Classes in biouml.standard.type used by biouml.model

Compartment           General definition of the compartment as a container for nodes and edges between them.

DefaultDiagramViewBuilder           Default implementation of DiagramViewBuilder.

Diagram

DiagramElement           Common definition of diagram element.

Edge           Edge is directed relation between two diagram nodes, called "input" and "output".

EquivalentNodeGroup           Group of equivalent nodes.

Node           Diagram node element

NodeInfo           Utility class for QueryEngine.

QueryEngineSupport

 

Classes in biouml.standard.type used by biouml.model.util

DiagramXmlReader

 

Classes in biouml.standard.type used by biouml.plugins.cellml

DiagramInfo

Reaction

Species           This is a wrapper class to handle RDF elemenet assotiated with CellML component.

 

Classes in biouml.standard.type used by biouml.plugins.ginsim

GinSimEdgeKernel

GinSimNodeKernel

 

Classes in biouml.standard.type used by biouml.plugins.sbml

Specie

 

Classes in biouml.standard.type used by biouml.standard

PathwayQueryEngine           Created by IntelliJ IDEA.

 

Classes in biouml.standard.type used by biouml.standard.diagram

PathwaySemanticController

 

Classes in biouml.standard.type used by biouml.standard.type

Base           General interface to be implemented by all classes to be used as BioUML diagram elements.

BaseSupport           Base class for all data element types.

Biopolymer

BiopolymerBeanInfo           Utility class containing common metada for all molecules.

Cell           Stub

CellBeanInfo           Utility class containing common metada for all molecules.

Compartment           Stub

CompartmentBeanInfo

Concept

ConceptBeanInfo

Constant           Some constant that can be used in kinetic or other equations.

ConstantBeanInfo

DatabaseInfo           Many data elements can refer to other databases through its database references field.

DatabaseInfoBeanInfo

DatabaseReference           General defintion of reference to external database.

DiagramInfo           Defines common properties for diagram description.

DiagramInfoBeanInfo

DiagramReference

Function           Molecular function is an activity or task performed by a gene product or other biological entity.

FunctionBeanInfo

Gene           Stub

GeneBeanInfo

GenericEntity

KineticLaw

KineticType           Definition of KinetReactionType defines: - meta information about reaction

KineticTypeBeanInfo           Utility class containing common metada for all generic entities.

Molecule

MoleculeBeanInfo           Utility class containing common metada for all molecules.

Process           Biological process is a biological goal that requires more than one function.

ProcessBeanInfo

Protein           Stub

ProteinBeanInfo

Reaction

ReactionBeanInfo

Referrer           Extention of GenericEntity that contains references to other databases and literature sources.

ReferrerBeanInfo

Relation           Intermediary class to generalize what is common for all relations/edges as well as to define common constants.

RNA           Stub

RNABeanInfo

SemanticRelation           SemanticRelatio specified semantic relationships between concepts (kernels) assotiated with two nodes on the diagram.

SemanticRelationBeanInfo

SpecieReference           SpecieReference specifies role of molecule involved in the Reaction.

SpecieReferenceBeanInfo

SpeciesSpecific           General interface for species specific entities.

State           State, stage or variant of biological system or its subunits.

StateBeanInfo

Stub

Stub.Note

Stub.NoteLink

Substance           Stub

SubstanceBeanInfo

UnitBeanInfo

 

Classes in biouml.standard.type used by biouml.workbench.diagram

DiagramElementInfo           Utility class for QueryEngine.