, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model5, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model5.base, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model6, biouml.plugins.sbml._test.semantic-test-suite.basic-reactions.model6.base, biouml.plugins.sbml._test.semantic-test-suite.basicRules, biouml.plugins.sbml._test.semantic-test-suite.basicRules.assignmentInconsistent-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.assignmentInitialize-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.assignment-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.assignmentUsedInAssignment-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.assignmentUsedInDifferential-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.assignmentUsedInReaction-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.differential-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.differentialUsedInAssignmentConsistent-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.differentialUsedInAssignment-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.differentialUsedInDifferential-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.differentialUsedInReaction-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.dynamicAssignmentUsedInDifferential-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.dynamicAssignmentUsedInReaction-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.noRule-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.reactionUsedInAssignment-Species, biouml.plugins.sbml._test.semantic-test-suite.basicRules.reactionUsedInDifferential-Species, biouml.plugins.sbml._test.semantic-test-suite.compartments, biouml.plugins.sbml._test.semantic-test-suite.compartments.nonUnitVolume-initialAmount, biouml.plugins.sbml._test.semantic-test-suite.compartments.nonUnitVolume-initialConcentration, biouml.plugins.sbml._test.semantic-test-suite.compartments.transportReaction, biouml.plugins.sbml._test.semantic-test-suite.complexReactions, biouml.plugins.sbml._test.semantic-test-suite.complexReactions.FeedbackCompetitive, biouml.plugins.sbml._test.semantic-test-suite.complexReactions.Hill, biouml.plugins.sbml._test.semantic-test-suite.complexReactions.linearNegFeedback, biouml.plugins.sbml._test.semantic-test-suite.complexReactions.ModifierNegativeFeedback, biouml.plugins.sbml._test.semantic-test-suite.complexReactions.NoProduct, biouml.plugins.sbml._test.semantic-test-suite.complexReactions.NoReactant, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.and, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.ceiling, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.delay, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.discontinuity, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.factorial, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.false, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.floor, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.geq, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.leq, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.lt, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.not, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.or, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.time, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.true, biouml.plugins.sbml._test.semantic-test-suite.discontinuityTimeAndDelays.xor, biouml.plugins.sbml._test.semantic-test-suite.events, biouml.plugins.sbml._test.semantic-test-suite.events.1-event-1-assignment, biouml.plugins.sbml._test.semantic-test-suite.events.1-event-2-assignments, biouml.plugins.sbml._test.semantic-test-suite.events.2-events-1-assignment, biouml.plugins.sbml._test.semantic-test-suite.events.complex-trigger, biouml.plugins.sbml._test.semantic-test-suite.events.increment, biouml.plugins.sbml._test.semantic-test-suite.events.increment.temp, biouml.plugins.sbml._test.semantic-test-suite.functions, biouml.plugins.sbml._test.semantic-test-suite.functions.algebraic-rule, biouml.plugins.sbml._test.semantic-test-suite.functions.basic-rules, biouml.plugins.sbml._test.semantic-test-suite.functions.event-assignment, biouml.plugins.sbml._test.semantic-test-suite.functions.function, biouml.plugins.sbml._test.semantic-test-suite.functions.kinetic-law, biouml.plugins.sbml._test.semantic-test-suite.functions.stoichiometry, biouml.plugins.sbml._test.semantic-test-suite.functions.trigger, biouml.plugins.sbml._test.semantic-test-suite.mathml, biouml.plugins.sbml._test.semantic-test-suite.mathml.abs, biouml.plugins.sbml._test.semantic-test-suite.mathml.arccos, biouml.plugins.sbml._test.semantic-test-suite.mathml.arccosh, biouml.plugins.sbml._test.semantic-test-suite.mathml.arccot, biouml.plugins.sbml._test.semantic-test-suite.mathml.arccoth, biouml.plugins.sbml._test.semantic-test-suite.mathml.arccsc, biouml.plugins.sbml._test.semantic-test-suite.mathml.arccsch, biouml.plugins.sbml._test.semantic-test-suite.mathml.arcsec, biouml.plugins.sbml._test.semantic-test-suite.mathml.arcsech, biouml.plugins.sbml._test.semantic-test-suite.mathml.arcsin, biouml.plugins.sbml._test.semantic-test-suite.mathml.arcsinh, biouml.plugins.sbml._test.semantic-test-suite.mathml.arctan, biouml.plugins.sbml._test.semantic-test-suite.mathml.arctanh, biouml.plugins.sbml._test.semantic-test-suite.mathml.cn-e-notation, biouml.plugins.sbml._test.semantic-test-suite.mathml.cn-integer, biouml.plugins.sbml._test.semantic-test-suite.mathml.cn-rational, biouml.plugins.sbml._test.semantic-test-suite.mathml.cn-real, biouml.plugins.sbml._test.semantic-test-suite.mathml.cos, biouml.plugins.sbml._test.semantic-test-suite.mathml.cosh, biouml.plugins.sbml._test.semantic-test-suite.mathml.cot, biouml.plugins.sbml._test.semantic-test-suite.mathml.coth, biouml.plugins.sbml._test.semantic-test-suite.mathml.csc, biouml.plugins.sbml._test.semantic-test-suite.mathml.csch, biouml.plugins.sbml._test.semantic-test-suite.mathml.divide, biouml.plugins.sbml._test.semantic-test-suite.mathml.exp, biouml.plugins.sbml._test.semantic-test-suite.mathml.exponentiale, biouml.plugins.sbml._test.semantic-test-suite.mathml.ln, biouml.plugins.sbml._test.semantic-test-suite.mathml.log, biouml.plugins.sbml._test.semantic-test-suite.mathml.logbase, biouml.plugins.sbml._test.semantic-test-suite.mathml.minus, biouml.plugins.sbml._test.semantic-test-suite.mathml.minus-unary, biouml.plugins.sbml._test.semantic-test-suite.mathml.pi, biouml.plugins.sbml._test.semantic-test-suite.mathml.plus, biouml.plugins.sbml._test.semantic-test-suite.mathml.power, biouml.plugins.sbml._test.semantic-test-suite.mathml.root, biouml.plugins.sbml._test.semantic-test-suite.mathml.root-degree, biouml.plugins.sbml._test.semantic-test-suite.mathml.sec, biouml.plugins.sbml._test.semantic-test-suite.mathml.sech, biouml.plugins.sbml._test.semantic-test-suite.mathml.sin, biouml.plugins.sbml._test.semantic-test-suite.mathml.sinh, biouml.plugins.sbml._test.semantic-test-suite.mathml.tan, biouml.plugins.sbml._test.semantic-test-suite.mathml.tanh, biouml.plugins.sbml._test.semantic-test-suite.mathml.times, biouml.plugins.sbml._test.semantic-test-suite.parameterNamespace, biouml.plugins.sbml._test.semantic-test-suite.parameterNamespace.global, biouml.plugins.sbml._test.semantic-test-suite.parameterNamespace.globalAndLocal, biouml.plugins.sbml._test.semantic-test-suite.parameterNamespace.local, biouml.plugins.sbml._test.semantic-test-suite.parameterNamespace.speciesAndLocal, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignment-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentInconsistent-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentInconsistent-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentInitialize-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentInitialize-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignment-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentUsedInDifferential-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentUsedInDifferential-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentUsedInReaction-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.assignmentUsedInReaction-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.differential-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.differential-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.differentialUsedInDifferential-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.differentialUsedInDifferential-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.differentialUsedInReaction-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.differentialUsedInReaction-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.reactionUsedInAssignment-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.reactionUsedInAssignment-Parameter, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.reactionUsedInDifferential-Compartment, biouml.plugins.sbml._test.semantic-test-suite.rulesForParametersAndCompartments.reactionUsedInDifferential-Parameter, biouml.plugins.sbml._test.semantic-test-suite.stoichiometry, biouml.plugins.sbml._test.semantic-test-suite.stoichiometry.floatingPoint, biouml.plugins.sbml._test.semantic-test-suite.stoichiometry.mathML, biouml.plugins.sbml.resources, biouml.plugins.sbw, biouml.plugins.simulation, biouml.plugins.simulation.access, biouml.plugins.simulation.ae, biouml.plugins.simulation.hybrid, biouml.plugins.simulation.java, biouml.plugins.simulation.ode, biouml.plugins.simulation.plot, biouml.plugins.simulation.plot.access, biouml.plugins.simulation.resources, biouml.plugins.svg, biouml.standard, biouml.standard.diagram, biouml.standard.diagram.legend, biouml.standard.diagram.resources, biouml.standard.filter, biouml.standard.type, biouml.standard.type.access, biouml.workbench, biouml.workbench.diagram, biouml.workbench.module, biouml.workbench.resources, com, com.developmentontheedge, com.developmentontheedge.application, com.developmentontheedge.application.action, com.developmentontheedge.application.action.resources, com.developmentontheedge.application.dialog, com.developmentontheedge.application.dialog.resources, com.developmentontheedge.jobcontrol, com.developmentontheedge.jobcontrol.action, com.developmentontheedge.jobcontrol.action.resources, com.developmentontheedge.log, com.developmentontheedge.print, ru, ru.biosoft, ru.biosoft.access, ru.biosoft.access.repository, ru.biosoft.access.repository.res, ru.biosoft.access.search, ru.biosoft.access.search.resources, ru.biosoft.access.support, ru.biosoft.graphics, ru.biosoft.graphics.editor, ru.biosoft.graphics.font, ru.biosoft.gui, ru.biosoft.gui.resources, ru.biosoft.gui.wizard, ru.biosoft.math, ru.biosoft.math.model, ru.biosoft.math.parser, ru.biosoft.math.view, ru.biosoft.math.xml, ru.biosoft.plugins, ru.biosoft.plugins.javascript, ru.biosoft.util, ru.biosoft.workbench

## Class Hierarchy

- class com.developmentontheedge.jobcontrol.AbstractJobControl (implements com.developmentontheedge.jobcontrol.JobControl)
  - class com.developmentontheedge.jobcontrol.ClassJobControl
  - class com.developmentontheedge.jobcontrol.FunctionJobControl
    - class biouml.plugins.simulation.SimulatorJobControl
- class ru.biosoft.math.model.AbstractParser (implements ru.biosoft.math.model.Parser)
  - class ru.biosoft.math.xml.MathMLParser (implements ru.biosoft.math.parser.ParserTreeConstants)
  - class ru.biosoft.math.parser.Parser (implements ru.biosoft.math.parser.ParserConstants, ru.biosoft.math.parser.ParserTreeConstants)
- class ru.biosoft.access.AbstractTransformer (implements ru.biosoft.access.Transformer)
  - class biouml.plugins.cellml.CellMLDiagramTransformer
  - class ru.biosoft.access.support.DatabaseEntryTransformer
  - class biouml.model.util.DiagramXmlTransformer
  - class biouml.plugins.ginsim.GinSimTransformer
  - class biouml.plugins.gxl.GxlTransformer
  - class biouml.plugins.sbml.SbmlDiagramTransformer
  - class ru.biosoft.access.support.TagEntryTransformer
    - class ru.biosoft.access.support.BeanInfoEntryTransformer
      - class biouml.plugins.simulation.plot.access.PlotTransformer
      - class biouml.standard.type.access.ReactionTransformer
      - class biouml.plugins.simulation.access.SimulationResultTransformer
  - class ru.biosoft.access.XMLTransformer
- class com.developmentontheedge.application.action.ActionInitializer
- class com.developmentontheedge.application.action.ActionManager
- class com.developmentontheedge.application.Application
- class ru.biosoft.util.ApplicationUtils
- class com.developmentontheedge.application.ApplicationUtils
- class ru.biosoft.access.search.ArrayPropertyValueFilterBeanInfo.FilterPropertyEditor (implements PropertyEditorEx)
- class ru.biosoft.graphics.ArrowView.Tip
- class biouml.workbench.BioUMLLauncher (implements IPlatformRunnable)
- class ru.biosoft.graphics.editor.BoxSelector (implements ru.biosoft.graphics.editor.ViewSelector)
  - class ru.biosoft.graphics.editor.ResizingBoxSelector
- class biouml.plugins.simulation.ode.Btableau
- class biouml.plugins.simulation.ode.BthDopr (implements biouml.plugins.simulation.ode.Btheta)
- class ru.biosoft.access.BTreeIndex.IntKey (implements ru.biosoft.access.Key)
- class ru.biosoft.access.BTreeIndex.NodeKey (implements Map.Entry)
- class biouml.plugins.cellml.CellMLImporter (implements biouml.model.DiagramImporter)
- class biouml.plugins.cellml.CellMLSupport (implements biouml.plugins.cellml.CellMLConstants)
  - class biouml.plugins.cellml.CellMLModelReader
  - class biouml.plugins.cellml.CellMLModelWriter
- class ru.biosoft.access.CollectionFactory
- class biouml.standard.filter.CompositeHighlightAction (implements biouml.standard.filter.Action)
- class com.developmentontheedge.jobcontrol.CurrentJobControl
- class biouml.model.dynamics.DAEModelUtilities
- class ru.biosoft.access.DataCollectionInfo
- class ru.biosoft.access.DataCollectionListenerSupport (implements ru.biosoft.access.DataCollectionListener)
- class ru.biosoft.access.repository.DataCollectionTreeModelAdapter (implements ru.biosoft.access.DataCollectionListener, TreeModel)
- class ru.biosoft.access.DataCollectionUndoListener (implements ru.biosoft.access.DataCollectionListener, PropertyChangeListener)
  - class biouml.workbench.RepositoryDocument.RepositoryUndoListener
- class ru.biosoft.access.DataElementSupport (implements ru.biosoft.access.DataElement)
  - class ru.biosoft.access.AbstractDataCollection (implements ru.biosoft.access.DataCollection)
    - class ru.biosoft.access.DataCollectionUnion (implements ru.biosoft.access.CollectionUnion)
    - class ru.biosoft.access.DerivedDataCollection
      - class ru.biosoft.access.FilteredDataCollection (implements ru.biosoft.access.DataCollectionListener)
      - class biouml.model.Module
      - class ru.biosoft.access.TransformedDataCollection (implements ru.biosoft.access.DataCollectionListener)
      - class biouml.model.dynamics.VariablesDataCollection
    - class ru.biosoft.access.EntryCollection
      - class ru.biosoft.access.FileEntryCollection
      - class ru.biosoft.access.FileEntryCollection2
    - class ru.biosoft.access.SqlDataCollection
    - class ru.biosoft.access.VectorDataCollection
      - class ru.biosoft.access.DataCollectionUnion2 (implements ru.biosoft.access.CollectionUnion, ru.biosoft.access.DataCollectionListener)
      - class ru.biosoft.access.FileCollection
      - class ru.biosoft.plugins.javascript.HostObjectInfo
        - class ru.biosoft.plugins.javascript.ClassInfo
      - class ru.biosoft.access.LocalRepository (implements ru.biosoft.access.Repository)
      - class ru.biosoft.plugins.Plugins
      - class biouml.plugins.sbw.SbwModule
      - class biouml.plugins.sbw.SbwService
      - class biouml.plugins.sbw.SbwServiceCategory
    - class ru.biosoft.plugins.VisiblePlugin
      - class ru.biosoft.plugins.javascript.JScriptVisiblePlugin
      - class biouml.plugins.sbw.SbwVisiblePlugin
  - class biouml.plugins.cellml.CellMLModuleType (implements biouml.model.ModuleType)
  - class ru.biosoft.access.DataElementRef
  - class ru.biosoft.access.Entry
  - class ru.biosoft.access.FileDataElement
  - class ru.biosoft.plugins.javascript.FunctionInfo
  - class ru.biosoft.plugins.javascript.PropertyInfo
  - class biouml.plugins.sbml.SbmlModuleType (implements biouml.model.ModuleType)
  - class biouml.plugins.simulation.SimulationResult
  - class biouml.standard.StandardModuleType (implements biouml.model.ModuleType)
    - class biouml.standard.SqlModuleType
- class biouml.model.DefaultDiagramViewBuilder (implements biouml.model.DiagramViewBuilder)
  - class biouml.model.dynamics.EModelDiagramViewBuilder
  - class biouml.plugins.ginsim.GinSimDiagramViewBuilder
  - class biouml.standard.diagram.PathwayDiagramViewBuilder
    - class biouml.standard.diagram.GeneNetworkDiagramType.GeneNetworkDiagramViewBuilder
    - class biouml.standard.diagram.MetabolicPathwayDiagramType.MetabolicPathwayDiagramViewBuilder
    - class biouml.standard.diagram.PathwaySimulationDiagramViewBuilder
      - class biouml.plugins.cellml.CellMLDiagramViewBuilder
      - class biouml.plugins.sbml.SbmlDiagramViewBuilder
    - class biouml.standard.diagram.SemanticNetworkDiagramType.SemanticNetworkDiagramViewBuilder
- class ru.biosoft.math.model.DefaultParserContext (implements ru.biosoft.math.model.ParserContext)
- class ru.biosoft.access.DefaultQuerySystem (implements ru.biosoft.access.QuerySystem)
- class biouml.model.DefaultSemanticController (implements biouml.model.SemanticController)
  - class biouml.standard.diagram.PathwaySemanticController
    - class biouml.standard.diagram.PathwaySimulationSemanticController
      - class biouml.plugins.cellml.CellMLSemanticController
      - class biouml.plugins.sbml.SbmlSemanticController
- class biouml.plugins.sbml._test.DefaultTestLogger (implements biouml.plugins.sbml._test.TestLogger)
  - class biouml.plugins.sbml._test.HtmlStatisticsLogger
- class ru.biosoft.graphics.editor.DefaultViewEditorHelper (implements ru.biosoft.graphics.editor.ViewEditorHelper)
- class biouml.workbench.diagram.DiagramEditorHelper (implements TransactionListener, ru.biosoft.graphics.editor.ViewEditorHelper)
- class biouml.workbench.diagram.DiagramElementInfo
- class biouml.workbench.diagram.DiagramExporterRegistry
- class biouml.workbench.diagram.DiagramExporterRegistry.ExporterInfo
- class biouml.workbench.diagram.DiagramFactory (implements com.developmentontheedge.application.DocumentFactory)
- class biouml.workbench.diagram.DiagramImageWriter (implements biouml.model.DiagramExporter)
- class biouml.workbench.diagram.DiagramImporterRegistry
- class biouml.workbench.diagram.DiagramImporterRegistry.ImporterInfo
- class biouml.standard.type.access.DiagramSqlTransformer.SqlReferenceGenerator (implements biouml.model.util.ReferenceGenerator)
- class biouml.plugins.jgraph.DiagramToJGraphTransformer
- class biouml.model.DiagramTypeConverter.NoConverter (implements biouml.model.DiagramTypeConverter)
- class biouml.model.DiagramTypeConverter.YesConverter (implements biouml.model.DiagramTypeConverter)
  - class biouml.model.DiagramTypeConverter.ConditionalConverter
- class biouml.workbench.diagram.DiagramTypeConverterRegistry
- class biouml.workbench.diagram.DiagramTypeConverterRegistry.Conversion
- class biouml.model.DiagramTypeSupport (implements biouml.model.DiagramType)
  - class biouml.plugins.cellml.CellMLDiagramType
  - class biouml.model.dynamics.EModelDiagramType
  - class biouml.plugins.ginsim.GinSimDiagramType
  - class biouml.standard.diagram.PathwayDiagramType
    - class biouml.standard.diagram.GeneNetworkDiagramType
    - class biouml.standard.diagram.MetabolicPathwayDiagramType
    - class biouml.standard.diagram.PathwaySimulationDiagramType
    - class biouml.standard.diagram.SemanticNetworkDiagramType
  - class biouml.plugins.sbml.SbmlDiagramType
    - class biouml.plugins.sbml.SbmlDiagramType_L1
    - class biouml.plugins.sbml.SbmlDiagramType_L2
- class biouml.model.util.DiagramXmlConstants
  - class biouml.model.util.DiagramXmlSupport
    - class biouml.model.util.DiagramXmlReader
    - class biouml.model.util.DiagramXmlWriter
- class ru.biosoft.gui.Document (implements com.developmentontheedge.application.ApplicationDocument)
  - class biouml.workbench.diagram.DiagramDocument (implements PropertyChangeListener)
  - class ru.biosoft.gui.RepositoryDocument (implements PropertyChangeListener, ru.biosoft.access.repository.RepositoryListener)
- class com.developmentontheedge.application.DocumentManager
  - class ru.biosoft.gui.DocumentManager
- class biouml.plugins.cellml.DomElementTransformer
- class biouml.plugins.cellml.DomHelperSupport (implements biouml.plugins.cellml.DomHelper)
  - class biouml.plugins.cellml.RdfHelper
- class biouml.plugins.simulation.ode.DormandPrince (implements biouml.plugins.simulation.Simulator)
- class biouml.plugins.simulation.ode.DormandPrince.Options
- class biouml.standard.type.EditionHistory (implements PropertyChangeListener)
- class biouml.standard.type.EditionHistory.Edition
- class ru.biosoft.gui.EditorsManager (implements ru.biosoft.gui.ViewPart)
- class biouml.model.dynamics.EModel.VariableFilter (implements ru.biosoft.access.Filter)
- class biouml.model.dynamics.EModelDiagramViewOptions
- class ru.biosoft.access.support.EntryParser
- class biouml.plugins.simulation.ode.ErrorEstimator
- class biouml.plugins.simulation.hybrid.Event
  - class biouml.plugins.simulation.hybrid.Transition
- class biouml.plugins.simulation.java.EventLoopSimulator (implements biouml.plugins.simulation.Simulator)
- class ru.biosoft.util.FileBuffer
  - class ru.biosoft.util.ConservativeFastFileBuffer
  - class ru.biosoft.util.FastFileBuffer
  - class ru.biosoft.util.SoftFileBuffer
- class ru.biosoft.util.FileChooserRegistry
- class ru.biosoft.access.Filter.IncludeAllFilter (implements ru.biosoft.access.Filter)
- class ru.biosoft.access.Filter.IncludeNoneFilter (implements ru.biosoft.access.Filter)
- class ru.biosoft.access.search.FilteringSettings
- class ru.biosoft.math.view.FormulaViewBuilder
- class biouml.model.util.Framework
- class ru.biosoft.plugins.javascript.FunctionInfo.Argument
- class ru.biosoft.plugins.javascript.FunctionInfo.Example
- class ru.biosoft.plugins.javascript.FunctionInfo.Exception
- class ru.biosoft.plugins.javascript.FunctionInfo.ReturnedValue
- class biouml.plugins.ginsim.GinMLExporter (implements biouml.model.DiagramExporter)
- class biouml.plugins.ginsim.GinMLImporter (implements biouml.model.DiagramImporter)
- class ru.biosoft.graphics.GraphicProperties
- class biouml.plugins.gxl.GxlExporter (implements biouml.model.DiagramExporter)
- class biouml.plugins.gxl.GxlParserContext
  - class biouml.plugins.ginsim.GinSimParserContext
- class biouml.plugins.gxl.GxlSupport (implements biouml.plugins.gxl.GxlConstants)
  - class biouml.plugins.gxl.GxlReader
    - class biouml.plugins.ginsim.GinSimReader
  - class biouml.plugins.gxl.GxlWriter
    - class biouml.plugins.ginsim.GinSimWriter
- class ru.biosoft.workbench.HelpRegistry
- class biouml.standard.filter.HideAction (implements biouml.standard.filter.Action)
- class biouml.standard.filter.HighlightAction (implements biouml.standard.filter.Action)
- class ru.biosoft.access.support.IdGenerator
- class biouml.model.util.ImageGenerator
- class ru.biosoft.access.Index.IndexEntry
  - class ru.biosoft.access.Index.StringIndexEntry
- class biouml.plugins.simulation.ode.Initsss
- class ru.biosoft.graphics.editor.InverseSelector (implements ru.biosoft.graphics.editor.ViewSelector)
- class biouml.plugins.simulation.java.JavaBaseModel (implements biouml.plugins.simulation.ae.AeModel, biouml.plugins.simulation.ode.OdeModel)
- class biouml.plugins.simulation.java.JavaError
- class biouml.plugins.matlab.JMatLinkFactory
- class biouml.plugins.matlab.JMatLinkJDK13 (implements biouml.plugins.matlab.JMatLinkInterface)
- class biouml.plugins.matlab.JMatLinkJDK14 (implements biouml.plugins.matlab.JMatLinkInterface)
- class com.developmentontheedge.jobcontrol.JobControlEvent
- class com.developmentontheedge.jobcontrol.JobControlListenerAdapter (implements com.developmentontheedge.jobcontrol.JobControlListener)
- class ru.biosoft.plugins.javascript.JScriptContext
- class ru.biosoft.plugins.javascript.JScriptHelp
- class ru.biosoft.plugins.javascript.JScriptRunner (implements IPlatformRunnable)
- class ru.biosoft.plugins.javascript.JScriptShell (implements IPlatformRunnable)
- class ru.biosoft.util.KeyValuePair
- class biouml.standard.type.KineticType.Element (implements ru.biosoft.access.support.SerializableAsText)
- class com.developmentontheedge.print.LargePageable (implements Pageable)
  - class com.developmentontheedge.print.JPrintableComponent (implements Printable)
- class com.developmentontheedge.print.LargePageable.TranslatedPrintable (implements Printable)
- class ru.biosoft.math.model.LinearFormatter (implements ru.biosoft.math.model.Formatter)
  - class ru.biosoft.math.model.PiecewiseExtFormatter
    - class ru.biosoft.math.model.JavaFormatter
    - class ru.biosoft.math.model.MatlabFormatter
- class ru.biosoft.math.xml.MathMLFormatter (implements ru.biosoft.math.model.Formatter)
- class ru.biosoft.math.MathRoutines
- class biouml.plugins.matlab.MatlabError
- class biouml.model.util.ModulePackager
- class biouml.plugins.simulation.ae.NewtonSolver
- class biouml.model.NodeInfo
- class java.lang.Object
  - class javax.swing.AbstractAction
    - class ru.biosoft.workbench.AboutAction
    - class com.developmentontheedge.application.action.ApplicationAction
      - class com.developmentontheedge.application.action.ApplicationAction.ActionAboutDialog
      - class com.developmentontheedge.application.action.ApplicationAction.ActionExit
      - class com.developmentontheedge.application.action.ApplicationAction.ActionHelp
      - class com.developmentontheedge.application.action.ApplicationAction.ActionPrint
      - class com.developmentontheedge.application.action.ApplicationAction.ActionPrintPreview
      - class com.developmentontheedge.application.action.ApplicationAction.ActionPrintSetup
    - class biouml.workbench.diagram.CloseDiagramAction
    - class biouml.workbench.diagram.ConvertDiagramAction
    - class ru.biosoft.access.search.DataSearchAction
    - class biouml.workbench.diagram.ExportDiagramAction
    - class biouml.workbench.module.ExportModuleAction
    - class biouml.model.htmlgen.GenerateHTMLAction
    - class ru.biosoft.workbench.HelpAction
    - class biouml.workbench.diagram.ImportDiagramAction
    - class ru.biosoft.graphics.editor.InsertAction
    - class com.developmentontheedge.jobcontrol.action.JobAction
    - class biouml.workbench.module.ModuleSetupAction
    - class biouml.workbench.NewDataElementAction
    - class biouml.workbench.diagram.NewDiagramAction
    - class biouml.workbench.module.NewModuleAction
    - class biouml.workbench.diagram.OpenDiagramAction
    - class biouml.workbench.PreferencesAction
    - class com.developmentontheedge.print.PrintAction
    - class com.developmentontheedge.print.PrintPreviewAction
    - class com.developmentontheedge.print.PrintSetupAction
    - class ru.biosoft.gui.RedoAction
    - class biouml.workbench.RemoveDataElementAction
    - class biouml.workbench.module.RemoveModuleAction
    - class biouml.plugins.simulation.RepositoryActionsProvider.ShowPlotAction
    - class biouml.workbench.diagram.SaveAsDiagramAction
    - class biouml.workbench.diagram.SaveDiagramAction
    - class com.developmentontheedge.application.action.SeparatorAction
    - class com.developmentontheedge.application.action.TogglePanelAction
    - class ru.biosoft.gui.UndoAction
    - class biouml.workbench.diagram.ZoomInAction
    - class biouml.workbench.diagram.ZoomOutAction
  - class javax.swing.AbstractListModel
    - class ru.biosoft.access.support.NameListToListModelAdapter (implements ru.biosoft.access.DataCollectionListener)
      - class ru.biosoft.access.support.NameListToComboBoxModelAdapter (implements ComboBoxModel, MutableComboBoxModel)
  - class java.util.AbstractMap
    - class ru.biosoft.access.BTreeIndex (implements ru.biosoft.access.Index)
      - class ru.biosoft.access.BTreeRangeIndex
    - class java.util.HashMap
      - class ru.biosoft.util.HashMapSoftValues
      - class ru.biosoft.util.HashMapWeakValues
      - class ru.biosoft.access.MemIndex (implements ru.biosoft.access.Index)
      - class biouml.standard.type.access.TitleSqlIndex (implements ComboBoxModel, ru.biosoft.access.DataCollectionListener, ru.biosoft.access.Index, ListModel)
  - class javax.swing.undo.AbstractUndoableEdit
    - class ru.biosoft.access.DataCollectionRemoveUndo
      - class ru.biosoft.access.DataCollectionAddUndo
  - class org.apache.log4j.AppenderSkeleton
    - class com.developmentontheedge.log.TextPaneAppender
  - class java.lang.ClassLoader
    - class java.security.SecureClassLoader
      - class java.net.URLClassLoader
        - class ru.biosoft.access.CollectionFactory.CollectionClassLoader
  - class java.awt.Component
    - class java.awt.Container
      - class javax.swing.JComponent
        - class javax.swing.AbstractButton
          - class javax.swing.JMenuItem
            - class javax.swing.JMenu
              - class com.developmentontheedge.application.ApplicationMenu
        - class ru.biosoft.graphics.font.FontChooser
        - class javax.swing.JLabel
          - class biouml.standard.filter.ActionEditor.ActionRenderer
        - class javax.swing.JMenuBar
          - class com.developmentontheedge.application.ApplicationMenuBar
        - class javax.swing.JPanel
          - class com.developmentontheedge.application.ApplicationStatusBar (implements ActionListener, com.developmentontheedge.jobcontrol.JobControlListener)
          - class ru.biosoft.access.support.DataCollectionMultyChoicePane
          - class biouml.standard.diagram.DiagramElementSelector
          - class biouml.workbench.diagram.DiagramsPane (implements ChangeListener)
          - class ru.biosoft.gui.DocumentPane (implements ChangeListener)
          - class com.developmentontheedge.jobcontrol.JobControlPane
          - class com.developmentontheedge.log.LogTextPanel
          - class biouml.plugins.matlab.MatlabErrorPane
          - class com.developmentontheedge.application.NamedPanel
          - class com.developmentontheedge.print.PagePreview
          - class com.developmentontheedge.application.PanelManager (implements PropertyChangeListener)
            - class ru.biosoft.math.ExpressionEditorPane
            - class ru.biosoft.workbench.WorkbenchPage
          - class biouml.plugins.simulation.plot.PlotEditorPane
          - class biouml.plugins.simulation.plot.PlotPane (implements PlotChangeListener, PropertyChangeListener, RowModelListener)
          - class biouml.standard.diagram.ReactionPane
          - class ru.biosoft.access.repository.RepositoryPane
          - class biouml.standard.diagram.SemanticRelationPane
            - class biouml.standard.diagram.NoteLinkPane
          - class biouml.plugins.simulation.SimulationPane
          - class com.developmentontheedge.application.dialog.TextButtonField
            - class com.developmentontheedge.application.dialog.BrowseTextField
          - class ru.biosoft.graphics.editor.ViewPane (implements MouseListener, MouseMotionListener)
            - class ru.biosoft.graphics.editor.ViewEditorPane (implements KeyListener, Transactable, TransactionListener)
          - class ru.biosoft.gui.ViewPartSupport (implements ru.biosoft.gui.ViewPart)
            - class biouml.workbench.diagram.ClipboardView (implements ListSelectionListener, ru.biosoft.graphics.editor.ViewPaneListener)
            - class ru.biosoft.gui.EditorPartSupport (implements ru.biosoft.gui.EditorPart)
              - class ru.biosoft.gui.EditorsTabbedPane
                - class ru.biosoft.gui.ExplorerPane
                - class ru.biosoft.gui.PluggedEditorsTabbedPane
              - class ru.biosoft.gui.HtmlEditor
                - class biouml.workbench.diagram.DiagramDescriptionEditor
              - class ru.biosoft.plugins.javascript.JScriptConsole
              - class biouml.plugins.simulation.SimulationEnginePane
                - class biouml.plugins.simulation.java.JavaEngineControl
                - class biouml.plugins.matlab.MatlabEngineControl
            - class biouml.workbench.diagram.FilterView
            - class ru.biosoft.gui.LogPane
          - class ru.biosoft.gui.wizard.WizardPanel (implements ru.biosoft.gui.wizard.Wizard)
        - class javax.swing.JPopupMenu
          - class com.developmentontheedge.application.ApplicationPopupMenu
        - class javax.swing.JProgressBar
          - class com.developmentontheedge.jobcontrol.JobProgressBar (implements com.developmentontheedge.jobcontrol.JobControlListener)
        - class javax.swing.JTabbedPane
          - class ru.biosoft.workbench.PageManager
        - class javax.swing.text.JTextComponent
          - class javax.swing.JTextArea
            - class ru.biosoft.plugins.javascript.EvalTextArea (implements DocumentListener, KeyListener)
        - class javax.swing.JToolBar
          - class com.developmentontheedge.application.ApplicationToolBar
      - class java.awt.Window
        - class java.awt.Dialog
          - class javax.swing.JDialog
            - class ru.biosoft.workbench.AboutDialog
            - class ru.biosoft.access.CreateDataCollectionDefaultController (implements ru.biosoft.access.CreateDataCollectionController)
            - class ru.biosoft.util.OkCancelDialog
              - class ru.biosoft.access.support.DataCollectionMultyChoiceDialog
              - class ru.biosoft.access.support.NewDataElementDialog
            - class com.developmentontheedge.application.dialog.OkCancelDialog
              - class ru.biosoft.access.support.AbstractExportDialog
              - class ru.biosoft.access.support.AbstractImportDialog
              - class biouml.workbench.AskIDDialog
              - class biouml.plugins.sbml.CreateDiagramElementDialog
              - class biouml.standard.diagram.CreateDiagramElementDialog
              - class biouml.standard.diagram.CreateEdgeDialog
              - class biouml.standard.diagram.CreateReactionDialog
              - class ru.biosoft.math.ExpressionEditorDialog
              - class biouml.model.htmlgen.GenerateHTMLDialog
              - class biouml.plugins.matlab.MatlabErrorDialog
              - class biouml.workbench.module.ModuleExportDialog
              - class biouml.workbench.module.ModuleInfoDialog
              - class biouml.workbench.module.ModuleReplaceDialog
              - class biouml.workbench.module.ModulesActivatingDialog
              - class biouml.workbench.diagram.NewDiagramDialog
              - class biouml.workbench.module.NewModuleDialog
              - class biouml.plugins.simulation.plot.PlotDialog
              - class biouml.workbench.diagram.ProcessDiagramDialog
                - class biouml.workbench.diagram.ConvertDiagramDialog
                - class biouml.workbench.diagram.ExportDiagramDialog
                - class biouml.workbench.diagram.ImportDiagramDialog
              - class biouml.workbench.module.StatusInfoDialog (implements com.developmentontheedge.jobcontrol.JobControlListener)
            - class biouml.workbench.PreferencesDialog
            - class com.developmentontheedge.print.PreviewDialog
            - class ru.biosoft.gui.wizard.WizardDialog (implements ru.biosoft.gui.wizard.Wizard)
        - class java.awt.Frame
          - class javax.swing.JFrame
            - class com.developmentontheedge.application.ApplicationFrame
              - class biouml.workbench.BioUMLApplication (implements ChangeListener)
              - class ru.biosoft.workbench.WorkbenchWindow
            - class ru.biosoft.access.search.DataSearch (implements PropertyChangeListener)
            - class ru.biosoft.gui.wizard.WizardFrame (implements ru.biosoft.gui.wizard.Wizard)
  - class java.util.Dictionary
    - class java.util.Hashtable
      - class ru.biosoft.access.IndexTable
      - class java.util.Properties
        - class ru.biosoft.util.ExProperties
        - class com.developmentontheedge.application.MapRegistry (implements com.developmentontheedge.application.ApplicationRegistry)
  - class java.util.EventObject
    - class java.awt.AWTEvent
      - class java.awt.event.ComponentEvent
        - class java.awt.event.InputEvent
          - class java.awt.event.MouseEvent
            - class ru.biosoft.graphics.editor.ViewPaneEvent
    - class ru.biosoft.access.DataCollectionEvent
  - class javax.swing.filechooser.FileFilter
    - class biouml.workbench.module.BMDFileFilter
    - class biouml.model.htmlgen.XSLFileFilter
  - class java.awt.event.FocusAdapter
    - class ru.biosoft.gui.HtmlEditor.DocumentFocusListener
  - class java.io.OutputStream
    - class java.io.ByteArrayOutputStream
      - class biouml.plugins.simulation.java.RunTimeCompiler.ErrorOutputStream
  - class java.awt.print.PageFormat
    - class com.developmentontheedge.print.FooterFormat
  - class java.beans.PropertyEditorSupport
    - class biouml.standard.type.MultiLineHtmlFieldEditor
  - class javax.swing.RepaintManager
    - class ru.biosoft.gui.RepaintManager
  - class java.util.ResourceBundle
    - class java.util.ListResourceBundle
      - class ru.biosoft.graphics.BrushMessageBundle
      - class ru.biosoft.graphics.font.ColorFontMessageBundle
      - class ru.biosoft.util.KeyValuePairMessageBundle
      - class biouml.plugins.cellml.MessageBundle
      - class ru.biosoft.workbench.MessageBundle
      - class biouml.plugins.simulation.java.MessageBundle
      - class biouml.plugins.sbw.MessageBundle
      - class ru.biosoft.access.support.MessageBundle
      - class biouml.plugins.simulation.resources.MessageBundle
      - class biouml.standard.MessageBundle
      - class ru.biosoft.access.MessageBundle
      - class biouml.standard.type.MessageBundle
      - class biouml.model.MessageBundle
      - class biouml.plugins.gxl.MessageBundle
      - class biouml.plugins.ginsim.MessageBundle
      - class biouml.workbench.resources.MessageBundle
      - class ru.biosoft.plugins.javascript.MessageBundle
      - class biouml.plugins.sbml.MessageBundle
      - class ru.biosoft.access.search.MessageBundle
      - class biouml.model.dynamics.resources.MessageBundle
      - class biouml.model.util.MessageBundle
      - class biouml.standard.filter.MessageBundle
      - class biouml.plugins.matlab.resources.MessageBundle
      - class biouml.standard.diagram.MessageBundle
      - class ru.biosoft.gui.resources.MessageBundle
      - class ru.biosoft.graphics.PenMessageBundle
      - class ru.biosoft.graphics.RulerOptionsMessageBundle
  - class java.lang.Throwable
    - class java.lang.Error
      - class ru.biosoft.math.parser.TokenMgrError
    - class java.lang.Exception
      - class ru.biosoft.access.DataCollectionVetoException
      - class com.developmentontheedge.jobcontrol.JobControlException
      - class ru.biosoft.math.parser.ParseException
      - class java.lang.RuntimeException
        - class ru.biosoft.util.ChainRuntimeException
  - class java.io.Writer
    - class biouml.plugins.simulation.MathWriter
    - class java.io.PrintWriter
      - class com.developmentontheedge.log.TextPaneAppender.TracerPrintWriter
- class biouml.plugins.simulation.ode.ODEFileWriter
- class biouml.plugins.simulation.ode.OdeSimulator (implements biouml.plugins.simulation.Simulator)
- class com.developmentontheedge.application.PanelInfo
- class ru.biosoft.math.parser.ParserTokenManager (implements ru.biosoft.math.parser.ParserConstants)
- class biouml.standard.diagram.PathwayDiagramViewOptions.RelationTypeColor
- class biouml.standard.diagram.PathwayDiagramViewOptions.RelationTypeStroke
- class ru.biosoft.workbench.PerspectiveDescriptor
- class ru.biosoft.workbench.PerspectiveDescriptor.View
- class ru.biosoft.workbench.PerspectiveRegistry
- class ru.biosoft.access.repository.PluginActions (implements ru.biosoft.access.repository.ActionsProvider)
- class ru.biosoft.math.model.PredefinedFunction (implements ru.biosoft.math.model.Function)
- class com.developmentontheedge.application.Preferences (implements DynamicPropertySet)
- class biouml.workbench.Preferences (implements com.developmentontheedge.application.ApplicationRegistry, Cloneable)
- class com.developmentontheedge.application.Preferences.PropertyComparator (implements Comparator)
- class com.developmentontheedge.print.PrintManager
- class ru.biosoft.access.search.PropertyValueFilterBeanInfo.FilterPropertyEditor (implements PropertyEditorEx)
- class biouml.model.QueryEngineSupport (implements biouml.model.QueryEngine)
  - class biouml.standard.PathwayQueryEngine
  - class biouml.standard.StandardQueryEngine
- class biouml.model.QueryOptions
  - class biouml.standard.PathwayQueryOptions
- class ru.biosoft.workbench.RegistryReader
- class ru.biosoft.access.search.RepositoryActionsProvider (implements ru.biosoft.access.repository.ActionsProvider)
- class biouml.workbench.RepositoryActionsProvider (implements ru.biosoft.access.repository.ActionsProvider)
- class biouml.plugins.simulation.RepositoryActionsProvider (implements ru.biosoft.access.repository.ActionsProvider)
- class biouml.plugins.simulation.ResultWriter (implements biouml.plugins.simulation.ResultListener)
- class biouml.plugins.simulation.ode.RootFinder
- class biouml.plugins.simulation.java.RunTimeCompiler
- class biouml.plugins.sbml.SbmlConstants
  - class biouml.plugins.sbml.SbmlSupport
    - class biouml.plugins.sbml.SbmlModelReader
      - class biouml.plugins.sbml.SbmlModelReader_11
        - class biouml.plugins.sbml.SbmlModelReader_12
      - class biouml.plugins.sbml.SbmlModelReader_21
    - class biouml.plugins.sbml.SbmlModelWriter
      - class biouml.plugins.sbml.SbmlModelWriter_21
      - class biouml.plugins.sbml.SbmlModelWriter_L1
        - class biouml.plugins.sbml.SbmlModelWriter_11
        - class biouml.plugins.sbml.SbmlModelWriter_12
- class biouml.plugins.sbml.SbmlExporter (implements biouml.model.DiagramExporter)
- class biouml.plugins.sbml.SbmlImporter (implements biouml.model.DiagramImporter)
- class biouml.plugins.sbml._test.SbmlJavaConsoleTest
- class biouml.plugins.sbml._test.SbmlJavaMain
- class biouml.plugins.sbml._test.SbmlJavaTestConsol
- class biouml.plugins.sbml._test.SbmlMatlabConsoleTest
- class biouml.plugins.sbml.SbmlModelFactory
- class biouml.plugins.sbml._test.SbmlSemanticCSVHander
- class biouml.plugins.sbml._test.SbmlTestSimulationEngineAdapter
- class biouml.plugins.sbw.SbwHost
- class biouml.plugins.sbw.SbwHost.SbmlModel
- class biouml.plugins.sbw.SbwServiceMethod (implements ru.biosoft.access.DataElement)
- class ru.biosoft.access.support.SetPropertyCommand (implements ru.biosoft.access.support.TagCommand)
  - class ru.biosoft.access.support.SetArrayPropertyCommand
- class ru.biosoft.math.parser.SimpleCharStream
- class ru.biosoft.math.model.SimpleNode (implements ru.biosoft.math.model.Node)
  - class ru.biosoft.math.model.AstConstant
  - class ru.biosoft.math.model.AstFunctionDeclaration (implements ru.biosoft.math.model.Function, ru.biosoft.math.model.ParserContext)
  - class ru.biosoft.math.model.AstFunNode
  - class ru.biosoft.math.model.AstPiece
  - class ru.biosoft.math.model.AstPiecewise
  - class ru.biosoft.math.model.AstStart
  - class ru.biosoft.math.model.AstVarNode
  - class ru.biosoft.math.model.ControlActions
  - class ru.biosoft.math.model.ControlTrigger
  - class ru.biosoft.math.model.StateChartControl
- class biouml.plugins.simulation.SimulationControl
- class biouml.plugins.simulation.SimulationEngine.VariableType
- class biouml.plugins.simulation.SimulatorInfo
- class biouml.plugins.simulation.Span
- class ru.biosoft.access.SqlConnectionPool
- class ru.biosoft.access.SqlTransformerSupport (implements ru.biosoft.access.SqlTransformer)
  - class biouml.plugins.simulation.plot.access.PlotSqlTransformer
  - class biouml.standard.type.access.ReferrerSqlTransformer
    - class biouml.standard.type.access.ConceptSqlTransformer
      - class biouml.standard.type.access.BiopolymerSqlTransformer
        - class biouml.standard.type.access.GeneSqlTransformer
        - class biouml.standard.type.access.ProteinSqlTransformer
        - class biouml.standard.type.access.RNASqlTransformer
      - class biouml.standard.type.access.CellSqlTransformer
      - class biouml.standard.type.access.CompartmentSqlTransformer
      - class biouml.standard.type.access.SubstanceSqlTransformer
    - class biouml.standard.type.access.DatabaseInfoSqlTransformer
    - class biouml.standard.type.access.DiagramSqlTransformer
    - class biouml.standard.type.access.ReactionSqlTransformer
    - class biouml.standard.type.access.RelationSqlTransformer
  - class biouml.standard.type.access.RelationTypeSqlTransformer
  - class biouml.plugins.simulation.access.SimulationResultSqlTransformer
  - class biouml.standard.type.access.SpeciesSqlTransformer
  - class biouml.standard.type.access.UnitSqlTransformer
- class biouml.standard.StandardModuleActivator (implements biouml.model.util.ModuleActivator)
- class biouml.plugins.simulation.hybrid.State
- class biouml.plugins.simulation.hybrid.StateChart
- class biouml.plugins.simulation.ode.StdMet
- class biouml.plugins.simulation.ode.StiffnessDetector
- class biouml.plugins.svg.SvgDiagramExporter (implements biouml.model.DiagramExporter)
- class ru.biosoft.access.support.TagCommandSupport (implements ru.biosoft.access.support.TagCommand)
- class biouml.plugins.sbml._test.TestListParser
- class biouml.plugins.sbml._test.TestListParser.Category
- class ru.biosoft.util.TextUtil
- class ru.biosoft.math.parser.Token
- class ru.biosoft.math.model.Token
- class biouml.plugins.simulation.hybrid.Trigger
- class ru.biosoft.math.model.UndeclaredFunction (implements ru.biosoft.math.model.Function)
- class ru.biosoft.graphics.View
  - class ru.biosoft.graphics.CompositeView
    - class ru.biosoft.graphics.ArrowView
    - class ru.biosoft.graphics.Ruler
  - class ru.biosoft.graphics.HtmlView
  - class ru.biosoft.graphics.ImageView (implements ImageObserver)
  - class ru.biosoft.graphics.LineView
  - class ru.biosoft.graphics.ShapeView
    - class ru.biosoft.graphics.BoxView
    - class ru.biosoft.graphics.EllipseView
    - class ru.biosoft.graphics.PathView
    - class ru.biosoft.graphics.PolygonView
      - class ru.biosoft.graphics.PolylineView
  - class ru.biosoft.graphics.TextView
- class ru.biosoft.workbench.ViewDescriptor
- class ru.biosoft.graphics.editor.ViewPaneAdapter (implements ru.biosoft.graphics.editor.ViewPaneListener)
  - class ru.biosoft.graphics.editor.SelectionManager
    - class ru.biosoft.graphics.editor.MultipleSelectionManager
      - class ru.biosoft.graphics.editor.ResizableSelectionManager
- class ru.biosoft.workbench.ViewRegistry
- class ru.biosoft.gui.wizard.WizardTools
- class ru.biosoft.workbench.Workbench (implements IPlatformRunnable)

## Interface Hierarchy

- interface biouml.standard.filter.Action
- interface biouml.standard.filter.ActionFilter
- interface ru.biosoft.access.repository.ActionsProvider
- interface biouml.plugins.simulation.ae.AeModel
- interface com.developmentontheedge.application.ApplicationDocument
- interface com.developmentontheedge.application.ApplicationRegistry
- interface biouml.plugins.simulation.ode.Btheta
- interface biouml.plugins.cellml.CellMLConstants
- interface ru.biosoft.access.CreateDataCollectionController
- interface ru.biosoft.access.DataElement
  - interface biouml.standard.type.Base (also extends biouml.standard.type.Type)
    - interface biouml.standard.type.Relation
  - interface ru.biosoft.access.DataCollection
    - interface ru.biosoft.access.CollectionUnion
  - interface biouml.model.ModuleType
  - interface ru.biosoft.access.MutableDataElement
- interface biouml.model.DiagramExporter
- interface biouml.model.DiagramFilter
- interface biouml.model.DiagramImporter
- interface biouml.model.DiagramType
- interface biouml.model.DiagramTypeConverter
- interface biouml.model.DiagramViewBuilder
- interface com.developmentontheedge.application.DocumentFactory
- interface biouml.plugins.cellml.DomHelper
- interface java.util.EventListener
  - interface ru.biosoft.access.DataCollectionListener
    - interface ru.biosoft.access.QuerySystem
- interface biouml.model.dynamics.ExpressionOwner
- interface ru.biosoft.access.Filter
  - interface ru.biosoft.access.QueryFilter
- interface ru.biosoft.math.model.Formatter
- interface biouml.model.dynamics.FormulaDelegate
- interface ru.biosoft.math.model.Function
- interface biouml.plugins.gxl.GxlConstants
  - interface biouml.plugins.ginsim.GinSimConstants
- interface biouml.model.util.ImageGenerator.ReferenceGenerator
- interface biouml.plugins.matlab.JMatLinkInterface
- interface com.developmentontheedge.jobcontrol.JobControlListener
- interface ru.biosoft.access.Key
- interface biouml.standard.type.LocalisedString
- interface java.util.Map
  - interface ru.biosoft.access.Index
- interface biouml.plugins.simulation.Model
  - interface biouml.plugins.simulation.ode.OdeModel
- interface ru.biosoft.gui.ModelValidator
- interface biouml.model.util.ModuleActivator
- interface ru.biosoft.math.model.Node
- interface ru.biosoft.math.model.Parser
- interface ru.biosoft.math.parser.ParserConstants
- interface ru.biosoft.math.model.ParserContext
- interface ru.biosoft.math.parser.ParserTreeConstants
- interface ru.biosoft.workbench.PerspectiveFactory
- interface biouml.standard.type.ProteinProperties
- interface biouml.model.QueryEngine
- interface ru.biosoft.access.Repository
- interface ru.biosoft.access.repository.RepositoryListener
- interface biouml.plugins.simulation.ResultListener
- interface biouml.model.Role
  - interface biouml.model.dynamics.EModelRole
- interface java.lang.Runnable
  - interface com.developmentontheedge.jobcontrol.JobControl
- interface biouml.model.SemanticController
- interface ru.biosoft.access.support.SerializableAsText
- interface biouml.plugins.simulation.Simulator
- interface biouml.standard.type.SpeciesSpecific
- interface ru.biosoft.access.SqlTransformer
- interface biouml.plugins.sbml._test.Status
- interface ru.biosoft.access.support.TagCommand
- interface biouml.plugins.sbml._test.TestLogger
- interface ru.biosoft.access.Transformer
- interface biouml.standard.type.Type
  - interface biouml.standard.type.Base (also extends ru.biosoft.access.DataElement)
    - interface biouml.standard.type.Relation
- interface ru.biosoft.math.model.VariableResolver
- interface ru.biosoft.graphics.editor.ViewEditorHelper
- interface ru.biosoft.graphics.editor.ViewPaneListener
- interface ru.biosoft.graphics.editor.ViewSelector
- interface ru.biosoft.gui.wizard.Wizard
- interface ru.biosoft.gui.wizard.WizardStep
- interface ru.biosoft.gui.wizard.WizardTarget

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