Package de.unirostock.sems.bives.cellml.parser

Class CellMLEntity

java.lang.Object

de.unirostock.sems.bives.cellml.parser.CellMLEntity

Direct Known Subclasses:

CellMLComponent, CellMLModel, CellMLReaction, CellMLReactionSubstance, CellMLReactionSubstance.Role, CellMLUnit, CellMLVariable

public abstract class CellMLEntity
extends Object

The Class CellMLEntity representing an entity in a CellML model.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
protected CellMLModel	model	The model.

Constructor Summary

Constructors

Constructor	Description
CellMLEntity(de.unirostock.sems.xmlutils.ds.DocumentNode node, CellMLModel model)	Instantiates a new CellML entity.

Method Summary

Modifier and Type	Method	Description
void	associateRdfDescription(de.unirostock.sems.bives.ds.rdf.RDFDescription descr)	Associate an rdf description.
boolean	flagMetaModifcations(de.unirostock.sems.bives.markup.MarkupElement me)	Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.
de.unirostock.sems.xmlutils.ds.DocumentNode	getDocumentNode()	Gets the document node.
String	getMetaId()	Gets the CellML meta id of this entity.
CellMLModel	getModel()	Gets the corresponding model.
List<de.unirostock.sems.bives.ds.rdf.RDF>	getRdfBlocks()	Gets the RDF descriptions, if there are any rooted in this entity.
List<de.unirostock.sems.bives.ds.rdf.RDFDescription>	getRdfDescriptions()	Gets the rdf descriptions.
boolean	setMetaId(String metaId)	Sets the meta id of this entity.
void	setModel(CellMLModel model)	Sets the model.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

model

protected CellMLModel model

The model.

Constructor Detail

CellMLEntity

public CellMLEntity(de.unirostock.sems.xmlutils.ds.DocumentNode node,
                    CellMLModel model)
             throws de.unirostock.sems.bives.exception.BivesLogicalException

Instantiates a new CellML entity.

Parameters:

node - the corresponding node in the XML document

model - the model

Throws:

de.unirostock.sems.bives.exception.BivesLogicalException

Method Detail

flagMetaModifcations

public boolean flagMetaModifcations(de.unirostock.sems.bives.markup.MarkupElement me)

Flags occuring modifcations of the meta information (notes, annotations) to the given MarkupElement.

Parameters:

me - the MarkupElement that should be flagged

Returns:

true, if flagged

getDocumentNode

public de.unirostock.sems.xmlutils.ds.DocumentNode getDocumentNode()

Gets the document node.

Returns:

the document node

getRdfBlocks

public List<de.unirostock.sems.bives.ds.rdf.RDF> getRdfBlocks()

Gets the RDF descriptions, if there are any rooted in this entity.

Returns:

the RDF descriptions

getModel

public CellMLModel getModel()

Gets the corresponding model.

Returns:

the model

setModel

public void setModel(CellMLModel model)
              throws de.unirostock.sems.bives.exception.BivesLogicalException

Sets the model.

Parameters:

model - the new model

Throws:

de.unirostock.sems.bives.exception.BivesLogicalException

setMetaId

public boolean setMetaId(String metaId)
                  throws de.unirostock.sems.bives.exception.BivesLogicalException

Sets the meta id of this entity. Must be unique in this model and

Parameters:

metaId - the meta id

Returns:

true, if successful

Throws:

de.unirostock.sems.bives.exception.BivesLogicalException

getMetaId

public String getMetaId()

Gets the CellML meta id of this entity. Might return null if not defined.

Returns:

the meta id

associateRdfDescription

public void associateRdfDescription(de.unirostock.sems.bives.ds.rdf.RDFDescription descr)

Associate an rdf description.

Parameters:

descr - the description

getRdfDescriptions

public List<de.unirostock.sems.bives.ds.rdf.RDFDescription> getRdfDescriptions()

Gets the rdf descriptions.

Returns:

the rdf descriptions