org.sbml.jsbml

Class SpeciesReference

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.SimpleSpeciesReference

org.sbml.jsbml.SpeciesReference

All Implemented Interfaces:

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

public class SpeciesReference
extends SimpleSpeciesReference
implements Variable

Represents the speciesReference XML element of a SBML file.

Since:

0.8

Version:

$Rev$

Author:

Andreas Dräger, Marine Dumousseau, Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.Boolean	constant Represents the 'constant' XML attribute of this SpeciesReference.
private java.lang.Integer	denominator Represents the 'denominator' XML attribute of this SpeciesReference.
private static java.lang.String	ILLEGAL_STOCHIOMETRY_VALUE Message to be displayed in case that an illegal stoichiometric value has been set.
private boolean	isSetConstant
private boolean	isSetDenominator Boolean value to know if the SpeciesReference denominator has been set.
private boolean	isSetStoichiometry
private static long	serialVersionUID Generated serial version identifier.
private java.lang.Double	stoichiometry Represents the 'stoichiometry' XML attribute of this SpeciesReference.
private StoichiometryMath	stoichiometryMath Deprecated.

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
SpeciesReference() Creates a SpeciesReference instance.
SpeciesReference(int level, int version) Creates a SpeciesReference instance.
SpeciesReference(Species species) Creates a SpeciesReference instance from a Species.
SpeciesReference(SpeciesReference speciesReference) Creates a SpeciesReference instance from a given SpeciesReference.
SpeciesReference(java.lang.String id) Creates a SpeciesReference instance.
SpeciesReference(java.lang.String id, int level, int version) Creates a SpeciesReference instance.
SpeciesReference(java.lang.String id, java.lang.String name, int level, int version) Creates a SpeciesReference instance.

Method Summary

Modifier and Type	Method and Description
SpeciesReference	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.
StoichiometryMath	createStoichiometryMath(ASTNode math) Deprecated. since SBML Level 3 this should not be used anymore.
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	getAllowsChildren()
double	getCalculatedStoichiometry() This method computes the fraction of the stoichiometry and the denominator.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
boolean	getConstant()
int	getDenominator() Deprecated. Use for Level 1 only.
UnitDefinition	getDerivedUnitDefinition() Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.
java.lang.String	getDerivedUnits() Derives the unit of this quantity.
java.lang.String	getElementName() Returns the XML element name of this object.
double	getStoichiometry()
StoichiometryMath	getStoichiometryMath() Deprecated. since SBML Level 3 this should not be used anymore.
double	getValue() Returns the value of this Quantity.
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 of this SpeciesReference.
void	initDefaults(int level, int version, boolean explicit)
boolean	isConstant()
boolean	isSetConstant()
boolean	isSetDenominator()
boolean	isSetStoichiometry()
boolean	isSetStoichiometryMath() Deprecated. since SBML L3V1
boolean	isSetValue() Returns true if the value of this Quantity is set.
java.lang.String	printSpeciesReference() Human-readable representation of this reference.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setConstant(boolean constant) Sets the constant boolean of this Variable.
void	setDenominator(int denominator) Deprecated.
void	setStoichiometry(double stoichiometry) Sets the stoichiometry of this SpeciesReference.
void	setStoichiometryMath(StoichiometryMath math) Deprecated.
void	setValue(double value) Sets the value of this Quantity.
void	unsetConstant() With this method the constant property of this variable will be set to an undefined state.
void	unsetStoichiometry() Unsets the stoichiometry property of this element.
boolean	unsetStoichiometryMath() Deprecated.
void	unsetValue() Unsets the value of this Quantity.
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.SimpleSpeciesReference

getSpecies, getSpeciesInstance, isIdMandatory, isSetSpecies, isSetSpeciesInstance, setSpecies, setSpecies

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, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, 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.NamedSBase

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

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, 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, getIndex, getParent, isLeaf

Field Detail

ILLEGAL_STOCHIOMETRY_VALUE

private static final java.lang.String ILLEGAL_STOCHIOMETRY_VALUE

Message to be displayed in case that an illegal stoichiometric value has been set.

See Also:

Constant Field Values

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

constant

private java.lang.Boolean constant

Represents the 'constant' XML attribute of this SpeciesReference.

denominator

private java.lang.Integer denominator

Represents the 'denominator' XML attribute of this SpeciesReference.

isSetConstant

private boolean isSetConstant

isSetDenominator

private boolean isSetDenominator

Boolean value to know if the SpeciesReference denominator has been set.

isSetStoichiometry

private boolean isSetStoichiometry

stoichiometry

private java.lang.Double stoichiometry

Represents the 'stoichiometry' XML attribute of this SpeciesReference.

stoichiometryMath

@Deprecated
private StoichiometryMath stoichiometryMath

Deprecated.

Contains the MathML expression for the stoichiometry of this SpeciesReference.

Constructor Detail

SpeciesReference

public SpeciesReference()

Creates a SpeciesReference instance. By default, if the level is superior or equal to 3, the constant, stoichiometryMath and stoichiometry are null.

SpeciesReference

public SpeciesReference(int level,
                        int version)

Creates a SpeciesReference instance.

Parameters:

level - the SBML level

version - the SBML version

SpeciesReference

public SpeciesReference(Species species)

Creates a SpeciesReference instance from a Species. By default, if the level is superior or equal to 3, the constant, stoichiometryMath and stoichiometry are null.

Parameters:

species -

SpeciesReference

public SpeciesReference(SpeciesReference speciesReference)

Creates a SpeciesReference instance from a given SpeciesReference.

Parameters:

speciesReference -

SpeciesReference

public SpeciesReference(java.lang.String id)

Creates a SpeciesReference instance.

Parameters:

id -

SpeciesReference

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

Creates a SpeciesReference instance.

Parameters:

id -

level - the SBML level

version - the SBML version

SpeciesReference

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

Creates a SpeciesReference instance.

Parameters:

id -

name -

level - the SBML level

version - the SBML version

Method Detail

clone

public SpeciesReference 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 AbstractSBase

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

Returns:

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

createStoichiometryMath

@Deprecated
public StoichiometryMath createStoichiometryMath(ASTNode math)

Deprecated. since SBML Level 3 this should not be used anymore.

Parameters:

math -

Returns:

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 SimpleSpeciesReference

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.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getCalculatedStoichiometry

public double getCalculatedStoichiometry()

This method computes the fraction of the stoichiometry and the denominator. Actually, the denominator is only defined in SBML Level 1. For convenience, this method might be usefull.

Returns:

The fraction between stoichiometry and denominator.

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

getConstant

public boolean getConstant()

Specified by:

getConstant in interface Variable

Returns:

the constant boolean of this variable.

getDenominator

@Deprecated
public int getDenominator()

Deprecated. Use for Level 1 only.

Returns:

the denominator value if it is set, 1 otherwise

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

Returns:

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

getDerivedUnits

public java.lang.String getDerivedUnits()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity. If the model that contains this quantity already contains a unit that is equivalent to the derived unit, the corresponding identifier will be returned. In case that the unit cannot be derived or that no equivalent unit exists within the model, or if the model has not been defined yet, null will be returned. In case that this quantity represents a basic Unit.Kind this method will return the String representation of this Unit.Kind.

Specified by:

getDerivedUnits in interface SBaseWithDerivedUnit

Returns:

a String that represent the id of a UnitDefinition. This UnitDefinition represent the derived unit of this quantity. If it is not possible to derive a unit for this quantity or if no equivalent UnitDefinition can be found in the Model, null is returned.

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.

getStoichiometry

public double getStoichiometry()

Returns:

the stoichiometry value of this SpeciesReference if it is set, otherwise, depending on the Level attribute, 1 for Level < 3 or Double.NaN.

getStoichiometryMath

@Deprecated
public StoichiometryMath getStoichiometryMath()

Deprecated. since SBML Level 3 this should not be used anymore.

Returns:

the stoichiometryMath of this SpeciesReference. Can be null if the stoichiometryMath is not set.

getValue

public double getValue()

Description copied from interface: Quantity

Returns the value of this Quantity. In Compartments the value is its size, in Species the value defines its initial amount or concentration, and in Parameters and LocalParameters this returns the value attribute from SBML.

Specified by:

getValue in interface Quantity

Returns:

the value

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 SimpleSpeciesReference

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 of this SpeciesReference.

Parameters:

level -

version -

initDefaults

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

Parameters:

level -

version -

explicit -

See Also:

Unit.initDefaults(int, int, boolean)

isConstant

public boolean isConstant()

Specified by:

isConstant in interface Variable

Returns:

the constant value if it is set, false otherwise.

isSetConstant

public boolean isSetConstant()

Specified by:

isSetConstant in interface Variable

Returns:

true if the constant boolean of this Variable is not null.

isSetDenominator

public boolean isSetDenominator()

Returns:

true if the denominator is not null.

isSetStoichiometry

public boolean isSetStoichiometry()

Returns:

true if the stoichiometry of this SpeciesReference has been explicitly set, false if it is not set at all or only a default value is available.

isSetStoichiometryMath

@Deprecated
public boolean isSetStoichiometryMath()

Deprecated. since SBML L3V1

Returns:

true if the StoichiometryMath of this SpeciesReference is not null.

isSetValue

public boolean isSetValue()

Description copied from interface: Quantity

Returns true if the value of this Quantity is set.

Specified by:

isSetValue in interface Quantity

Returns:

true if the value of this Quantity is set.

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 SimpleSpeciesReference

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.

setConstant

public void setConstant(boolean constant)

Description copied from interface: Variable

Sets the constant boolean of this Variable.

Specified by:

setConstant in interface Variable

setDenominator

@Deprecated
public void setDenominator(int denominator)

Deprecated.

Sets the denominator of this SpeciesReference.

Parameters:

denominator -

setStoichiometry

public void setStoichiometry(double stoichiometry)

Sets the stoichiometry of this SpeciesReference.

Parameters:

stoichiometry -

setStoichiometryMath

@Deprecated
public void setStoichiometryMath(StoichiometryMath math)

Deprecated.

Sets the StoichiometryMath of this SpeciesReference.

Parameters:

math -

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

Parameters:

value - the value to set

printSpeciesReference

public java.lang.String printSpeciesReference()

Description copied from class: SimpleSpeciesReference

Human-readable representation of this reference.

Overrides:

printSpeciesReference in class SimpleSpeciesReference

Returns:

unsetConstant

public void unsetConstant()

Description copied from interface: Variable

With this method the constant property of this variable will be set to an undefined state.

Specified by:

unsetConstant in interface Variable

unsetStoichiometry

public void unsetStoichiometry()

Unsets the stoichiometry property of this element.

unsetStoichiometryMath

@Deprecated
public boolean unsetStoichiometryMath()

Deprecated.

Returns:

unsetValue

public void unsetValue()

Description copied from interface: Quantity

Unsets the value of this Quantity.

Specified by:

unsetValue in interface Quantity

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 SimpleSpeciesReference

Returns:

a Map containing the XML attributes of this object.