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## Uses of Package
biouml.model

Packages that use biouml.model
biouml.editor |
biouml.editor.graphlayout |
biouml.editor.module |
biouml.model |
biouml.model.dynamics |
biouml.model.htmlgen |
biouml.model.util |
biouml.modules.genenet |
biouml.modules.kegg |
biouml.modules.kegg.type.access |
biouml.modules.transpath |
biouml.standard |
biouml.standard.diagram.pathway |
biouml.standard.filter |

Classes in biouml.model used by biouml.editor
BioUMLApplication General class for different BioUML applications.
BioUMLEditor
DiagramDocument
DiagramEditorHelper This class is used to provide all neccessary changes and validations in diagram model.
MatlabErrorDialog
NewDiagramDialog
NewDiagramElementDialog
NodeInfo
QueryEngine
SaveAsImageAction
SearchEngine
SearchLinkedPanel
SearchOptions
ViewerDiagramFilter

Classes in biouml.model used by biouml.editor.graphlayout
CellLayoutManager
ForceDirectedLayoutManager
GraphLayout
LayeredLayoutManager
LayeredOptimizedLayoutManager

Classes in biouml.model used by biouml.editor.module
ModuleExportDialog

Classes in biouml.model used by biouml.model
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.
DiagramType Formalyze the diagram attributes.
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
QueryEngine
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
MatlabOdeModel
Reaction
Variable 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
ModuleActivator This class is used to activate the module during the process of module instalation.
ModulePackager

Classes in biouml.model used by biouml.modules.genenet
GeneNetDiagramType
GeneNetDiagramViewBuilder Default implementation of `DiagramViewBuilder`.
GeneNetModuleActivator Definition of GeneNet module creator.
GeneNetModuleType Definition of GeneNet module.
GeneNetQueryEngine
GeneNetSemanticController

Classes in biouml.model used by biouml.modules.kegg
KeggPathwayDiagramType
KeggPathwayDiagramViewBuilder Default implementation of `DiagramViewBuilder`.
KeggPathwayModuleActivator
KeggPathwayModuleType Definition of KEGG Pathways module.
KeggPathwayQueryEngine
KeggPathwaySemanticController

Classes in biouml.model used by biouml.modules.kegg.type.access
DiagramReader

Classes in biouml.model used by biouml.modules.transpath
TranspathDiagramType
TranspathDiagramViewBuilder Default implementation of `DiagramViewBuilder`.
TranspathModuleActivator Definition of Transpath module.
TranspathModuleType Definition of Transpath module.
TranspathQueryEngine
TranspathSemanticController

Classes in biouml.model used by biouml.standard
StandardModuleActivator
StandardModuleType Definition of standard BioUML module.
StandardQueryEngine

Classes in biouml.model used by biouml.standard.diagram.pathway
PathwayDiagramType
PathwayDiagramViewBuilder Default implementation of `DiagramViewBuilder`.
PathwayDiagramViewOptions
PathwaySemanticController
PathwaySimulationDiagramType

Classes in biouml.model used by biouml.standard.filter
BiopolimerDiagramFilter Common purpose diagram filter allowing to filter Biopolimers by species, cell types and inducers.

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