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

Class CellMLComponent

java.lang.Object

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

de.unirostock.sems.bives.cellml.parser.CellMLComponent

public class CellMLComponent
extends CellMLEntity

The Class CellMLComponent representing a single component in a CellML model.

Author:

Martin Scharm

Field Summary

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

model

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	getDependencies(Map<CellMLUserUnit,List<CellMLEntity>> list)	Adds the units the variables in this component depend on to a global list of dependencies.
List<de.unirostock.sems.bives.ds.MathML>	getMath()	Gets the mathematical equations defined in this component.
String	getName()	Gets the name of this component.
List<CellMLReaction>	getReactions()	Gets the reactions defined in this component.
CellMLUnit	getUnit(String name)	Gets the unit.
CellMLVariable	getVariable(String name)	Gets the variable.
HashMap<String,CellMLVariable>	getVariables()	Gets the variables of this component.
void	setName(String name)	Sets the name of this component.
void	unconnect()	Unconnect all variables in this component.

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

CellMLComponent

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

Instantiates a new CellML component.

Parameters:

model - the model this component belongs to

node - the corresponding document node in the XML tree

Throws:

BivesCellMLParseException - the bives cell ml parse exception

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

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

Method Detail

getVariable

public CellMLVariable getVariable(String name)
                           throws de.unirostock.sems.bives.exception.BivesDocumentConsistencyException

Gets the variable.

Parameters:

name - the name of the variable

Returns:

the variable

Throws:

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

getUnit

public CellMLUnit getUnit(String name)

Gets the unit.

Parameters:

name - the name of the unit

Returns:

the unit

getName

public String getName()

Gets the name of this component.

Returns:

the name

setName

public void setName(String name)

Sets the name of this component.

Parameters:

name - the new name

unconnect

public void unconnect()

Unconnect all variables in this component.

getDependencies

public void getDependencies(Map<CellMLUserUnit,List<CellMLEntity>> list)

Adds the units the variables in this component depend on to a global list of dependencies.

Parameters:

list - the global list of dependencies

getReactions

public List<CellMLReaction> getReactions()

Gets the reactions defined in this component.

Returns:

the reactions

getVariables

public HashMap<String,CellMLVariable> getVariables()

Gets the variables of this component.

Returns:

the variables

getMath

public List<de.unirostock.sems.bives.ds.MathML> getMath()

Gets the mathematical equations defined in this component.

Returns:

the math