Overview | Package | Class | Use | Tree | Help
| HEADER
PREV NEXT | FRAMES NO FRAMES

## Uses of Package
biouml.model

Packages that use biouml.model
biouml.model |
biouml.model.dynamics |
biouml.model.htmlgen |
biouml.model.util |
biouml.plugins.cellml |
biouml.plugins.ginsim |
biouml.plugins.gxl |
biouml.plugins.jgraph |
biouml.plugins.matlab |
biouml.plugins.sbml |
biouml.plugins.simulation |
biouml.plugins.simulation.java |
biouml.plugins.simulation.plot |
biouml.plugins.svg |
biouml.standard |
biouml.standard.diagram |
biouml.standard.filter |
biouml.workbench |
biouml.workbench.diagram |
biouml.workbench.module |

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 `Diagram`s.
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.diagram
CreateDiagramElementDialog
CreateEdgeDialog
DiagramElementSelector
GeneNetworkDiagramType
GeneNetworkDiagramType.GeneNetworkDiagramViewBuilder
GeneNetworkDiagramType.GeneNetworkDiagramViewOptions We have redefined ViewOptions to have an ability specify corresponding bean info.
MetabolicPathwayDiagramType
MetabolicPathwayDiagramType.MetabolicPathwayDiagramViewBuilder
MetabolicPathwayDiagramType.MetabolicPathwayDiagramViewOptions We have redefined ViewOptions to have an ability specify corresponding bean info.
NoteLinkPane
PathwayDiagramType This is basic class for formal description of biological pathways.
PathwayDiagramViewBuilder Default implementation of `DiagramViewBuilder`.
PathwayDiagramViewOptions
PathwaySemanticController
PathwaySimulationDiagramType PathwaySimulationDiagramType is extension of PathwayDiagramType.
PathwaySimulationDiagramViewBuilder
PathwaySimulationSemanticController
ReactionPane
SemanticNetworkDiagramType
SemanticNetworkDiagramType.SemanticNetworkDiagramViewBuilder
SemanticNetworkDiagramType.SemanticNetworkDiagramViewOptions We have defined SemanticNetworkDiagramViewOptions to have an ability specify corresponding bean info.
SemanticRelationPane

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

Overview | Package | Class | Use | Tree | Help
| FOOTER
PREV NEXT | FRAMES NO FRAMES

BOTTOM