org.sbml.jsbml

Class Compartment

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.AbstractNamedSBaseWithUnit

org.sbml.jsbml.QuantityWithUnit

org.sbml.jsbml.Symbol

org.sbml.jsbml.Compartment

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, CallableSBase, NamedSBase, NamedSBaseWithDerivedUnit, Quantity, SBase, SBaseWithDerivedUnit, SBaseWithUnit, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport, Variable

public class Compartment
extends Symbol

Represents the compartment in a model, i.e., a variable element with name, identifier, unit, and value that may change during a simulation. This is the container for reacting species.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	compartmentTypeID Deprecated.
private boolean	isSetSpatialDimensions Helper variable to check if spatial dimensions has been set by the user.
private static org.apache.log4j.Logger	logger A Logger for this class.
private java.lang.String	outsideID Deprecated.
private static long	serialVersionUID Generated serial version identifier.
private java.lang.Double	spatialDimensions Represents the spatialDimensions XML attribute of a compartment element.

Fields inherited from class org.sbml.jsbml.Symbol

constant, isSetConstant

Fields inherited from class org.sbml.jsbml.QuantityWithUnit

value

Fields inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

unitsID

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
Compartment() Creates a Compartment instance.
Compartment(Compartment compartment) Creates a Compartment instance from a given compartment.
Compartment(int level, int version) Creates a Compartment instance from a level and version.
Compartment(java.lang.String id) Creates a Compartment instance with the given id.
Compartment(java.lang.String id, int level, int version) Creates a Compartment instance from an id, level and version.
Compartment(java.lang.String id, java.lang.String name, int level, int version) Creates a Compartment instance from an id, name, level and version.

Method Summary

Modifier and Type	Method and Description
Compartment	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	containsUndeclaredUnits() Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.lang.String	getCompartmentType() Deprecated. Only defined in SBML Level 2 Versions 2 through 4.
CompartmentType	getCompartmentTypeInstance() Deprecated.
UnitDefinition	getDerivedUnitDefinition() Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.
java.lang.String	getOutside() Returns the outside id of this compartment.
Compartment	getOutsideInstance() Returns the compartment instance which matches the outside id in Model.
java.lang.String	getPredefinedUnitID() Returns the predefined unit identifier for this data type with the current level/version combination.
double	getSize() Returns the size of this compartment.
double	getSpatialDimensions() Returns the spatialDimensions of this Compartment.
double	getSpatialDimensionsAsDouble() Deprecated. use getSpatialDimensions()
java.lang.String	getUnits()
UnitDefinition	getUnitsInstance()
double	getVolume() Deprecated. The volume attribute is only defined in SBML Level 1. Please use getSize().
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults() Initializes the default values using the current Level/Version configuration.
void	initDefaults(int level, int version) Initializes the default values using the current Level/Version configuration.
void	initDefaults(int level, int version, boolean explicit)
boolean	isSetCompartmentType() Returns true if the compartmentID of this compartment is not null.
boolean	isSetCompartmentTypeInstance() Deprecated.
boolean	isSetOutside() Returns true if the outsideID of this compartment is not null.
boolean	isSetOutsideInstance() Returns true if the compartment instance which matches the outsideID of this compartment is not null.
boolean	isSetSize() Returns true if the size of this compartment has been set by a user.
boolean	isSetSpatialDimensions() Returns true if the spatialDimensions of this compartment has been set by a user.
boolean	isSetVolume() Deprecated. The volume attribute is only defined in SBML Level 1. Please use isSetSize()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setCompartmentType(CompartmentType compartmentType) Deprecated.
void	setCompartmentType(java.lang.String compartmentTypeID) Deprecated. Only valid in Level 2.
void	setOutside(Compartment outside) Deprecated.
void	setOutside(java.lang.String outside) Deprecated. since Level 3 Version 1
void	setSize(double size) Sets the size of this compartment to 'size'.
void	setSpatialDimensions(double spatialDimension) Sets the spatialDimensions of this compartment to 'i'.
void	setSpatialDimensions(int spatialDimensions)
void	setSpatialDimensions(short spatialDimensions) Sets the spatialDimensions of this compartment to 'spatialDimensiosn'.
void	setUnits(java.lang.String units) Sets the unitsID of this QuantityWithUnit.
void	setUnits(Unit.Kind unitKind) Sets the unit of this Compartment.
void	setUnits(Unit unit) Sets the Unit of this Compartment.
void	setUnits(UnitDefinition unitDefinition) Set the unit attribute of this Compartment to the given unit definition.
void	setValue(double value) Sets the value of this Quantity.
void	setVolume(double value) Deprecated. This method is only available for SBML Level 1. You should either use setSize(double) or setValue(double).
void	unsetCompartmentType() Sets the compartmentTypeID of this Compartment to null.
void	unsetOutside() Deprecated. since Level 3 Version 1
void	unsetSize() Unsets the value of the 'size' attribute of this Compartment.
void	unsetSpatialDimensions() Sets the spatialDimensions of this compartment to null.
void	unsetVolume() Deprecated. The volume attribute is only defined in SBML Level 1. Please use unsetSize()
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.Symbol

getConstant, isConstant, isSetConstant, setConstant, unsetConstant

Methods inherited from class org.sbml.jsbml.QuantityWithUnit

getValue, isIdMandatory, isSetValue, unsetValue

Methods inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

getDerivedUnits, isPredefinedUnitsID, isSetUnits, isSetUnitsInstance, unsetUnits

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setLevelAndVersion, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageNamespaceAndVersion, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.Quantity

getValue, isSetValue, unsetValue

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isIdMandatory, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBaseWithDerivedUnit

getDerivedUnits

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

logger

private static final transient org.apache.log4j.Logger logger

A Logger for this class.

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

compartmentTypeID

@Deprecated
private java.lang.String compartmentTypeID

Deprecated.

Represents the compartmentType XML attribute of a compartment element. It matches a compartmentType id in the model.

isSetSpatialDimensions

private boolean isSetSpatialDimensions

Helper variable to check if spatial dimensions has been set by the user.

outsideID

@Deprecated
private java.lang.String outsideID

Deprecated.

Represents the outside XML attribute of a compartment element. It matches a compartment id in the model instance.

spatialDimensions

private java.lang.Double spatialDimensions

Represents the spatialDimensions XML attribute of a compartment element.

Constructor Detail

Compartment

public Compartment()

Creates a Compartment instance. By default, if the level is set and is superior or equal to 3, sets the compartmentType, outsideID and spatialDimension to null.

Compartment

public Compartment(Compartment compartment)

Creates a Compartment instance from a given compartment.

Parameters:

compartment - the compartment object to clone.

Compartment

public Compartment(int level,
                   int version)

Creates a Compartment instance from a level and version. By default, if the level is set and is superior or equal to 3, sets the compartmentType, outsideID and spatialDimension to null.

Parameters:

level - the SBML level

version - the SBML level

Compartment

public Compartment(java.lang.String id)

Creates a Compartment instance with the given id.

Parameters:

id - the compartment id.

Compartment

public Compartment(java.lang.String id,
                   int level,
                   int version)

Creates a Compartment instance from an id, level and version. By default, sets the compartmentType, outsideID and spatialDimension to null.

Parameters:

id - the compartment id.

level - the SBML level

version - the SBML level

Compartment

public Compartment(java.lang.String id,
                   java.lang.String name,
                   int level,
                   int version)

Creates a Compartment instance from an id, name, level and version. By default, if the level is set and is superior or equal to 3, sets the compartmentType, outsideID and spatialDimension to null.

Parameters:

id - the compartment id.

name - the compartment name.

level - the SBML level

version - the SBML level

Method Detail

clone

public Compartment clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class Symbol

Returns:

a copy of this object

containsUndeclaredUnits

public boolean containsUndeclaredUnits()

Description copied from interface: SBaseWithDerivedUnit

Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units. A return value of true indicates that the UnitDefinition returned by SBaseWithDerivedUnit.getDerivedUnitDefinition() may not accurately represent the units of the expression.

Specified by:

containsUndeclaredUnits in interface SBaseWithDerivedUnit

Overrides:

containsUndeclaredUnits in class AbstractNamedSBaseWithUnit

Returns:

true if the math expression of this SBaseWithDerivedUnit includes parameters/numbers with undeclared units, false otherwise.

equals

public boolean equals(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class Symbol

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getCompartmentType

@Deprecated
public java.lang.String getCompartmentType()

Deprecated. Only defined in SBML Level 2 Versions 2 through 4.

Returns the compartmentType id of this compartment. Return an empty String if it is not set.

Returns:

the compartmentType id of this compartment. Return an empty String if it is not set.

getCompartmentTypeInstance

@Deprecated
public CompartmentType getCompartmentTypeInstance()

Deprecated.

Returns the compartmentType instance in Model for this compartment compartmentTypeID. Return null if there is no compartmentType instance which matches this compartmentTypeID.

Returns:

the compartmentType instance in Model for this compartment compartmentTypeID. Return null if there is no compartmentType instance which matches this compartmentTypeID.

getDerivedUnitDefinition

public UnitDefinition getDerivedUnitDefinition()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model. If no equivalent unit definition can be found, a new unit definition will be created that is not part of the model but represents the unit of this quantity. If it is not possible to derive a unit for this quantity, null will be returned.

Specified by:

getDerivedUnitDefinition in interface SBaseWithDerivedUnit

Overrides:

getDerivedUnitDefinition in class AbstractNamedSBaseWithUnit

Returns:

a UnitDefinition that represent the derived unit of this quantity, or null if it is not possible to derive a unit.

getOutside

public java.lang.String getOutside()

Returns the outside id of this compartment. Return "" if it is not set.

Returns:

the outside id of this compartment. Return "" if it is not set.

getOutsideInstance

public Compartment getOutsideInstance()

Returns the compartment instance which matches the outside id in Model. Return null if no compartment instance matches the outside id.

Returns:

the compartment instance which matches the outside id in Model. Return null if no compartment instance matches the outside id.

getPredefinedUnitID

public java.lang.String getPredefinedUnitID()

Description copied from class: AbstractNamedSBaseWithUnit

Returns the predefined unit identifier for this data type with the current level/version combination.

Specified by:

getPredefinedUnitID in class AbstractNamedSBaseWithUnit

Returns:

an identifier of a unit in the containing Model. This can be one of the predefined unit identifiers if there are any.

getSize

public double getSize()

Returns the size of this compartment.

Returns:

the size of this compartment.

getSpatialDimensions

public double getSpatialDimensions()

Returns the spatialDimensions of this Compartment. If it is not set and the level of this Compartment is either one or two it returns the default SBML Level 2 value, which is 3. In all other cases, Double.NaN will be returned.

Returns:

the spatialDimensions of this Compartment or 3 if spatialDimensions is not set and level is 1 or 2.

getSpatialDimensionsAsDouble

@Deprecated
public double getSpatialDimensionsAsDouble()

Deprecated. use getSpatialDimensions()

Returns:

getUnits

public java.lang.String getUnits()

Specified by:

getUnits in interface SBaseWithUnit

Overrides:

getUnits in class AbstractNamedSBaseWithUnit

Returns:

the unitsID of this SBaseWithUnit. The empty String if it is not set.

getUnitsInstance

public UnitDefinition getUnitsInstance()

Specified by:

getUnitsInstance in interface SBaseWithUnit

Overrides:

getUnitsInstance in class AbstractNamedSBaseWithUnit

Returns:

The UnitDefinition instance which has the unitsID of this SBaseWithUnit as id. Null if it doesn't exist. In case that the unit of this SBaseWithUnit represents a base Unit, a new UnitDefinition will be created and returned by this method. This new UnitDefinition will only contain the one unit represented by the unit identifier in this SBaseWithUnit. Note that the corresponding model will not contain this UnitDefinition. The identifier of this new UnitDefinition will be set to the same value as the name of the base Unit.

getVolume

@Deprecated
public double getVolume()

Deprecated. The volume attribute is only defined in SBML Level 1. Please use getSize().

Gets the volume of this Compartment This method is identical to getSize(). In SBML Level 1, compartments are always three-dimensional constructs and only have volumes, whereas in SBML Level 2, compartments may be other than three-dimensional and therefore the 'volume' attribute is named 'size' in Level 2. LibSBML provides both getSize() and getVolume() for easier compatibility between SBML Levels.

Returns:

the volume of this Compartment

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class Symbol

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

initDefaults

public void initDefaults()

Initializes the default values using the current Level/Version configuration.

initDefaults

public void initDefaults(int level,
                         int version)

Initializes the default values using the current Level/Version configuration.

Parameters:

level -

version -

initDefaults

public void initDefaults(int level,
                         int version,
                         boolean explicit)

Parameters:

level -

version -

explicit -

isSetCompartmentType

public boolean isSetCompartmentType()

Returns true if the compartmentID of this compartment is not null.

Returns:

true if the compartmentID of this compartment is not null.

isSetCompartmentTypeInstance

@Deprecated
public boolean isSetCompartmentTypeInstance()

Deprecated.

Returns true if the compartmentType instance which matches the compartmentTypeID of this compartment is not null.

Returns:

true if the compartmentType instance which matches the compartmentTypeID of this compartment is not null.

isSetOutside

public boolean isSetOutside()

Returns true if the outsideID of this compartment is not null.

Returns:

true if the outsideID of this compartment is not null.

isSetOutsideInstance

public boolean isSetOutsideInstance()

Returns true if the compartment instance which matches the outsideID of this compartment is not null.

Returns:

true if the compartment instance which matches the outsideID of this compartment is not null.

isSetSize

public boolean isSetSize()

Returns true if the size of this compartment has been set by a user.

Returns:

true if the size of this compartment has been set by a user.

isSetSpatialDimensions

public boolean isSetSpatialDimensions()

Returns true if the spatialDimensions of this compartment has been set by a user.

Returns:

true if the spatialDimensions of this compartment has been set by a user.

isSetVolume

@Deprecated
public boolean isSetVolume()

Deprecated. The volume attribute is only defined in SBML Level 1. Please use isSetSize()

Returns true or false depending on whether this Compartment's 'volume' attribute has been set.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

This method is similar but not identical to isSetSize(). The latter should not be used in the context of SBML Level 1 models because this method (isSetVolume()) performs extra processing to take into account the difference in default values between SBML Levels 1 and 2.

Returns:

true if the 'volume' attribute ('size' in L2) of this Compartment has been set, false otherwise.

See Also:

isSetSize()

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

setCompartmentType

@Deprecated
public void setCompartmentType(CompartmentType compartmentType)

Deprecated.

Sets the compartmentTypeID value of this compartment to the id of 'compartmentType'

Parameters:

compartmentType -

setCompartmentType

@Deprecated
public void setCompartmentType(java.lang.String compartmentTypeID)

Deprecated. Only valid in Level 2.

Sets the compartmentTypeID of this compartment to 'compartmentTypeID'

Parameters:

compartmentTypeID -

Throws:

PropertyNotAvailableException - if Level is not 2.

setOutside

@Deprecated
public void setOutside(Compartment outside)

Deprecated.

Sets the outsideID of this compartment to the id of 'outside'.

Parameters:

outside -

setOutside

@Deprecated
public void setOutside(java.lang.String outside)

Deprecated. since Level 3 Version 1

Sets the outsideID of this compartment to 'outside'.

Parameters:

outside -

Throws:

PropertyNotAvailableException - if Level greater than 2.

setSize

public void setSize(double size)

Sets the size of this compartment to 'size'.

Parameters:

size -

Throws:

PropertyNotAvailableException - in case of Level < 2.

setSpatialDimensions

public void setSpatialDimensions(double spatialDimension)

Sets the spatialDimensions of this compartment to 'i'.

Parameters:

spatialDimension -

Throws:

java.lang.IllegalArgumentException - if spatialDimension < 0 or if spatialDimension > 3

PropertyNotAvailableException - if Level < 2.

setSpatialDimensions

public void setSpatialDimensions(int spatialDimensions)

Parameters:

spatialDimensions -

setSpatialDimensions

public void setSpatialDimensions(short spatialDimensions)

Sets the spatialDimensions of this compartment to 'spatialDimensiosn'.

Parameters:

spatialDimensions -

Throws:

java.lang.IllegalArgumentException - if spatialDimension < 0 or if spatialDimension > 3

setUnits

public void setUnits(java.lang.String units)

Sets the unitsID of this QuantityWithUnit. Only valid unit kind names or identifiers of already existing UnitDefinitions are allowed arguments of this function.

Specified by:

setUnits in interface SBaseWithUnit

Overrides:

setUnits in class AbstractNamedSBaseWithUnit

Parameters:

units - the identifier of an already existing UnitDefinition or an Unit.Kind identifier for the current level/version combination of this unit. Passing a null value to this method is equivalent to calling AbstractNamedSBaseWithUnit.unsetUnits().

Throws:

java.lang.IllegalArgumentException - if the unit is not valid or if spatialDimensions = 0.

setUnits

public void setUnits(Unit unit)

Sets the Unit of this Compartment.

Specified by:

setUnits in interface SBaseWithUnit

Overrides:

setUnits in class AbstractNamedSBaseWithUnit

Parameters:

unit -

Throws:

java.lang.IllegalArgumentException - if spatialDimensions = 0.

setUnits

public void setUnits(Unit.Kind unitKind)

Sets the unit of this Compartment. A new Unit object will be created base on this kind.

Specified by:

setUnits in interface SBaseWithUnit

Overrides:

setUnits in class AbstractNamedSBaseWithUnit

Parameters:

unitKind -

Throws:

java.lang.IllegalArgumentException - if spatialDimensions = 0.

setUnits

public void setUnits(UnitDefinition unitDefinition)

Set the unit attribute of this Compartment to the given unit definition.

Specified by:

setUnits in interface SBaseWithUnit

Overrides:

setUnits in class AbstractNamedSBaseWithUnit

Parameters:

unitDefinition -

Throws:

java.lang.IllegalArgumentException - if spatialDimensions <= 0.

setValue

public void setValue(double value)

Description copied from interface: Quantity

Sets the value of this Quantity. Note that the meaning of the value can be different in all derived classes. In Compartments the value defines its size. In Species the value describes either the initial amount or the initial concentration. Only the class Parameter and LocalParameter really define a value attribute with this name.

Specified by:

setValue in interface Quantity

Overrides:

setValue in class QuantityWithUnit

Parameters:

value - the value to set

setVolume

@Deprecated
public void setVolume(double value)

Deprecated. This method is only available for SBML Level 1. You should either use setSize(double) or setValue(double).

Sets the 'volume' attribute (or 'size' in SBML Level 2) of this Compartment.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

This method is identical to setSize(double) and is provided for compatibility between SBML Level 1 and Level 2.

Parameters:

value - a double representing the volume of this compartment instance in whatever units are in effect for the compartment.

Throws:

PropertyNotAvailableException - if Level is not 1.

unsetCompartmentType

public void unsetCompartmentType()

Sets the compartmentTypeID of this Compartment to null.

unsetOutside

@Deprecated
public void unsetOutside()

Deprecated. since Level 3 Version 1

Sets the outsideID of this compartment to null.

unsetSize

public void unsetSize()

Unsets the value of the 'size' attribute of this Compartment.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

unsetSpatialDimensions

public void unsetSpatialDimensions()

Sets the spatialDimensions of this compartment to null.

unsetVolume

@Deprecated
public void unsetVolume()

Deprecated. The volume attribute is only defined in SBML Level 1. Please use unsetSize()

Unsets the value of the 'volume' attribute of this Compartment.

Some words of explanation about the set/unset/isSet methods: SBML Levels 1 and 2 define certain attributes on some classes of objects as optional. This requires an application to be careful about the distinction between two cases: (1) a given attribute has never been set to a value, and therefore should be assumed to have the SBML-defined default value, and (2) a given attribute has been set to a value, but the value happens to be an empty string. LibSBML supports these distinctions by providing methods to set, unset, and query the status of attributes that are optional. The methods have names of the form setAttribute(...), unsetAttribute(), and isSetAttribute(), where Attribute is the the name of the optional attribute in question.

In SBML Level 1, a Compartment volume has a default value (1.0) and therefore should always be set. In Level 2, 'size' is optional with no default value and as such may or may not be set.

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:

a Map containing the XML attributes of this object.