Reaction

java.lang.Object
- org.sbml.jsbml.AbstractTreeNode
- - org.sbml.jsbml.AbstractSBase
  - - org.sbml.jsbml.AbstractNamedSBase
    - - org.sbml.jsbml.Reaction

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, CallableSBase, NamedSBase, NamedSBaseWithDerivedUnit, SBase, SBaseWithDerivedUnit, UniqueNamedSBase, TreeNodeWithChangeSupport
```
public class Reaction
extends AbstractNamedSBase
implements CallableSBase, UniqueNamedSBase
```
Represents the reaction XML element of a SBML file.

Since:

0.8

Version:

$Rev: 1966 $

Author:

Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`private java.lang.String`	`compartmentID` Represents the 'compartment' XML attribute of a reaction element.
`private java.lang.Boolean`	`fast` Represents the 'fast' XML attribute of a reaction element.
`private boolean`	`isSetFast` Checks whether the `fast` attribute has been set by using a default or by changing its value.
`private boolean`	`isSetReversible` Checks whether the `reversible` attribute has been set by using a default or by changing its value.
`private KineticLaw`	`kineticLaw` Represents the 'kineticLaw' XML subNode of a reaction element.
`private ListOf<ModifierSpeciesReference>`	`listOfModifiers` Represents the 'listOfModifiers' XML subNode of a reaction element.
`private ListOf<SpeciesReference>`	`listOfProducts` Represents the 'listOfProducts' XML subNode of a reaction element.
`private ListOf<SpeciesReference>`	`listOfReactants` Represents the 'listOfReactants' XML subNode of a reaction element.
`private java.lang.Boolean`	`reversible` Represents the 'reversible' XML attribute of a reaction element.
`private static long`	`serialVersionUID` Generated serial version identifier.

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
`Reaction()` Creates a Reaction instance.
`Reaction(int level, int version)` Creates a new Reaction instance from a given SBML level and version.
`Reaction(Reaction reaction)` Creates a Reaction instance from a given reaction.
`Reaction(java.lang.String id)`
`Reaction(java.lang.String id, int level, int version)` Creates a `Reaction` instance from an id, level and version.

Method Summary

Methods
Modifier and Type	Method and Description
`boolean`	`addModifier(ModifierSpeciesReference modspecref)` Adds a `ModifierSpeciesReference` instance to this `Reaction`.
`boolean`	`addProduct(SpeciesReference specref)` Adds a `SpeciesReference` instance to the listOfProducts of this `Reaction`.
`boolean`	`addReactant(SpeciesReference specref)` Adds a `SpeciesReference` instance to the listOfReactants of this `Reaction`.
`Reaction`	`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.
`KineticLaw`	`createKineticLaw()` Creates a new `KineticLaw` object, installs it as this `Reaction`'s 'kineticLaw' sub-element, and returns it.
`ModifierSpeciesReference`	`createModifier()` Creates a new `ModifierSpeciesReference`, adds it to this `Reaction`'s list of modifiers and returns it.
`ModifierSpeciesReference`	`createModifier(Species species)` Creates a new `ModifierSpeciesReference`, which points to the given `Species`, adds it to this `Reaction`'s `listOfModifiers`, and returns a pointer to it.
`ModifierSpeciesReference`	`createModifier(java.lang.String id)`
`ModifierSpeciesReference`	`createModifier(java.lang.String id, Species species)` Creates a new `ModifierSpeciesReference` with the given `id` as its identifier, which points to the given `Species`, adds it to this `Reaction`'s `listOfModifiers`, and returns a pointer to it.
`ModifierSpeciesReference`	`createModifier(java.lang.String id, java.lang.String species)` Creates a new `ModifierSpeciesReference` with the given `id` as its identifier, which points to the `Species` with the given `id`, adds it to this `Reaction`'s `listOfModifiers`, and returns a pointer to it.
`SpeciesReference`	`createProduct()` Creates a new `SpeciesReference`, adds it to this `Reaction`'s `listOfProducts` and returns it.
`SpeciesReference`	`createProduct(Species species)` Creates a new `SpeciesReference`, which points to the given `Species`, adds it to this `Reaction`'s `listOfProducts` and returns a pointer to it.
`SpeciesReference`	`createProduct(java.lang.String id)`
`SpeciesReference`	`createProduct(java.lang.String id, Species species)` Creates a new `SpeciesReference` with the given `id` as its identifier, which points to the given `Species`, adds it to this `Reaction`'s `listOfProducts` and returns a pointer to it.
`SpeciesReference`	`createProduct(java.lang.String id, java.lang.String species)`
`SpeciesReference`	`createReactant()` Creates a new `SpeciesReference`, adds it to this `Reaction`'s `listOfReactants` and returns it.
`SpeciesReference`	`createReactant(Species species)` Creates a new `SpeciesReference` to the given `Species` and adds it to the `listOfReactants`.
`SpeciesReference`	`createReactant(java.lang.String id)` Creates a new `SpeciesReference` with the given identifier and adds it to this `Reaction`'s `listOfReactants`.
`SpeciesReference`	`createReactant(java.lang.String id, Species species)` Creates a new `SpeciesReference` with the given `id` as identifier, which points to the given `Species` and adds it to the `listOfReactants`.
`SpeciesReference`	`createReactant(java.lang.String id, java.lang.String species)`
`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()`
`javax.swing.tree.TreeNode`	`getChildAt(int index)`
`int`	`getChildCount()`
`java.lang.String`	`getCompartment()` Only available if Level >= 3.
`Compartment`	`getCompartmentInstance()`
`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.
`boolean`	`getFast()`
`KineticLaw`	`getKineticLaw()`
`ListOf<ModifierSpeciesReference>`	`getListOfModifiers()`
`ListOf<SpeciesReference>`	`getListOfProducts()`
`ListOf<SpeciesReference>`	`getListOfReactants()`
`ModifierSpeciesReference`	`getModifier(int i)`
`ModifierSpeciesReference`	`getModifier(java.lang.String id)` Searches the first `ModifierSpeciesReference` in the `listOfModifiers` of this `Reaction` with the given identifier.
`int`	`getModifierCount()`
`ModifierSpeciesReference`	`getModifierForSpecies(java.lang.String id)` Returns the first `ModifierSpeciesReference` in the `listOfModifiers` of this `Reaction` whose 'species' attribute points to a `Species` with the given identifier.
`int`	`getNumModifiers()`
`int`	`getNumProducts()`
`int`	`getNumReactants()`
`ListOf<Reaction>`	`getParent()` This is equivalent to calling `AbstractSBase.getParentSBMLObject()`, but this method is needed for `TreeNode`.
`SpeciesReference`	`getProduct(int i)`
`SpeciesReference`	`getProduct(java.lang.String id)` Searches the first `SpeciesReference` in the listOfProducts of this `Reaction` with the given identifier.
`int`	`getProductCount()`
`SpeciesReference`	`getProductForSpecies(java.lang.String id)` Returns the first `SpeciesReference` in the `listOfProducts` of this `Reaction` whose 'species' attribute points to a `Species` with the given identifier.
`SpeciesReference`	`getReactant(int i)`
`SpeciesReference`	`getReactant(java.lang.String id)` Searches the first `SpeciesReference` in the listOfReactants of this `Reaction` with the given identifier.
`int`	`getReactantCount()`
`SpeciesReference`	`getReactantForSpecies(java.lang.String id)` Returns the first `SpeciesReference` in the `listOfReactants` of this `Reaction` whose 'species' attribute points to a `Species` with the given identifier.
`boolean`	`getReversible()`
`int`	`hashCode()` Returns a hash code value for this `SBase` instance.
`boolean`	`hasModifier(Species s)`
`boolean`	`hasProduct(Species s)`
`boolean`	`hasReactant(Species s)`
`void`	`initDefaults()` Initializes the default values using the current Level/Version configuration.
`void`	`initDefaults(int level, int version)` Initializes the default variables of this Reaction.
`boolean`	`involves(Species s)` Convenient test if the given species takes part in this reaction as a reactant, product, or modifier.
`boolean`	`isFast()`
`boolean`	`isIdMandatory()` This method can be used to query if the identifier of this `NamedSBase` is required to be defined (i.e., not `null`) in the definition of SBML.
`boolean`	`isReversible()`
`boolean`	`isSetCompartment()`
`boolean`	`isSetCompartmentInstance()`
`boolean`	`isSetFast()`
`boolean`	`isSetKineticLaw()`
`boolean`	`isSetListOfModifiers()`
`boolean`	`isSetListOfProducts()`
`boolean`	`isSetListOfReactants()`
`boolean`	`isSetReversible()`
`boolean`	`readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)` Sets the given attribute in this `SBase`.
`private boolean`	`references(ListOf<? extends SimpleSpeciesReference> list, Species s)` Checks whether the given list references the given species.
`private <T extends SimpleSpeciesReference> T`	`remove(ListOf<T> list, java.lang.String id)`
`ModifierSpeciesReference`	`removeModifier(int i)` Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns it.
`boolean`	`removeModifier(ModifierSpeciesReference modspecref)` Removes the ModifierSpeciesReference 'modspecref' from this Reaction.
`ModifierSpeciesReference`	`removeModifier(java.lang.String id)` Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in the list of modifiers in this Reaction and returns it.
`SpeciesReference`	`removeProduct(int i)` Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns it.
`void`	`removeProduct(SpeciesReference specref)` Removes the SpeciesReference 'modspecref' from the listOfProducts of this Reaction.
`SpeciesReference`	`removeProduct(java.lang.String id)` Removes the product species (SpeciesReference object) having the given 'species' attribute in the list of products in this Reaction and returns it.
`SpeciesReference`	`removeReactant(int i)` Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns it.
`boolean`	`removeReactant(SpeciesReference specref)` Removes the SpeciesReference 'modspecref' from the listOfReactants of this Reaction.
`SpeciesReference`	`removeReactant(java.lang.String id)` Removes the reactant species (SpeciesReference object) having the given 'species' attribute in the list of reactants in this Reaction and returns it.
`void`	`setCompartment(Compartment compartment)` Sets the compartmentID of this `Reaction` to the id of the `Compartment` 'compartment'.
`void`	`setCompartment(java.lang.String compartmentID)` Sets the compartmentID of this Reaction to 'compartmentID'.
`void`	`setFast(boolean fast)` Sets the fast Boolean of this `Reaction`.
`void`	`setKineticLaw(KineticLaw kineticLaw)` Sets the kineticLaw of this `Reaction`.
`void`	`setListOfModifiers(ListOf<ModifierSpeciesReference> listOfModifiers)` Sets the listOfModifiers of this `Reaction`.
`void`	`setListOfProducts(ListOf<SpeciesReference> listOfProducts)` Sets the `listOfProducts` of this `Reaction`.
`void`	`setListOfReactants(ListOf<SpeciesReference> listOfReactants)` Sets the listOfReactants of this `Reaction`.
`void`	`setReversible(boolean reversible)` Sets the reversible Boolean of this `Reaction`.
`void`	`unsetFast()` Sets the fast Boolean of this Reaction to `null`.
`boolean`	`unsetKineticLaw()` Sets the `KineticLaw` of this `Reaction` to null and notifies all `TreeNodeChangeListener` about changes.
`boolean`	`unsetListOfModifiers()` Removes the `listOfModifiers` from this `Reaction` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfProducts()` Removes the `listOfProducts` from this `Reaction` and notifies all registered instances of `TreeNodeChangeListener`.
`boolean`	`unsetListOfReactants()` Removes the `listOfReactants` from this `Reaction` and notifies all registered instances of `TreeNodeChangeListener`.
`void`	`unsetReversible()` Sets the reversible Boolean of this `Reaction` to `null`.
`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.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, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, 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, 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 java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

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, getElementName, 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 javax.swing.tree.TreeNode
children, getIndex, isLeaf

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    Generated serial version identifier.
    
    See Also:
    Constant Field Values
  - compartmentID
```
private java.lang.String compartmentID
```
    Represents the 'compartment' XML attribute of a reaction element.
  - fast
```
private java.lang.Boolean fast
```
    Represents the 'fast' XML attribute of a reaction element.
  - isSetFast
```
private boolean isSetFast
```
    Checks whether the fast attribute has been set by using a default or by changing its value.
  - isSetReversible
```
private boolean isSetReversible
```
    Checks whether the reversible attribute has been set by using a default or by changing its value.
  - kineticLaw
```
private KineticLaw kineticLaw
```
    Represents the 'kineticLaw' XML subNode of a reaction element.
  - listOfModifiers
```
private ListOf<ModifierSpeciesReference> listOfModifiers
```
    Represents the 'listOfModifiers' XML subNode of a reaction element.
  - listOfProducts
```
private ListOf<SpeciesReference> listOfProducts
```
    Represents the 'listOfProducts' XML subNode of a reaction element.
  - listOfReactants
```
private ListOf<SpeciesReference> listOfReactants
```
    Represents the 'listOfReactants' XML subNode of a reaction element.
  - reversible
```
private java.lang.Boolean reversible
```
    Represents the 'reversible' XML attribute of a reaction element.
- Constructor Detail
  - Reaction
```
public Reaction()
```
    Creates a Reaction instance. By default, the compartmentID, kineticLaw, listOfReactants, listOfProducts and listOfModifiers are empty.
  - Reaction
```
public Reaction(int level,
        int version)
```
    Creates a new Reaction instance from a given SBML level and version.
    
    Parameters:
    level - the SBML level
    version - the SBML version
  - Reaction
```
public Reaction(Reaction reaction)
```
    Creates a Reaction instance from a given reaction.
    
    Parameters:
    reaction -
  - Reaction
```
public Reaction(java.lang.String id)
```
    Parameters:
    id -
  - Reaction
```
public Reaction(java.lang.String id,
        int level,
        int version)
```
    Creates a Reaction instance from an id, level and version. By default, the compartmentID, kineticLaw, listOfReactants, listOfProducts and listOfModifiers are empty.
    
    Parameters:
    id -
    level -
    version -
- Method Detail
  - addModifier
```
public boolean addModifier(ModifierSpeciesReference modspecref)
```
    Adds a ModifierSpeciesReference instance to this Reaction.
    
    Parameters:
    modspecref -
    
    Returns:
    true if the listOfModifiers was changed as a result of this call.
  - addProduct
```
public boolean addProduct(SpeciesReference specref)
```
    Adds a SpeciesReference instance to the listOfProducts of this Reaction.
    
    Parameters:
    specref -
    
    Returns:
    true if the listOfProducts was changed as a result of this call.
  - addReactant
```
public boolean addReactant(SpeciesReference specref)
```
    Adds a SpeciesReference instance to the listOfReactants of this Reaction.
    
    Parameters:
    specref -
    
    Returns:
    true if the listOfReactants was changed as a result of this call.
  - clone
```
public Reaction 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.
  - createKineticLaw
```
public KineticLaw createKineticLaw()
```
    Creates a new KineticLaw object, installs it as this Reaction's 'kineticLaw' sub-element, and returns it. If this Reaction had a previous KineticLaw, it will be destroyed.
    
    Returns:
    the new KineticLaw object
  - createModifier
```
public ModifierSpeciesReference createModifier()
```
    Creates a new ModifierSpeciesReference, adds it to this Reaction's list of modifiers and returns it.
    
    Returns:
    a new ModifierSpeciesReference object.
  - createModifier
```
public ModifierSpeciesReference createModifier(Species species)
```
    Creates a new ModifierSpeciesReference, which points to the given Species, adds it to this Reaction's listOfModifiers, and returns a pointer to it.
    
    Parameters:
    species - the Species to which this modifier should point.
    See Also:
    createModifier(String, Species)
  - createModifier
```
public ModifierSpeciesReference createModifier(java.lang.String id)
```
    Parameters:
    id -
    
    Returns:
  - createModifier
```
public ModifierSpeciesReference createModifier(java.lang.String id,
                                      Species species)
```
    Creates a new ModifierSpeciesReference with the given id as its identifier, which points to the given Species, adds it to this Reaction's listOfModifiers, and returns a pointer to it.
    
    Parameters:
    id - the identifier of the ModifierSpeciesReference to be created.
    species - the Species to which this modifier should point.
    
    Returns:
    a pointer to the newly created ModifierSpeciesReference.
  - createModifier
```
public ModifierSpeciesReference createModifier(java.lang.String id,
                                      java.lang.String species)
```
    Creates a new ModifierSpeciesReference with the given id as its identifier, which points to the Species with the given id, adds it to this Reaction's listOfModifiers, and returns a pointer to it.
    
    Parameters:
    id - the identifier of the ModifierSpeciesReference to be created.
    species - the identifier of the Species to be referenced.
    
    Returns:
    a pointer to the newly created ModifierSpeciesReference.
  - createProduct
```
public SpeciesReference createProduct()
```
    Creates a new SpeciesReference, adds it to this Reaction's listOfProducts and returns it.
    
    Returns:
    a new SpeciesReference object.
  - createProduct
```
public SpeciesReference createProduct(Species species)
```
    Creates a new SpeciesReference, which points to the given Species, adds it to this Reaction's listOfProducts and returns a pointer to it.
    
    Parameters:
    species - the Species to which the SpeciesReference should point.
    
    Returns:
    a pointer to a newly created SpeciesReference that has been added to this Reaction's listOfProducts.
    See Also:
    createProduct(String, Species)
  - createProduct
```
public SpeciesReference createProduct(java.lang.String id)
```
    Parameters:
    id -
    
    Returns:
  - createProduct
```
public SpeciesReference createProduct(java.lang.String id,
                             Species species)
```
    Creates a new SpeciesReference with the given id as its identifier, which points to the given Species, adds it to this Reaction's listOfProducts and returns a pointer to it.
    
    Parameters:
    id - the identifier of the SpeciesReference to be created.
    species - the Species to which the SpeciesReference should point.
    
    Returns:
    a pointer to a newly created SpeciesReference that has been added to this Reaction's listOfProducts.
  - createProduct
```
public SpeciesReference createProduct(java.lang.String id,
                             java.lang.String species)
```
    Parameters:
    id -
    species -
    
    Returns:
  - createReactant
```
public SpeciesReference createReactant()
```
    Creates a new SpeciesReference, adds it to this Reaction's listOfReactants and returns it.
    
    Returns:
    a new SpeciesReference object.
  - createReactant
```
public SpeciesReference createReactant(Species species)
```
    Creates a new SpeciesReference to the given Species and adds it to the listOfReactants.
    
    Parameters:
    species -
    
    Returns:
    the newly created instance of SpeciesReference that points to the given Species.
    See Also:
    createReactant(String, Species)
  - createReactant
```
public SpeciesReference createReactant(java.lang.String id)
```
    Creates a new SpeciesReference with the given identifier and adds it to this Reaction's listOfReactants.
    
    Parameters:
    id - the id of the SpeciesReference that is to be created.
    
    Returns:
    a new instance of SpeciesReference, which is already linked to this Reaction.
  - createReactant
```
public SpeciesReference createReactant(java.lang.String id,
                              Species species)
```
    Creates a new SpeciesReference with the given id as identifier, which points to the given Species and adds it to the listOfReactants.
    
    Parameters:
    id - the identifier of the SpeciesReference to be created.
    species - the Species to which this reactant should point.
    
    Returns:
    a pointer to the newly created SpeciesReference.
  - createReactant
```
public SpeciesReference createReactant(java.lang.String id,
                              java.lang.String species)
```
    Parameters:
    id -
    species -
    
    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 AbstractNamedSBase
    
    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
  - 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
  - getCompartment
```
public java.lang.String getCompartment()
```
    Only available if Level >= 3.
    
    Returns:
    the compartmentID of this Reaction. The empty String if it is not set.
  - getCompartmentInstance
```
public Compartment getCompartmentInstance()
```
    Returns:
    the Compartment instance which has the compartmentID of this Reaction as id. Can be 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
    
    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.
  - getFast
```
public boolean getFast()
```
    Returns:
    the fast Boolean of this Reaction.
  - getKineticLaw
```
public KineticLaw getKineticLaw()
```
    Returns:
    the kineticLaw of this Reaction. Can be null if not set.
  - getListOfModifiers
```
public ListOf<ModifierSpeciesReference> getListOfModifiers()
```
    Returns:
    the listOfModifiers of this Reaction. Is initialized here if not yet set.
  - getListOfProducts
```
public ListOf<SpeciesReference> getListOfProducts()
```
    Returns:
    the listOfProducts of this Reaction. Is initialized here if not yet set.
  - getListOfReactants
```
public ListOf<SpeciesReference> getListOfReactants()
```
    Returns:
    the listOfReactants of this Reaction. Is initialized here if not yet set.
  - getModifier
```
public ModifierSpeciesReference getModifier(int i)
```
    Parameters:
    i -
    
    Returns:
    the ith ModifierSpeciesReference of the listOfModifiers. Can be null if it doesn't exist.
  - getModifier
```
public ModifierSpeciesReference getModifier(java.lang.String id)
```
    Searches the first ModifierSpeciesReference in the listOfModifiers of this Reaction with the given identifier.
    
    Parameters:
    id - identifier of the desired ModifierSpeciesReference. Note that this is not the identifier of the Species.
    
    Returns:
    the ModifierSpeciesReference of the listOfModifiers which has 'id' as id (or name depending on the level and version). Can be null if it doesn't exist.
  - getModifierCount
```
public int getModifierCount()
```
    Returns:
    the number of ModifierSpeciesReferences of this Reaction.
  - getModifierForSpecies
```
public ModifierSpeciesReference getModifierForSpecies(java.lang.String id)
```
    Returns the first ModifierSpeciesReference in the listOfModifiers of this Reaction whose 'species' attribute points to a Species with the given identifier.
    
    Parameters:
    id - The identifier of a referenced Species
    
    Returns:
    the ModifierSpeciesReference of the listOfModifiers which has 'id' as species attribute (or name depending on the level and version). Can be null if it doesn't exist.
  - getNumModifiers
```
public int getNumModifiers()
```
    Returns:
    the number of ModifierSpeciesReferences of this Reaction.
  - getNumProducts
```
public int getNumProducts()
```
    Returns:
    the number of products SpeciesReference.
  - getNumReactants
```
public int getNumReactants()
```
    Returns:
    the number of reactants SpeciesReference.
  - getParent
```
public ListOf<Reaction> getParent()
```
    Description copied from class: AbstractSBase
    
    This is equivalent to calling AbstractSBase.getParentSBMLObject(), but this method is needed for TreeNode.
    
    Specified by:
    
    getParent in interface javax.swing.tree.TreeNode
    
    Overrides:
    
    getParent in class AbstractSBase
    
    Returns:
    the parent element of this element.
    See Also:
    AbstractSBase.getParentSBMLObject()
  - getProduct
```
public SpeciesReference getProduct(int i)
```
    Parameters:
    i -
    
    Returns:
    the ith product SpeciesReference of the listOfProducts. Can be null if it doesn't exist.
  - getProduct
```
public SpeciesReference getProduct(java.lang.String id)
```
    Searches the first SpeciesReference in the listOfProducts of this Reaction with the given identifier.
    
    Parameters:
    id - identifier of the desired SpeciesReference. Note that this is not the identifier of the Species.
    
    Returns:
    the SpeciesReference of the listOfProducts which has 'id' as id (or name depending on the level and version). Can be null if it doesn't exist.
  - getProductCount
```
public int getProductCount()
```
    Returns:
    the number of products SpeciesReference.
  - getProductForSpecies
```
public SpeciesReference getProductForSpecies(java.lang.String id)
```
    Returns the first SpeciesReference in the listOfProducts of this Reaction whose 'species' attribute points to a Species with the given identifier.
    
    Parameters:
    id - The identifier of a referenced Species
    
    Returns:
    the SpeciesReference of the listOfProducts which has 'id' as species attribute (or name depending on the level and version). Can be null if it doesn't exist.
  - getReactant
```
public SpeciesReference getReactant(int i)
```
    Parameters:
    i -
    
    Returns:
    the ith reactant SpeciesReference of the listOfReactants. Can be null if it doesn't exist.
  - getReactant
```
public SpeciesReference getReactant(java.lang.String id)
```
    Searches the first SpeciesReference in the listOfReactants of this Reaction with the given identifier.
    
    Parameters:
    id - identifier of the desired SpeciesReference. Note that this is not the identifier of the Species.
    
    Returns:
    the SpeciesReference of the listOfReactants which has 'id' as id (or name depending on the level and version). Can be null if it doesn't exist.
  - getReactantCount
```
public int getReactantCount()
```
    Returns:
    the number of reactants SpeciesReference.
  - getReactantForSpecies
```
public SpeciesReference getReactantForSpecies(java.lang.String id)
```
    Returns the first SpeciesReference in the listOfReactants of this Reaction whose 'species' attribute points to a Species with the given identifier.
    
    Parameters:
    id - The identifier of a referenced Species
    
    Returns:
    the SpeciesReference of the listOfReactants which has 'id' as species attribute (or name depending on the level and version). Can be null if it doesn't exist.
  - getReversible
```
public boolean getReversible()
```
    Returns:
    the reversible Boolean of this reaction.
  - 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 AbstractNamedSBase
    
    Returns:
    a hash code value for this SBase instance.
    See Also:
    Object.hashCode()
  - hasModifier
```
public boolean hasModifier(Species s)
```
    Parameters:
    s -
    
    Returns:
  - hasProduct
```
public boolean hasProduct(Species s)
```
    Parameters:
    s -
    
    Returns:
  - hasReactant
```
public boolean hasReactant(Species s)
```
    Parameters:
    s -
    
    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 variables of this Reaction.
  - involves
```
public boolean involves(Species s)
```
    Convenient test if the given species takes part in this reaction as a reactant, product, or modifier.
    
    Parameters:
    s -
    
    Returns:
  - isFast
```
public boolean isFast()
```
    Returns:
    the boolean value of fast if it is set, false otherwise.
  - isIdMandatory
```
public boolean isIdMandatory()
```
    Description copied from interface: NamedSBase
    
    This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
    
    Specified by:
    
    isIdMandatory in interface NamedSBase
    
    Returns:
    true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.
  - isReversible
```
public boolean isReversible()
```
    Returns:
    the value of reversible if it is set, false otherwise.
  - isSetCompartment
```
public boolean isSetCompartment()
```
    Returns:
    true if the compartmentID of this Reaction is not null.
  - isSetCompartmentInstance
```
public boolean isSetCompartmentInstance()
```
    Returns:
    true if the Compartment which has the compartmentID of this Reaction as id is not null;
  - isSetFast
```
public boolean isSetFast()
```
    Returns:
    true if fast is not null.
  - isSetKineticLaw
```
public boolean isSetKineticLaw()
```
    Returns:
    true if the kineticLaw of this Reaction is not null.
  - isSetListOfModifiers
```
public boolean isSetListOfModifiers()
```
    Returns:
    true if the listOfModifiers of this Reaction is not true and not empty.
  - isSetListOfProducts
```
public boolean isSetListOfProducts()
```
    Returns:
    true if the listOfProducts of this reaction is not true and not empty.
  - isSetListOfReactants
```
public boolean isSetListOfReactants()
```
    Returns:
    true if the listOfReactants of this Reaction is not true and not empty.
  - isSetReversible
```
public boolean isSetReversible()
```
    Returns:
    true if reversible 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.
  - references
```
private boolean references(ListOf<? extends SimpleSpeciesReference> list,
                 Species s)
```
    Checks whether the given list references the given species.
    
    Parameters:
    list -
    s -
    
    Returns:
  - remove
```
private <T extends SimpleSpeciesReference> T remove(ListOf<T> list,
                                          java.lang.String id)
```
    Parameters:
    list -
    id -
    
    Returns:
  - removeModifier
```
public ModifierSpeciesReference removeModifier(int i)
```
    Removes the nth modifier species (ModifierSpeciesReference object) in the list of modifiers in this Reaction and returns it.
    
    Parameters:
    i - the index of the ModifierSpeciesReference object to remove.
    
    Returns:
    the removed ModifierSpeciesReference object, or null if the given index is out of range.
  - removeModifier
```
public boolean removeModifier(ModifierSpeciesReference modspecref)
```
    Removes the ModifierSpeciesReference 'modspecref' from this Reaction.
    
    Parameters:
    modspecref -
  - removeModifier
```
public ModifierSpeciesReference removeModifier(java.lang.String id)
```
    Removes the modifier species (ModifierSpeciesReference object) having the given 'species' attribute in the list of modifiers in this Reaction and returns it.
    
    Parameters:
    id - the 'species' attribute of the ModifierSpeciesReference object (which correspond to a species id).
    
    Returns:
  - removeProduct
```
public SpeciesReference removeProduct(int i)
```
    Removes the nth product species (SpeciesReference object) in the list of products in this Reaction and returns it.
    
    Parameters:
    i - the index of the SpeciesReference object to remove.
    
    Returns:
    the removed SpeciesReference object, or null if the given index is out of range.
  - removeProduct
```
public void removeProduct(SpeciesReference specref)
```
    Removes the SpeciesReference 'modspecref' from the listOfProducts of this Reaction.
    
    Parameters:
    specref -
  - removeProduct
```
public SpeciesReference removeProduct(java.lang.String id)
```
    Removes the product species (SpeciesReference object) having the given 'species' attribute in the list of products in this Reaction and returns it.
    
    Parameters:
    id - the 'species' attribute of the SpeciesReference object (which correspond to a species id).
    
    Returns:
  - removeReactant
```
public SpeciesReference removeReactant(int i)
```
    Removes the nth reactant species (SpeciesReference object) in the list of reactants in this Reaction and returns it.
    
    Parameters:
    i - the index of the SpeciesReference object to remove.
    
    Returns:
    the removed SpeciesReference object, or null if the given index is out of range.
  - removeReactant
```
public boolean removeReactant(SpeciesReference specref)
```
    Removes the SpeciesReference 'modspecref' from the listOfReactants of this Reaction.
    
    Parameters:
    specref -
  - removeReactant
```
public SpeciesReference removeReactant(java.lang.String id)
```
    Removes the reactant species (SpeciesReference object) having the given 'species' attribute in the list of reactants in this Reaction and returns it.
    
    Parameters:
    id - the 'species' attribute of the SpeciesReference object (which correspond to a species id).
    
    Returns:
  - setCompartment
```
public void setCompartment(Compartment compartment)
```
    Sets the compartmentID of this Reaction to the id of the Compartment 'compartment'.
    
    Parameters:
    compartment -
  - setCompartment
```
public void setCompartment(java.lang.String compartmentID)
```
    Sets the compartmentID of this Reaction to 'compartmentID'. This method is only available for Level >= 3.
    
    Parameters:
    compartmentID -
    
    Throws:
    
    PropertyNotAvailableException - if Level < 3.
  - setFast
```
public void setFast(boolean fast)
```
    Sets the fast Boolean of this Reaction.
    
    Parameters:
    fast -
  - setKineticLaw
```
public void setKineticLaw(KineticLaw kineticLaw)
```
    Sets the kineticLaw of this Reaction.
    
    Parameters:
    kineticLaw -
  - setListOfModifiers
```
public void setListOfModifiers(ListOf<ModifierSpeciesReference> listOfModifiers)
```
    Sets the listOfModifiers of this Reaction. Automatically sets the parentSBML object of the list to this Reaction instance.
    
    Parameters:
    listOfModifiers -
  - setListOfProducts
```
public void setListOfProducts(ListOf<SpeciesReference> listOfProducts)
```
    Sets the listOfProducts of this Reaction. Automatically sets the parentSBML object of the list to this Reaction instance.
    
    Parameters:
    listOfProducts -
  - setListOfReactants
```
public void setListOfReactants(ListOf<SpeciesReference> listOfReactants)
```
    Sets the listOfReactants of this Reaction. Automatically sets the parentSBML object of the list to this Reaction instance.
    
    Parameters:
    listOfReactants -
  - setReversible
```
public void setReversible(boolean reversible)
```
    Sets the reversible Boolean of this Reaction.
    
    Parameters:
    reversible -
  - unsetFast
```
public void unsetFast()
```
    Sets the fast Boolean of this Reaction to null.
  - unsetKineticLaw
```
public boolean unsetKineticLaw()
```
    Sets the KineticLaw of this Reaction to null and notifies all TreeNodeChangeListener about changes.
    
    Returns:
    true if calling this method changed the properties of this element.
  - unsetListOfModifiers
```
public boolean unsetListOfModifiers()
```
    Removes the listOfModifiers from this Reaction and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfProducts
```
public boolean unsetListOfProducts()
```
    Removes the listOfProducts from this Reaction and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetListOfReactants
```
public boolean unsetListOfReactants()
```
    Removes the listOfReactants from this Reaction and notifies all registered instances of TreeNodeChangeListener.
    
    Returns:
    true if calling this method lead to a change in this data structure.
  - unsetReversible
```
public void unsetReversible()
```
    Sets the reversible Boolean of this Reaction to null.
  - 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.

Class Reaction

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

Methods inherited from class org.sbml.jsbml.AbstractSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.NamedSBase

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from interface javax.swing.tree.TreeNode

Field Detail

serialVersionUID

compartmentID

fast

isSetFast

isSetReversible

kineticLaw

listOfModifiers

listOfProducts

listOfReactants

reversible

Constructor Detail

Reaction

Reaction

Reaction

Reaction

Reaction

Method Detail

addModifier

addProduct

addReactant

clone

containsUndeclaredUnits

createKineticLaw

createModifier

createModifier

createModifier

createModifier

createModifier

createProduct

createProduct

createProduct

createProduct

createProduct

createReactant

createReactant

createReactant

createReactant

createReactant

equals

getAllowsChildren

getChildAt

getChildCount

getCompartment

getCompartmentInstance

getDerivedUnitDefinition

getDerivedUnits

getFast

getKineticLaw

getListOfModifiers

getListOfProducts

getListOfReactants

getModifier

getModifier

getModifierCount

getModifierForSpecies

getNumModifiers

getNumProducts

getNumReactants

getParent

getProduct

getProduct

getProductCount

getProductForSpecies

getReactant

getReactant