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

Class CellMLModel

java.lang.Object

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

de.unirostock.sems.bives.cellml.parser.CellMLModel

public class CellMLModel
extends CellMLEntity

The Class CellMLModel representing a computational model that was encoded in CellML.

Author:

Martin Scharm

Field Summary

Fields inherited from class de.unirostock.sems.bives.cellml.parser.CellMLEntity

model

Constructor Summary

Constructors

Constructor	Description
CellMLModel(CellMLDocument doc, de.unirostock.sems.xmlutils.ds.DocumentNode rootNode)	Instantiates a new model.

Method Summary

Modifier and Type	Method	Description
void	addComponent(CellMLComponent component)	Adds a component.
void	addUnit(CellMLUserUnit unit, boolean imported)	Adds a unit.
boolean	containsImports()	Does this model contain imports?.
void	flatten()	Flatten this model.
CellMLComponent	getComponent(String name)	Gets the component having a specified name.
HashMap<String,CellMLComponent>	getComponents()	Gets the components.
List<de.unirostock.sems.bives.ds.rdf.RDFDescription>	getDescriptions(CellMLEntity entity)	Gets the RDF descriptions for an entity.
CellMLDocument	getDocument()	Gets the document.
CellMLEntity	getEntityByMetaId(String metaId)	Get an entity by its meta id.
CellMLEntity	getFromNode(de.unirostock.sems.xmlutils.ds.TreeNode node)	Gets an entity given a node in an XML tree.
CellMLHierarchy	getHierarchy()	Gets the hierarchy.
String	getName()	Gets the name of the model.
CellMLUnitDictionary	getUnits()	Gets the units.
void	importComponent(CellMLComponent component)	Import a component from another document.
void	importUnit(CellMLUserUnit unit)	Imports a unit from another document.
void	mapNode(de.unirostock.sems.xmlutils.ds.DocumentNode node, CellMLEntity entity)	Map document node to a CellML entity.
void	registerMetaId(String metaId, CellMLEntity cellMLEntity)	Register an entity by its meta id.
void	registerRdfBlock(de.unirostock.sems.bives.ds.rdf.RDF rdf)	Register an rdf block.
void	unregisterMetaId(String metaId)	Unregister a meta id.

Methods inherited from class de.unirostock.sems.bives.cellml.parser.CellMLEntity

associateRdfDescription, flagMetaModifcations, getDocumentNode, getMetaId, getModel, getRdfBlocks, getRdfDescriptions, setMetaId, setModel

Methods inherited from class java.lang.Object

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

Constructor Detail

CellMLModel

public CellMLModel(CellMLDocument doc,
                   de.unirostock.sems.xmlutils.ds.DocumentNode rootNode)
            throws BivesCellMLParseException,
                   de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                   de.unirostock.sems.bives.exception.BivesLogicalException,
                   IOException,
                   URISyntaxException,
                   de.unirostock.sems.bives.exception.BivesImportException

Instantiates a new model.

Parameters:

doc - the document containing this model

rootNode - the root node of the model

Throws:

BivesCellMLParseException - the bives cell ml parse exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

IOException - Signals that an I/O exception has occurred.

URISyntaxException - the uRI syntax exception

de.unirostock.sems.bives.exception.BivesImportException - the bives import exception

Method Detail

getName

public String getName()

Gets the name of the model.

Returns:

the name

containsImports

public boolean containsImports()

Does this model contain imports?.

Returns:

true, if it contains imports

importUnit

public void importUnit(CellMLUserUnit unit)
                throws de.unirostock.sems.bives.exception.BivesDocumentConsistencyException

Imports a unit from another document. Runs some additional code (in cmp to addUnit) in order to flatten a document.

Parameters:

unit - the unit

Throws:

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

addUnit

public void addUnit(CellMLUserUnit unit,
                    boolean imported)
             throws de.unirostock.sems.bives.exception.BivesDocumentConsistencyException

Adds a unit.

Parameters:

unit - the unit

imported - is that an import?

Throws:

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

getUnits

public CellMLUnitDictionary getUnits()

Gets the units.

Returns:

the unit dictionary

getDocument

public CellMLDocument getDocument()

Gets the document.

Returns:

the document

getComponents

public HashMap<String,CellMLComponent> getComponents()

Gets the components.

Returns:

the components

getComponent

public CellMLComponent getComponent(String name)

Gets the component having a specified name.

Parameters:

name - the name of the component

Returns:

the component

addComponent

public void addComponent(CellMLComponent component)
                  throws de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                         de.unirostock.sems.bives.exception.BivesLogicalException

Adds a component.

Parameters:

component - the component to add

Throws:

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

importComponent

public void importComponent(CellMLComponent component)
                     throws de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                            de.unirostock.sems.bives.exception.BivesLogicalException

Import a component from another document.

Parameters:

component - the component to import

Throws:

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

de.unirostock.sems.bives.exception.BivesLogicalException - the bives logical exception

flatten

public void flatten()
             throws de.unirostock.sems.bives.exception.BivesFlattenException,
                    de.unirostock.sems.bives.exception.BivesDocumentConsistencyException,
                    de.unirostock.sems.xmlutils.exception.XmlDocumentConsistencyException,
                    de.unirostock.sems.bives.exception.BivesLogicalException

Flatten this model. Write all imported entities to this tree.

Throws:

de.unirostock.sems.bives.exception.BivesFlattenException - the bives flatten exception

de.unirostock.sems.bives.exception.BivesDocumentConsistencyException - the bives document consistency exception

de.unirostock.sems.xmlutils.exception.XmlDocumentConsistencyException - the xml document consistency exception

de.unirostock.sems.bives.exception.BivesLogicalException

getHierarchy

public CellMLHierarchy getHierarchy()

Gets the hierarchy.

Returns:

the hierarchy

mapNode

public void mapNode(de.unirostock.sems.xmlutils.ds.DocumentNode node,
                    CellMLEntity entity)

Map document node to a CellML entity.

Parameters:

node - the document node

entity - the entity

getFromNode

public CellMLEntity getFromNode(de.unirostock.sems.xmlutils.ds.TreeNode node)

Gets an entity given a node in an XML tree.

Parameters:

node - the node

Returns:

the from node

getEntityByMetaId

public CellMLEntity getEntityByMetaId(String metaId)

Get an entity by its meta id.

Parameters:

metaId - the meta id

Returns:

the corresponding entity

registerMetaId

public void registerMetaId(String metaId,
                           CellMLEntity cellMLEntity)
                    throws de.unirostock.sems.bives.exception.BivesLogicalException

Register an entity by its meta id.

Parameters:

metaId - the meta id

cellMLEntity - the CellML entity

Throws:

de.unirostock.sems.bives.exception.BivesLogicalException

registerRdfBlock

public void registerRdfBlock(de.unirostock.sems.bives.ds.rdf.RDF rdf)

Register an rdf block.

Parameters:

rdf - the rdf block

getDescriptions

public List<de.unirostock.sems.bives.ds.rdf.RDFDescription> getDescriptions(CellMLEntity entity)

Gets the RDF descriptions for an entity.

Parameters:

entity - the entity

Returns:

the descriptions, or null if there aren't any

unregisterMetaId

public void unregisterMetaId(String metaId)

Unregister a meta id.

Parameters:

metaId - the meta id to remove from mapper