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 Diagrams.

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.