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| Classes in biouml.model used by biouml.model | |
| AbstractFilter Utility class that provides support for basic diagram filter operations. | |
| Compartment General definition of the compartment as a container for nodes and edges between them. | |
| CompartmentBeanInfo | |
| DefaultDiagramViewBuilder Default implementation of DiagramViewBuilder. | |
| DefaultSemanticController | |
| Diagram | |
| DiagramBeanInfo | |
| DiagramElement Common definition of diagram element. | |
| DiagramExporter General interface to export digaram in the specified format, for example in SBML format or as PNG image. | |
| DiagramFilter Filter cab be applied to any diagram view. | |
| DiagramImporter General interface to import digaram, for example from SBML or CellML file. | |
| DiagramType Formalyze the diagram attributes. | |
| DiagramTypeConverter General interface to convert diagram type. | |
| DiagramTypeConverter.ConditionalConverter Checks whether data types of all kernels on the diagram can be used in new diagram. | |
| DiagramTypeConverter.NoConverter | |
| DiagramTypeConverter.YesConverter | |
| DiagramTypeSupport Stub implementation of DiagramType interface. | |
| DiagramViewBuilder | |
| Edge Edge is directed relation between two diagram nodes, called "input" and "output". | |
| EdgeBeanInfo | |
| EquivalentNodeGroup Group of equivalent nodes. | |
| EquivalentNodeGroupBeanInfo | |
| Module The module data is hierarchically organised in following manner: Diagrams DataCollection of Diagrams. | |
| ModuleType | |
| Node Diagram node element | |
| NodeBeanInfo | |
| NodeInfo Utility class for QueryEngine. | |
| QueryEngine | |
| QueryEngineSupport | |
| Role | |
| SemanticController | |
| Classes in biouml.model used by biouml.model.dynamics | |
| EModel Genrally this role should be assotiated with Diagram. | |
| EModelDiagramType Type for executable model diagram. | |
| EModelDiagramViewBuilder View builder for executable model diagram. | |
| EModelRole Executable model role. | |
| EModelRoleSupport | |
| Equation | |
| Event | |
| Function Wrapper for MathML lambda element. | |
| State | |
| Transition | |
| VariableRole General variable definition. | |
| VariablesDataCollection | |
| Classes in biouml.model used by biouml.model.htmlgen | |
| GenerateHTMLDialog | |
| Classes in biouml.model used by biouml.model.util | |
| DiagramXmlReader | |
| DiagramXmlWriter | |
| ImageGenerator Utility class to generate diagram image. | |
| ModuleActivator This class is used to activate the module during the process of module instalation. | |
| ModulePackager | |
| Classes in biouml.model used by biouml.plugins.cellml | |
| CellMLDiagramType | |
| CellMLImporter | |
| CellMLModelReader | |
| CellMLModelWriter Writes diagram in SBML format. | |
| CellMLModuleType Module type that process CellML 1.0 and 1.1 biochemical models. | |
| Classes in biouml.model used by biouml.plugins.ginsim | |
| GinMLExporter | |
| GinMLImporter | |
| GinSimDiagramType | |
| GinSimDiagramViewBuilder | |
| Classes in biouml.model used by biouml.plugins.gxl | |
| GxlExporter | |
| GxlParserContext The simpliest implementation of SAX parser context for parsing supported sibset of GXL. | |
| GxlReader | |
| GxlWriter Extracts only GXL-representable part of the digram. | |
| Classes in biouml.model used by biouml.plugins.jgraph | |
| DiagramToJGraphTransformer Converts BioUML diagram or its part into org.jgraph.graph for usage by graph layout algorithm. | |
| Classes in biouml.model used by biouml.plugins.matlab | |
| MatlabErrorDialog | |
| MatlabSimulationEngine | |
| Classes in biouml.model used by biouml.plugins.sbml | |
| CreateDiagramElementDialog Creates SBML specie or compartment diagram element. | |
| SbmlDiagramType | |
| SbmlExporter | |
| SbmlImporter | |
| SbmlModelFactory Utility class to read/write diagrams in SBML format. | |
| SbmlModelReader | |
| SbmlModelWriter Writes diagram in SBML format. | |
| SbmlModelWriter_21 | |
| SbmlModelWriter_L1 | |
| SbmlModuleType Module type that process SBML diagrams. | |
| SbmlSemanticController | |
| SbmlSupport | |
| Classes in biouml.model used by biouml.plugins.simulation | |
| MathWriter | |
| SimulationEngine General class for simulation engine. | |
| Classes in biouml.model used by biouml.plugins.simulation.java | |
| JavaSimulationEngine | |
| Classes in biouml.model used by biouml.plugins.simulation.plot | |
| PlotDialog | |
| PlotEx It supports extened views of plot in property inspector. | |
| Classes in biouml.model used by biouml.plugins.svg | |
| SvgDiagramExporter Exports diagram image in SVG format. | |
| Classes in biouml.model used by biouml.standard | |
| PathwayQueryEngine Created by IntelliJ IDEA. | |
| PathwayQueryOptions | |
| PathwayQueryOptionsBeanInfo Created by IntelliJ IDEA. | |
| StandardModuleActivator | |
| StandardModuleType Definition of standard BioUML module. | |
| StandardQueryEngine | |
| Classes in biouml.model used by biouml.standard.filter | |
| Action Public interface that is used to specify what action should be applied to digarm element if it satisfies to the filter condition. | |
| ActionFilter This filter generates some action (currently hide or highlight) if the processed node satisfies to the filter condition. | |
| BiopolimerDiagramFilter Common purpose diagram filter allowing to filter Biopolimers by species, cell types and inducers. | |
| CompositeHighlightAction If some diagram element satisfies to conditions of several filters simultaneously, then it can be highlighted by several colors. | |
| HideAction If diagram element satisfies to the filter condition it will be highlighted. | |
| HighlightAction If diagram element satisfies to the filter condition it will be highlighted. | |
| ValueActionFilter Filter condition is specified as a set of ActionValuess. | |
| Classes in biouml.model used by biouml.workbench | |
| BioUMLApplication General class for different BioUML applications. | |
| Classes in biouml.model used by biouml.workbench.diagram | |
| ConvertDiagramDialog | |
| DiagramDocument | |
| DiagramEditorHelper This class is used to provide all neccessary changes and validations in diagram model. | |
| DiagramElementInfo Utility class for QueryEngine. | |
| DiagramExporterRegistry | |
| DiagramExporterRegistry.ExporterInfo Utility class that stores information about DiagramExporter. | |
| DiagramImageWriter Exports diagram image in formats supported by javax.imageio.ImageIO. | |
| DiagramImporterRegistry | |
| DiagramsPane | |
| ExportDiagramDialog | |
| ImportDiagramDialog | |
| NewDiagramDialog | |
| Classes in biouml.model used by biouml.workbench.module | |
| ModuleExportDialog | |
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