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

Class CellMLVariable

java.lang.Object

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

de.unirostock.sems.bives.cellml.parser.CellMLVariable

All Implemented Interfaces:

de.unirostock.sems.bives.algorithm.DiffReporter

public class CellMLVariable
extends CellMLEntity
implements de.unirostock.sems.bives.algorithm.DiffReporter

The Class CellMLVariable representing a variable of a CellML model.

Author:

Martin Scharm

Field Summary

Fields

Modifier and Type	Field	Description
static int	INTERFACE_IN	The flag INTERFACE_IN = incoming interface.
static int	INTERFACE_NONE	The flag INTERFACE_NONE = no interface.
static int	INTERFACE_OUT	The flag INTERFACE_OUT = outgoing interface.

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

model

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	addPrivateInterfaceConnection(CellMLVariable var)	Adds the private interface connection to annother CellML variable.
void	addPublicInterfaceConnection(CellMLVariable var)	Adds a public interface connection to annother CellML variable.
CellMLComponent	getComponent()	Gets the component.
void	getDependencies(Map<CellMLUserUnit,List<CellMLEntity>> list)	Adds the unit this variable depends on to a global list of dependencies.
Double	getInitialValue()	Gets the initial value, if explicitly specified by a scalar value.
CellMLVariable	getInitialValueVariable()	Gets the initial value, if specified by a variable.
String	getName()	Gets the name of this variable.
int	getPrivateInterface()	Gets the private interface flag.
List<CellMLVariable>	getPrivateInterfaceConnections()	Gets the private interface connections as a list of CellML variables.
String	getPrivateInterfaceStr()	Gets the textual representation (in, out, or none) of the private interface.
int	getPublicInterface()	Gets the public interface flag.
List<CellMLVariable>	getPublicInterfaceConnections()	Gets the public interface connections as a list of CellML variables.
String	getPublicInterfaceStr()	Gets the textual representation (in, out, or none) of the public interface.
CellMLVariable	getRootVariable()	Gets the root variable, obtained by traversing the interface connections.
void	renameUnit(String original, String newName)	Rename the corresponding unit.
de.unirostock.sems.bives.markup.MarkupElement	reportDelete()
de.unirostock.sems.bives.markup.MarkupElement	reportInsert()
de.unirostock.sems.bives.markup.MarkupElement	reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt, de.unirostock.sems.bives.algorithm.DiffReporter docA, de.unirostock.sems.bives.algorithm.DiffReporter docB)
void	unconnect()	Unconnect all interface connections.

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

Field Detail

INTERFACE_NONE

public static final int INTERFACE_NONE

The flag INTERFACE_NONE = no interface.

See Also:

Constant Field Values

INTERFACE_IN

public static final int INTERFACE_IN

The flag INTERFACE_IN = incoming interface.

See Also:

Constant Field Values

INTERFACE_OUT

public static final int INTERFACE_OUT

The flag INTERFACE_OUT = outgoing interface.

See Also:

Constant Field Values

Constructor Detail

CellMLVariable

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

Instantiates a new CellML variable.

Parameters:

model - the corresponding model

component - the component containing this variable

node - the corresponding node which defines this variable

Throws:

BivesCellMLParseException - the bives cell ml parse exception

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

Method Detail

getComponent

public CellMLComponent getComponent()

Gets the component.

Returns:

the component

getPublicInterface

public int getPublicInterface()

Gets the public interface flag. (CellMLVariable.INTERFACE_IN, CellMLVariable.INTERFACE_OUT, or CellMLVariable.INTERFACE_NONE)

Returns:

the public interface flag

getPrivateInterface

public int getPrivateInterface()

Gets the private interface flag. (CellMLVariable.INTERFACE_IN, CellMLVariable.INTERFACE_OUT, or CellMLVariable.INTERFACE_NONE)

Returns:

the private interface flag

getPublicInterfaceStr

public String getPublicInterfaceStr()

Gets the textual representation (in, out, or none) of the public interface.

Returns:

the public interface

getPrivateInterfaceStr

public String getPrivateInterfaceStr()

Gets the textual representation (in, out, or none) of the private interface.

Returns:

the private interface

addPublicInterfaceConnection

public void addPublicInterfaceConnection(CellMLVariable var)
                                  throws de.unirostock.sems.bives.exception.BivesLogicalException

Adds a public interface connection to annother CellML variable.

Parameters:

var - the variable

Throws:

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

addPrivateInterfaceConnection

public void addPrivateInterfaceConnection(CellMLVariable var)
                                   throws de.unirostock.sems.bives.exception.BivesLogicalException

Adds the private interface connection to annother CellML variable.

Parameters:

var - the variable

Throws:

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

getPublicInterfaceConnections

public List<CellMLVariable> getPublicInterfaceConnections()

Gets the public interface connections as a list of CellML variables.

Returns:

the public interface connections

getPrivateInterfaceConnections

public List<CellMLVariable> getPrivateInterfaceConnections()

Gets the private interface connections as a list of CellML variables.

Returns:

the private interface connections

getRootVariable

public CellMLVariable getRootVariable()

Gets the root variable, obtained by traversing the interface connections.

Returns:

the root variable

getInitialValueVariable

public CellMLVariable getInitialValueVariable()

Gets the initial value, if specified by a variable.

Returns:

the initial value variable

getInitialValue

public Double getInitialValue()

Gets the initial value, if explicitly specified by a scalar value.

Returns:

the initial value

unconnect

public void unconnect()

Unconnect all interface connections.

getName

public String getName()

Gets the name of this variable.

Returns:

the name

getDependencies

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

Adds the unit this variable depends on to a global list of dependencies.

Parameters:

list - the global list of dependencies

reportModification

public de.unirostock.sems.bives.markup.MarkupElement reportModification(de.unirostock.sems.bives.algorithm.SimpleConnectionManager conMgmt,
                                                                        de.unirostock.sems.bives.algorithm.DiffReporter docA,
                                                                        de.unirostock.sems.bives.algorithm.DiffReporter docB)

Specified by:

reportModification in interface de.unirostock.sems.bives.algorithm.DiffReporter

reportInsert

public de.unirostock.sems.bives.markup.MarkupElement reportInsert()

Specified by:

reportInsert in interface de.unirostock.sems.bives.algorithm.DiffReporter

reportDelete

public de.unirostock.sems.bives.markup.MarkupElement reportDelete()

Specified by:

reportDelete in interface de.unirostock.sems.bives.algorithm.DiffReporter

renameUnit

public void renameUnit(String original,
                       String newName)
                throws de.unirostock.sems.bives.exception.BivesLogicalException

Rename the corresponding unit. (Intended to be used for flattening)

Parameters:

original - the original name

newName - the new name

Throws:

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