Uses of Interface
biouml.standard.type.Base

Packages that use Base

biouml.model
biouml.plugins.cellml
biouml.plugins.ginsim
biouml.plugins.sbml
biouml.standard
biouml.standard.diagram
biouml.standard.filter
biouml.standard.type
biouml.workbench.diagram

Uses of Base in biouml.model

Fields in biouml.model declared as Base

protected Base

DiagramElement.kernel

Methods in biouml.model that return Base

Base	NodeInfo.getBase()
Base[]	EquivalentNodeGroup.getKernels() We would like to get access for kernels through the property to display it in property inspector.
Base	DiagramElement.getKernel()

Methods in biouml.model with parameters of type Base

Compartment	QueryEngineSupport.getCompartment(Node start, Base kernel) Should return the most suitable compartment where new node should be located.
protected Node	QueryEngineSupport.findNearestNode(Compartment c, Node node, Base kernel)
void	DiagramElement.setKernel(Base kernel)
void	Diagram.setKernel(Base newKernel)
boolean	DefaultDiagramViewBuilder.isReaction(Base kernel)
boolean	Compartment.containsKernel(Base kernel)
java.util.List	Compartment.getKernelNodes(Base kernel)

Constructors in biouml.model with parameters of type Base

NodeInfo(Base base)

Node(DataCollection parent, java.lang.String name, Base kernel)

Node(DataCollection parent, Base kernel)

Edge(DataCollection parent, java.lang.String id, Base kernel, Node input, Node output)

Edge(DataCollection parent, Base kernel, Node input, Node output)

DiagramElement(DataCollection parent, java.lang.String name, Base kernel)
Constructs the diagram element.

DiagramElement(DataCollection parent, Base kernel)
Constructs the diagram element.

Diagram(DataCollection origin, Base kernel, DiagramType type)
Creates the diagram of the specified type.

Compartment(DataCollection parent, java.lang.String id, Base kernel)

Compartment(DataCollection parent, Base kernel)

Uses of Base in biouml.plugins.cellml

Classes in biouml.plugins.cellml that implement Base

class

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

Uses of Base in biouml.plugins.ginsim

Classes in biouml.plugins.ginsim that implement Base

class	GinSimEdgeKernel
class	GinSimNodeKernel

Uses of Base in biouml.plugins.sbml

Classes in biouml.plugins.sbml that implement Base

class

Specie

Uses of Base in biouml.standard

Methods in biouml.standard with parameters of type Base

boolean

PathwayQueryEngine.isSmallMolecule(Base base, java.lang.Object obj)

Uses of Base in biouml.standard.diagram

Fields in biouml.standard.diagram declared as Base

protected Base

SemanticRelationPane.relation

Methods in biouml.standard.diagram with parameters of type Base

DiagramElement	PathwaySemanticController.createDiagramElement(Base kernel, java.util.Set elements)
protected Node	PathwaySemanticController.getNode(Base kernel, java.util.Set elements)
protected Brush	PathwayDiagramViewBuilder.getReactionBrush(Base reaction, PathwayDiagramViewOptions options)

Uses of Base in biouml.standard.filter

Methods in biouml.standard.filter with parameters of type Base

protected boolean

HideAction.isReaction(Base kernel)

Uses of Base in biouml.standard.type

Subinterfaces of Base in biouml.standard.type

interface

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

Classes in biouml.standard.type that implement Base

class	BaseSupport Base class for all data element types.
class	Biopolymer
class	Cell Stub
class	Compartment Stub
class	Concept
class	Constant Some constant that can be used in kinetic or other equations.
class	DatabaseInfo Many data elements can refer to other databases through its database references field.
class	DiagramInfo Defines common properties for diagram description.
class	DiagramReference
class	Function Molecular function is an activity or task performed by a gene product or other biological entity.
class	Gene Stub
class	GenericEntity
class	Molecule
class	Process Biological process is a biological goal that requires more than one function.
class	Protein Stub
class	Reaction
class	Referrer Extention of GenericEntity that contains references to other databases and literature sources.
class	RNA Stub
class	SemanticRelation SemanticRelatio specified semantic relationships between concepts (kernels) assotiated with two nodes on the diagram.
class	SpecieReference SpecieReference specifies role of molecule involved in the Reaction.
class	State State, stage or variant of biological system or its subunits.
class	Stub
static class	Stub.Note
static class	Stub.NoteLink
class	Substance Stub

Uses of Base in biouml.workbench.diagram

Methods in biouml.workbench.diagram that return Base

Base	DiagramElementInfo.getKernel()

Methods in biouml.workbench.diagram with parameters of type Base

protected void

DiagramDocument.saveKernel(Base de)