org.sbml.jsbml

Class Species

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.Species

All Implemented Interfaces:

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

public class Species
extends Symbol

Represents the species XML element of a SBML file.

Since:

0.8

Version:

$Rev: 1968 $

Author:

Andreas Dräger, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	amount True means initial amount is set.
private java.lang.Boolean	boundaryCondition Represents the 'boundaryCondition' attribute of a Species element.
private java.lang.Integer	charge Deprecated.
private java.lang.String	compartmentID Represents the 'compartment' attribute of a Species element.
private java.lang.String	conversionFactorID Represents the 'conversionFactor' attribute of a Species element.
private java.lang.Boolean	hasOnlySubstanceUnits Represents the 'hasOnlySubstanceUnits' attribute of a Species element.
private boolean	isSetBoundaryCondition
private boolean	isSetCharge Boolean value to test if the charge has been set.
private boolean	isSetHasOnlySubstanceUnits
private static org.apache.log4j.Logger	logger A Logger for this class.
private static long	serialVersionUID Generated serial version identifier.
private java.lang.String	spatialSizeUnitsID Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
private java.lang.String	speciesTypeID Deprecated.

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, lv

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
Species() Creates a Species instance.
Species(int level, int version) Creates a Species instance from a level and version.
Species(Species species) Creates a Species instance from a Species.
Species(java.lang.String id)
Species(java.lang.String id, int level, int version) Creates a Species instance from a level and verison.
Species(java.lang.String id, java.lang.String name, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
Species	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.
boolean	getBoundaryCondition()
int	getCharge() Deprecated.
java.lang.String	getCompartment()
Compartment	getCompartmentInstance()
java.lang.String	getConversionFactor()
Parameter	getConversionFactorInstance()
UnitDefinition	getDerivedUnitDefinition() Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.
java.lang.String	getElementName() Returns the XML element name of this object.
boolean	getHasOnlySubstanceUnits()
double	getInitialAmount()
double	getInitialConcentration()
java.lang.String	getPredefinedUnitID() Returns the predefined unit identifier for this data type with the current level/version combination.
java.lang.String	getSpatialSizeUnits() Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
UnitDefinition	getSpatialSizeUnitsInstance() Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
java.lang.String	getSpeciesType() Deprecated. Only valid for SBML Level 2 Versions 2, 3, and 4.
SpeciesType	getSpeciesTypeInstance() Deprecated. Only valid for SBML Level 2 Versions 2, 3, and 4.
java.lang.String	getSubstanceUnits()
UnitDefinition	getSubstanceUnitsInstance()
int	hashCode() Returns a hash code value for this SBase instance.
boolean	hasOnlySubstanceUnits()
void	initDefaults() Initializes the default values using the current Level/Version configuration.
void	initDefaults(int level, int version) Initializes the default values of this Species.
boolean	isBoundaryCondition()
boolean	isHasOnlySubstanceUnits()
boolean	isSetBoundaryCondition()
boolean	isSetCharge()
boolean	isSetCompartment()
boolean	isSetCompartmentInstance()
boolean	isSetConversionFactor()
boolean	isSetConversionFactorInstance()
boolean	isSetHasOnlySubstanceUnits()
boolean	isSetInitialAmount()
boolean	isSetInitialConcentration()
boolean	isSetSpatialSizeUnits() Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
boolean	isSetSpatialSizeUnitsInstance() Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
boolean	isSetSpeciesType() Deprecated.
boolean	isSetSpeciesTypeInstance() Deprecated.
boolean	isSetSubstanceUnits()
boolean	isSetSubstanceUnitsInstance()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setBoundaryCondition(boolean boundaryCondition) Sets the boundaryCondition Boolean.
void	setCharge(int charge) Deprecated. Only defined in SBML Level 1, Version 1 and 2, and Level 2 Version 1. Since Level 2 Version 2 it has been marked as a deprecated property, but has been completely removed in SBML Level 3.
void	setCompartment(Compartment compartment) Sets the compartmentID of this Species to the id of 'compartment'.
void	setCompartment(java.lang.String compartment) Sets the compartmentID of this Species to 'compartment'.
void	setConversionFactor(Parameter conversionFactor) Sets the conversionFactorID of this Species to the id of 'conversionFactor'.
void	setConversionFactor(java.lang.String conversionFactorID) Sets the conversionFactorID of this Species to 'conversionFactorID'.
void	setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits) Sets hasOnlySubstanceUnits Boolean
void	setInitialAmount(double initialAmount) Sets the initialAmount of this Species.
void	setInitialConcentration(double initialConcentration) Sets the initialConcentration of this Species.
void	setSpatialSizeUnits(java.lang.String spatialSizeUnits) Deprecated. This property is only valid for SBML Level 2 Versions 1 and 2.
void	setSpatialSizeUnits(UnitDefinition spatialSizeUnits) Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
void	setSpeciesType(SpeciesType speciesType) Deprecated.
void	setSpeciesType(java.lang.String speciesType) Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.
void	setSubstanceUnits(java.lang.String unit) Sets the substanceUnitsID to 'unit'.
void	setSubstanceUnits(Unit.Kind unitKind) Sets the substanceUnits.
void	setSubstanceUnits(Unit unit) Sets the substanceUnits.
void	setSubstanceUnits(UnitDefinition units) Sets the substanceUnitsID to the id of 'units'.
void	unsetCharge() Deprecated.
void	unsetCompartment() Remove the reference to a comparmtent.
void	unsetConversionFactor() Unsets the conversionFactorID of this Species.
void	unsetInitialAmount() Unsets the initialAmount of this Species.
void	unsetInitialConcentration() Unsets the initialConcentration of this Species.
void	unsetSpatialSizeUnits() Deprecated. Only valid for SBML Level 2 Versions 1 and 2.
void	unsetSubstanceUnits() Unsets the substanceUnits of this Species.
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, setValue, unsetValue

Methods inherited from class org.sbml.jsbml.AbstractNamedSBaseWithUnit

getDerivedUnits, getUnits, getUnitsInstance, isPredefinedUnitsID, isSetUnits, isSetUnitsInstance, setUnits, setUnits, setUnits, setUnits, unsetUnits

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

checkIdentifier, getId, getName, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setLevelAndVersion, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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, 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, setValue, 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, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

logger

private static final org.apache.log4j.Logger logger

A Logger for this class.

amount

private boolean amount

True means initial amount is set. False means that an initial concentration is set.

boundaryCondition

private java.lang.Boolean boundaryCondition

Represents the 'boundaryCondition' attribute of a Species element.

charge

@Deprecated
private java.lang.Integer charge

Deprecated.

Represents the 'charge' attribute of a Species element.

compartmentID

private java.lang.String compartmentID

Represents the 'compartment' attribute of a Species element.

conversionFactorID

private java.lang.String conversionFactorID

Represents the 'conversionFactor' attribute of a Species element.

hasOnlySubstanceUnits

private java.lang.Boolean hasOnlySubstanceUnits

Represents the 'hasOnlySubstanceUnits' attribute of a Species element.

isSetBoundaryCondition

private boolean isSetBoundaryCondition

isSetCharge

private boolean isSetCharge

Boolean value to test if the charge has been set.

isSetHasOnlySubstanceUnits

private boolean isSetHasOnlySubstanceUnits

spatialSizeUnitsID

@Deprecated
private java.lang.String spatialSizeUnitsID

Deprecated. Only valid for SBML Level 2 Versions 1 and 2.

Represents the 'spatialSizeUnits' attribute of a Species element.

speciesTypeID

@Deprecated
private java.lang.String speciesTypeID

Deprecated.

Represents the 'speciesType' attribute of a Species element.

Constructor Detail

Species

public Species()

Creates a Species instance. By default, the charge, compartmentID, speciesTypeID, conversionFactorID, hasOnlySubstanceUnits, boundaryCondition are null.

Species

public Species(int level,
       int version)

Creates a Species instance from a level and version. By default, the charge, compartmentID, speciesTypeID, conversionFactorID, hasOnlySubstanceUnits, boundaryCondition are null.

Parameters:

level -

version -

Species

public Species(Species species)

Creates a Species instance from a Species.

Parameters:

species -

Species

public Species(java.lang.String id)

Parameters:

id -

Species

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

Creates a Species instance from a level and verison. By default, the charge, compartmentID, speciesTypeID, conversionFactorID, hasOnlySubstanceUnits, boundaryCondition are null.

Parameters:

id -

level -

version -

Species

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

Parameters:

id -

name -

level -

version -

Method Detail

clone

public Species 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.

getBoundaryCondition

public boolean getBoundaryCondition()

Returns:

the boundaryCondition Boolean of this Species.

getCharge

@Deprecated
public int getCharge()

Deprecated.

Returns:

the charge value of this Species if it is set, 0 otherwise.

getCompartment

public java.lang.String getCompartment()

Returns:

the compartmentID of this Species. The empty String if it is not set.

getCompartmentInstance

public Compartment getCompartmentInstance()

Returns:

The Compartment instance which as the compartmentID of this Species as id. Null if it doesn't exist.

getConversionFactor

public java.lang.String getConversionFactor()

Returns:

the conversionFactorID of this Species.

getConversionFactorInstance

public Parameter getConversionFactorInstance()

Returns:

the Parameter instance which has the conversionFactorID of this Species as id, null if it doesn't exist.

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.

getElementName

public java.lang.String getElementName()

Description copied from interface: SBase

Returns the XML element name of this object.

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class AbstractSBase

Returns:

the XML element name of this object.

getHasOnlySubstanceUnits

public boolean getHasOnlySubstanceUnits()

Returns:

the hasOnlySubstanceUnits Boolean of this Species.

getInitialAmount

public double getInitialAmount()

Returns:

the initialAmount of this Species if it has been set, o otherwise.

getInitialConcentration

public double getInitialConcentration()

Returns:

the initialConcentration of this Species if it has been set, o otherwise.

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.

getSpatialSizeUnits

@Deprecated
public java.lang.String getSpatialSizeUnits()

Deprecated. Only valid for SBML Level 2 Versions 1 and 2.

If determined, this method first checks the explicitly set spatial size units of this Species. If no such value is defined, it will return the units of the surrounding Compartment. Only if this is also not possible, an empty String will be returned.

Returns:

the spatialSizeUnits of this Species.

getSpatialSizeUnitsInstance

@Deprecated
public UnitDefinition getSpatialSizeUnitsInstance()

Deprecated. Only valid for SBML Level 2 Versions 1 and 2.

Determines the spatial units of this Species. If the spatial units have been set explicitly using spatialSizeUnitsID the corresponding UnitDefinition from the Model to which this Species belongs will be returned. Otherwise, the size unit from the surrounding Compartment of this Species will be returned. If this also fails, null will be returned.

Returns:

The UnitDefinition instance which as the spatialSizeUnitsID of this Species as id or the size unit of the surrounding Compartment. null if it doesn't exist.

getSpeciesType

@Deprecated
public java.lang.String getSpeciesType()

Deprecated. Only valid for SBML Level 2 Versions 2, 3, and 4.

Returns:

the speciesTypeID of this Species. The empty String if it is not set.

getSpeciesTypeInstance

@Deprecated
public SpeciesType getSpeciesTypeInstance()

Deprecated. Only valid for SBML Level 2 Versions 2, 3, and 4.

Returns:

the SpeciesType instance which has the speciesTypeID of this Species as id. Null if it doesn't exist.

getSubstanceUnits

public java.lang.String getSubstanceUnits()

Returns:

the substanceUnitsID of this Species.

getSubstanceUnitsInstance

public UnitDefinition getSubstanceUnitsInstance()

Returns:

The UnitsDefinition instance which has the substanceUnistID of this Species as id.

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()

hasOnlySubstanceUnits

public boolean hasOnlySubstanceUnits()

Returns:

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 of this Species.

isBoundaryCondition

public boolean isBoundaryCondition()

Returns:

the value of the boundaryCondition Boolean if it is set, false otherwise.

isHasOnlySubstanceUnits

public boolean isHasOnlySubstanceUnits()

Returns:

the value of the hasOnlySubstanceUnits Boolean if it is set, false otherwise.

isSetBoundaryCondition

public boolean isSetBoundaryCondition()

Returns:

true if the boundaryCondition of this Species is not null.

isSetCharge

public boolean isSetCharge()

Returns:

true if the charge of this Species if not null.

isSetCompartment

public boolean isSetCompartment()

Returns:

true if the compartmentID of this Species is not null.

isSetCompartmentInstance

public boolean isSetCompartmentInstance()

Returns:

true if the Compartment instance which has the compartmentID of this Species as id is not null.

isSetConversionFactor

public boolean isSetConversionFactor()

Returns:

true if the conversionFactorID of this Species is not null.

isSetConversionFactorInstance

public boolean isSetConversionFactorInstance()

Returns:

true if the Parameter which has the conversionFactorID of this Species as id is not null.

isSetHasOnlySubstanceUnits

public boolean isSetHasOnlySubstanceUnits()

Returns:

true if the hasOnlySubstanceUnits of this Species is not null.

isSetInitialAmount

public boolean isSetInitialAmount()

Returns:

true if an initial amount has been set for this species.

isSetInitialConcentration

public boolean isSetInitialConcentration()

Returns:

true if an initial concentration has been set for this species.

isSetSpatialSizeUnits

@Deprecated
public boolean isSetSpatialSizeUnits()

Deprecated. Only valid for SBML Level 2 Versions 1 and 2.

Returns:

true if the spatialSizeUnits of this Species is not null.

isSetSpatialSizeUnitsInstance

@Deprecated
public boolean isSetSpatialSizeUnitsInstance()

Deprecated. Only valid for SBML Level 2 Versions 1 and 2.

Returns:

true if the UnitDefinition which has the spatialSizeUnitsID of this Species as id is not null.

isSetSpeciesType

@Deprecated
public boolean isSetSpeciesType()

Deprecated.

Returns:

true if the speciesTypeID of this Species is not null.

isSetSpeciesTypeInstance

@Deprecated
public boolean isSetSpeciesTypeInstance()

Deprecated.

Returns:

true if the SpeciesType instance which has the speciesTypeID of this Species as id is not null.

isSetSubstanceUnits

public boolean isSetSubstanceUnits()

Returns:

true if the substanceUnitsID of this species is not null.

isSetSubstanceUnitsInstance

public boolean isSetSubstanceUnitsInstance()

Returns:

true if the UnitDefinition which has the substanceUnitsID of this Species as id is not null.

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 AbstractNamedSBase

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.

setBoundaryCondition

public void setBoundaryCondition(boolean boundaryCondition)

Sets the boundaryCondition Boolean.

Parameters:

boundaryCondition -

setCharge

@Deprecated
public void setCharge(int charge)

Deprecated. Only defined in SBML Level 1, Version 1 and 2, and Level 2 Version 1. Since Level 2 Version 2 it has been marked as a deprecated property, but has been completely removed in SBML Level 3.

Sets the charge of this Species.

Parameters:

charge -

Throws:

PropertyNotAvailableException - if Level >= 3.

setCompartment

public void setCompartment(Compartment compartment)

Sets the compartmentID of this Species to the id of 'compartment'.

Parameters:

compartment -

setCompartment

public void setCompartment(java.lang.String compartment)

Sets the compartmentID of this Species to 'compartment'.

Parameters:

compartment -

setConversionFactor

public void setConversionFactor(Parameter conversionFactor)

Sets the conversionFactorID of this Species to the id of 'conversionFactor'. This is only possible if Level >= 3.

Parameters:

conversionFactor -

setConversionFactor

public void setConversionFactor(java.lang.String conversionFactorID)

Sets the conversionFactorID of this Species to 'conversionFactorID'. This is only possible if Level >= 3.

Parameters:

conversionFactorID -

Throws:

PropertyNotAvailableException - if Level < 3.

setHasOnlySubstanceUnits

public void setHasOnlySubstanceUnits(boolean hasOnlySubstanceUnits)

Sets hasOnlySubstanceUnits Boolean

Parameters:

hasOnlySubstanceUnits -

Throws:

PropertyNotAvailableException - if Level < 2.

setInitialAmount

public void setInitialAmount(double initialAmount)

Sets the initialAmount of this Species.

Parameters:

initialAmount -

setInitialConcentration

public void setInitialConcentration(double initialConcentration)

Sets the initialConcentration of this Species.

Parameters:

initialConcentration -

setSpatialSizeUnits

@Deprecated
public void setSpatialSizeUnits(java.lang.String spatialSizeUnits)
                         throws PropertyNotAvailableException,
                                SBMLException

Deprecated. This property is only valid for SBML Level 2 Versions 1 and 2.

Sets the spatialSizeUnitsID of this Species to 'spatialSizeUnits'.

Parameters:

spatialSizeUnits -

Throws:

PropertyNotAvailableException - for inapropriate Level/Version combinations.

SBMLException - in case that hasOnlySubstanceUnits() is set to true or the spatial dimensions of the surrounding compartment are zero.

setSpatialSizeUnits

@Deprecated
public void setSpatialSizeUnits(UnitDefinition spatialSizeUnits)
                         throws PropertyNotAvailableException,
                                SBMLException

Deprecated. Only valid for SBML Level 2 Versions 1 and 2.

Sets the spatialSizeUnitsID of this Species to the id of 'spatialSizeUnits'.

Parameters:

spatialSizeUnits -

Throws:

PropertyNotAvailableException - for inapropriate Level/Version combinations.

SBMLException - in case that hasOnlySubstanceUnits() is set to true or the spatial dimensions of the surrounding compartment are zero.

setSpeciesType

@Deprecated
public void setSpeciesType(SpeciesType speciesType)

Deprecated.

Sets the speciesTypeID of this Species to the id of 'speciesType'.

Parameters:

speciesType -

setSpeciesType

@Deprecated
public void setSpeciesType(java.lang.String speciesType)

Deprecated. Only valid in SBML Level 2 for Versions 2 through 4.

Sets the speciesTypeID of this Species to 'speciesType'.

Parameters:

speciesType -

Throws:

PropertyNotAvailableException - for inapropriate Level/Version combinations.

setSubstanceUnits

public void setSubstanceUnits(java.lang.String unit)

Sets the substanceUnitsID to 'unit'.

Parameters:

unit -

setSubstanceUnits

public void setSubstanceUnits(Unit unit)

Sets the substanceUnits.

Parameters:

unit -

setSubstanceUnits

public void setSubstanceUnits(Unit.Kind unitKind)

Sets the substanceUnits.

Parameters:

unitKind -

setSubstanceUnits

public void setSubstanceUnits(UnitDefinition units)

Sets the substanceUnitsID to the id of 'units'.

Parameters:

units -

unsetCharge

@Deprecated
public void unsetCharge()

Deprecated.

Unsets the charge of this Species

unsetCompartment

public void unsetCompartment()

Remove the reference to a comparmtent.

unsetConversionFactor

public void unsetConversionFactor()

Unsets the conversionFactorID of this Species.

unsetInitialAmount

public void unsetInitialAmount()

Unsets the initialAmount of this Species.

unsetInitialConcentration

public void unsetInitialConcentration()

Unsets the initialConcentration of this Species.

unsetSpatialSizeUnits

@Deprecated
public void unsetSpatialSizeUnits()

Deprecated. Only valid for SBML Level 2 Versions 1 and 2.

Unsets the spatialSizeUnits of this Species

unsetSubstanceUnits

public void unsetSubstanceUnits()

Unsets the substanceUnits of this Species.

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 AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.