KineticLaw (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.KineticLaw

```
public class KineticLaw
extends SBase
```
The rate expression for an SBML reaction.
An object of class KineticLaw is used to describe the rate at which the process defined by a given Reaction takes place. KineticLaw has subelements called 'math' (for MathML content) and 'listOfParameters' (of class ListOfParameters), in addition to the attributes and subelements it inherits from SBase.
KineticLaw's 'math' subelement for holding a MathML formula defines the rate of the reaction. The formula may refer to other entities in a model as well as local parameter definitions within the scope of the Reaction (see below). It is important to keep in mind, however, that the only Species identifiers that can be used in this formula are those declared in the lists of reactants, products and modifiers in the Reaction structure. (In other words, before a species can be referenced in the KineticLaw, it must be declared in one of those lists.)
KineticLaw provides a way to define local parameters whose identifiers can be used in the 'math' formula of that KineticLaw instance. Prior to SBML Level 3, these parameter definitions are stored inside a 'listOfParameters' subelement containing Parameter objects in SBML Level 3, this is achieved using a specialized object class called LocalParameter and the containing subelement is called 'listOfLocalParameters'. In both cases, the parameters so defined are only visible within the KineticLaw they cannot be accessed outside. A local parameter within one reaction is not visible from within another reaction, nor is it visible to any other construct outside of the KineticLaw in which it is defined. In addition, another important feature is that if such a Parameter (or in Level 3, LocalParameter) object has the same identifier as another object in the scope of the enclosing Model, the definition inside the KineticLaw takes precedence. In other words, within the KineticLaw's 'math' formula, references to local parameter identifiers shadow any identical global identifiers.
The values of local parameters defined within KineticLaw objects cannot change. In SBML Level 3, this quality is built into the LocalParameter construct. In Level 2, where the same kind of Parameter object class is used as for global parameters, the Parameter objects' 'constant' attribute must always have a value of true (either explicitly or left to its default value).

A warning about identifier shadowing

A common misconception is that different classes of objects (e.g., species, compartments, parameters) in SBML have different identifier scopes. They do not. The implication is that if a KineticLaw's local parameter definition uses an identifier identical to any other identifier defined in the model outside the KineticLaw, even if the other identifier does not belong to a parameter type of object, the local parameter's identifier takes precedence within that KineticLaw's 'math' formula. It is not an error in SBML for identifiers to shadow each other this way, but can lead to confusing and subtle errors.

SBML Level/Version differences

In SBML Level 2 Version 1, the SBML specification included two additional attributes on KineticLaw called 'substanceUnits' and 'timeUnits'. They were removed beginning with SBML Level 2 Version 2 because further research determined they introduced many problems. The most significant problem was that their use could easily lead to the creation of valid models whose reactions nevertheless could not be integrated into a system of equations without outside knowledge for converting the quantities used. Examination of real-life models revealed that a common reason for using 'substanceUnits' on KineticLaw was to set the units of all reactions to the same set of substance units, something that is better achieved by using UnitDefinition to redefine 'substance' for the whole Model.
As mentioned above, in SBML Level 2 Versions 2&ndash4, local parameters are of class Parameter. In SBML Level 3, the class of object is LocalParameter.

Constructor Summary

Constructors
Constructor and Description
`KineticLaw(KineticLaw orig)` Copy constructor creates a copy of this `KineticLaw`.
`KineticLaw(long level, long version)` Creates a new `KineticLaw` using the given SBML `level` and `version` values.
`KineticLaw(SBMLNamespaces sbmlns)` Creates a new `KineticLaw` using the given `SBMLNamespaces` object `sbmlns`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addLocalParameter(LocalParameter p)` Adds a copy of the given `LocalParameter` object to the list of local parameters in this `KineticLaw`.
`int`	`addParameter(Parameter p)` Adds a copy of the given `Parameter` object to the list of local parameters in this `KineticLaw`.
`KineticLaw`	`cloneObject()` Creates and returns a deep copy of this `KineticLaw` object.
`void`	`connectToChild()`
`boolean`	`containsUndeclaredUnits()` Predicate returning `true` if the math expression of this `KineticLaw` contains parameters/numbers with undeclared units.
`LocalParameter`	`createLocalParameter()` Creates a new `LocalParameter` object, adds it to this `KineticLaw`'s list of local parameters, and returns the `LocalParameter` object created.
`Parameter`	`createParameter()` Creates a new `Parameter` object, adds it to this `KineticLaw`'s list of local parameters, and returns the `Parameter` object created.
`void`	`delete()` Explicitly deletes the underlying native object.
`UnitDefinition`	`getDerivedUnitDefinition()` Calculates and returns a `UnitDefinition` that expresses the units of measurement assumed for the 'math' expression of this `KineticLaw`.
`SBase`	`getElementByMetaId(java.lang.String metaid)` Returns the first child element it can find with the given `metaid`, or `null` if no such object is found.
`SBase`	`getElementBySId(java.lang.String id)` Returns the first child element found that has the given `id` in the model-wide SId namespace, or `null` if no such object is found.
`java.lang.String`	`getElementName()` Returns the XML element name of this object, which for `Species`, is always `'kineticLaw'.`
`java.lang.String`	`getFormula()` Returns the mathematical formula for this `KineticLaw` object and return it as as a text string.
`ListOfLocalParameters`	`getListOfLocalParameters()` Returns the list of local parameters in this `KineticLaw` object.
`ListOfParameters`	`getListOfParameters()` Returns the list of local parameters in this `KineticLaw` object.
`LocalParameter`	`getLocalParameter(long n)` Returns the nth `LocalParameter` object in the list of local parameters in this `KineticLaw` instance.
`LocalParameter`	`getLocalParameter(java.lang.String sid)` Returns a local parameter based on its identifier.
`ASTNode`	`getMath()` Returns the mathematical formula for this `KineticLaw` object and return it as as an AST.
`long`	`getNumLocalParameters()` Returns the number of local parameters in this `KineticLaw` instance.
`long`	`getNumParameters()` Returns the number of local parameters in this `KineticLaw` instance.
`Parameter`	`getParameter(long n)` Returns the nth `Parameter` object in the list of local parameters in this `KineticLaw` instance.
`Parameter`	`getParameter(java.lang.String sid)` Returns a local parameter based on its identifier.
`java.lang.String`	`getSubstanceUnits()` (SBML Level 2 Version 1 only) Returns the value of the 'substanceUnits' attribute of this `KineticLaw` object.
`java.lang.String`	`getTimeUnits()` (SBML Level 2 Version 1 only) Returns the value of the 'timeUnits' attribute of this `KineticLaw` object.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`boolean`	`hasRequiredAttributes()` Predicate returning `true` if all the required attributes for this `KineticLaw` object have been set.
`boolean`	`hasRequiredElements()` Predicate returning `true` if all the required elements for this `KineticLaw` object have been set.
`boolean`	`isSetFormula()` Predicate returning `true` if this `KineticLaw`'s 'formula' attribute is set.
`boolean`	`isSetMath()` Predicate returning `true` if this Kinetic's 'math' subelement is set.
`boolean`	`isSetSubstanceUnits()` (SBML Level 2 Version 1 only) Predicate returning `true` if this `SpeciesReference`'s 'substanceUnits' attribute is set.
`boolean`	`isSetTimeUnits()` (SBML Level 2 Version 1 only) Predicate returning `true` if this `SpeciesReference`'s 'timeUnits' attribute is set.
`int`	`removeFromParentAndDelete()` Finds this `KineticLaw`'s `Reaction` parent and calls unsetKineticLaw() on it, indirectly deleting itself.
`LocalParameter`	`removeLocalParameter(long n)` Removes the nth `LocalParameter` object in the list of local parameters in this `KineticLaw` instance and returns a pointer to it.
`LocalParameter`	`removeLocalParameter(java.lang.String sid)` Removes a `LocalParameter` object with the given identifier in the list of local parameters in this `KineticLaw` instance and returns a pointer to it.
`Parameter`	`removeParameter(long n)` Removes the nth `Parameter` object in the list of local parameters in this `KineticLaw` instance and returns a pointer to it.
`Parameter`	`removeParameter(java.lang.String sid)` Removes a `Parameter` object with the given identifier in the list of local parameters in this `KineticLaw` instance and returns a pointer to it.
`void`	`renameSIdRefs(java.lang.String oldid, java.lang.String newid)` Replaces all uses of a given `SIdRef` type attribute value with another value.
`void`	`renameUnitSIdRefs(java.lang.String oldid, java.lang.String newid)` Replaces all uses of a given `UnitSIdRef` type attribute value with another value.
`int`	`setFormula(java.lang.String formula)` Sets the mathematical expression of this `KineticLaw` instance to the given `formula`.
`int`	`setMath(ASTNode math)` Sets the mathematical expression of this `KineticLaw` instance to a copy of the given `ASTNode`.
`int`	`setSubstanceUnits(java.lang.String sid)` (SBML Level 2 Version 1 only) Sets the 'substanceUnits' attribute of this `KineticLaw` object to a copy of the identifier given in `sid`.
`int`	`setTimeUnits(java.lang.String sid)` (SBML Level 2 Version 1 only) Sets the 'timeUnits' attribute of this `KineticLaw` object to a copy of the identifier in `sid`.
`int`	`unsetSubstanceUnits()` (SBML Level 2 Version 1 only) Unsets the 'substanceUnits' attribute of this `KineticLaw` object.
`int`	`unsetTimeUnits()` (SBML Level 2 Version 1 only) Unsets the 'timeUnits' attribugte of this `KineticLaw` object.

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - KineticLaw
```
public KineticLaw(long level,
                  long version)
           throws SBMLConstructorException
```
    Creates a new KineticLaw using the given SBML level and version values.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this KineticLaw
    
    version - a long integer, the SBML Version to assign to this KineticLaw
    
    Throws:
    
    SBMLConstructorException - Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version.
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.
  - KineticLaw
```
public KineticLaw(SBMLNamespaces sbmlns)
           throws SBMLConstructorException
```
    Creates a new KineticLaw using the given SBMLNamespaces object sbmlns.
    
    The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
    
    Parameters:
    
    sbmlns - an SBMLNamespaces object.
    
    Throws:
    
    SBMLConstructorException - Thrown if the given sbmlns is inconsistent or incompatible with this object.
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.
  - KineticLaw
```
public KineticLaw(KineticLaw orig)
           throws SBMLConstructorException
```
    Copy constructor creates a copy of this KineticLaw.
    
    Parameters:
    
    orig - the object to copy.
    
    Throws:
    
    SBMLConstructorException
- Method Detail
  - delete
```
public void delete()
```
    Explicitly deletes the underlying native object.
    In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the KineticLaw.delete() method on the libSBML object.
    This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke KineticLaw.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public KineticLaw cloneObject()
```
    Creates and returns a deep copy of this KineticLaw object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    the (deep) copy of this KineticLaw object.
  - getElementBySId
```
public SBase getElementBySId(java.lang.String id)
```
    Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
    
    Overrides:
    
    getElementBySId in class SBase
    
    Parameters:
    
    id - string representing the id of objects to find.
    
    Returns:
    
    pointer to the first element found with the given id.
  - getElementByMetaId
```
public SBase getElementByMetaId(java.lang.String metaid)
```
    Returns the first child element it can find with the given metaid, or null if no such object is found.
    
    Overrides:
    
    getElementByMetaId in class SBase
    
    Parameters:
    
    metaid - string representing the metaid of objects to find
    
    Returns:
    
    pointer to the first element found with the given metaid.
  - getFormula
```
public java.lang.String getFormula()
```
    Returns the mathematical formula for this KineticLaw object and return it as as a text string.
    This is fundamentally equivalent to KineticLaw.getMath(). This variant is provided principally for compatibility compatibility with SBML Level 1.
    
    Returns:
    
    a string representing the formula of this KineticLaw.
    
    See Also:
    
    KineticLaw.getMath()
    
    "Note:"
    
    SBML Level 1 uses a text-string format for mathematical formulas. SBML Level 2 uses MathML, an XML format for representing mathematical expressions. LibSBML provides an Abstract Syntax Tree API for working with mathematical expressions this API is more powerful than working with formulas directly in text form, and ASTs can be translated into either MathML or the text-string syntax. The libSBML methods that accept text-string formulas directly (such as this constructor) are provided for SBML Level 1 compatibility, but developers are encouraged to use the AST mechanisms.
  - getMath
```
public ASTNode getMath()
```
    Returns the mathematical formula for this KineticLaw object and return it as as an AST.
    This is fundamentally equivalent to KineticLaw.getFormula(). The latter is provided principally for compatibility compatibility with SBML Level 1, which represented mathematical formulas in text-string form.
    
    Returns:
    
    the ASTNode representation of the mathematical formula.
    
    See Also:
    
    KineticLaw.getFormula()
  - getTimeUnits
```
public java.lang.String getTimeUnits()
```
    (SBML Level 2 Version 1 only) Returns the value of the 'timeUnits' attribute of this KineticLaw object.
    
    Returns:
    
    the 'timeUnits' attribute value.
    
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - getSubstanceUnits
```
public java.lang.String getSubstanceUnits()
```
    (SBML Level 2 Version 1 only) Returns the value of the 'substanceUnits' attribute of this KineticLaw object.
    
    Returns:
    
    the 'substanceUnits' attribute value.
    
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - isSetFormula
```
public boolean isSetFormula()
```
    Predicate returning true if this KineticLaw's 'formula' attribute is set.
    This is functionally identical to the method KineticLaw.isSetMath(). It is provided in order to mirror the parallel between KineticLaw.getFormula() and KineticLaw.getMath().
    
    Returns:
    
    true if the formula (meaning the math subelement) of this KineticLaw is set, false otherwise.
    
    See Also:
    
    KineticLaw.isSetMath()
    
    "Note:"
    
    SBML Level 1 uses a text-string format for mathematical formulas. SBML Level 2 uses MathML, an XML format for representing mathematical expressions. LibSBML provides an Abstract Syntax Tree API for working with mathematical expressions this API is more powerful than working with formulas directly in text form, and ASTs can be translated into either MathML or the text-string syntax. The libSBML methods that accept text-string formulas directly (such as this constructor) are provided for SBML Level 1 compatibility, but developers are encouraged to use the AST mechanisms.
  - isSetMath
```
public boolean isSetMath()
```
    Predicate returning true if this Kinetic's 'math' subelement is set.
    This is identical to the method KineticLaw.isSetFormula(). It is provided in order to mirror the parallel between KineticLaw.getFormula() and KineticLaw.getMath().
    
    Returns:
    
    true if the formula (meaning the math subelement) of this KineticLaw is set, false otherwise.
    
    See Also:
    
    KineticLaw.isSetFormula()
  - isSetTimeUnits
```
public boolean isSetTimeUnits()
```
    (SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's 'timeUnits' attribute is set.
    
    Returns:
    
    true if the 'timeUnits' attribute of this KineticLaw object is set, false otherwise.
    
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - isSetSubstanceUnits
```
public boolean isSetSubstanceUnits()
```
    (SBML Level 2 Version 1 only) Predicate returning true if this SpeciesReference's 'substanceUnits' attribute is set.
    
    Returns:
    
    true if the 'substanceUnits' attribute of this KineticLaw object is set, false otherwise.
    
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - setFormula
```
public int setFormula(java.lang.String formula)
```
    Sets the mathematical expression of this KineticLaw instance to the given formula.
    The given formula string is copied. Internally, libSBML stores the mathematical expression as an ASTNode.
    Parameters:
    
    formula - the mathematical expression to use, represented in text-string form.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT
    See Also:
    
    KineticLaw.setMath(ASTNode math)
    
    "Note:"
    
    SBML Level 1 uses a text-string format for mathematical formulas. SBML Level 2 uses MathML, an XML format for representing mathematical expressions. LibSBML provides an Abstract Syntax Tree API for working with mathematical expressions this API is more powerful than working with formulas directly in text form, and ASTs can be translated into either MathML or the text-string syntax. The libSBML methods that accept text-string formulas directly (such as this constructor) are provided for SBML Level 1 compatibility, but developers are encouraged to use the AST mechanisms.
  - setMath
```
public int setMath(ASTNode math)
```
    Sets the mathematical expression of this KineticLaw instance to a copy of the given ASTNode.
    This is fundamentally identical to KineticLaw.setFormula(String formula). The latter is provided principally for compatibility compatibility with SBML Level 1, which represented mathematical formulas in text-string form.
    Parameters:
    
    math - an ASTNode representing a formula tree.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT
    See Also:
    
    KineticLaw.setFormula(String formula)
  - setTimeUnits
```
public int setTimeUnits(java.lang.String sid)
```
    (SBML Level 2 Version 1 only) Sets the 'timeUnits' attribute of this KineticLaw object to a copy of the identifier in sid.
    Parameters:
    
    sid - the identifier of the units to use.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    LIBSBML_UNEXPECTED_ATTRIBUTE
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - setSubstanceUnits
```
public int setSubstanceUnits(java.lang.String sid)
```
    (SBML Level 2 Version 1 only) Sets the 'substanceUnits' attribute of this KineticLaw object to a copy of the identifier given in sid.
    Parameters:
    
    sid - the identifier of the units to use.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    LIBSBML_UNEXPECTED_ATTRIBUTE
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - unsetTimeUnits
```
public int unsetTimeUnits()
```
    (SBML Level 2 Version 1 only) Unsets the 'timeUnits' attribugte of this KineticLaw object.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_UNEXPECTED_ATTRIBUTE
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - unsetSubstanceUnits
```
public int unsetSubstanceUnits()
```
    (SBML Level 2 Version 1 only) Unsets the 'substanceUnits' attribute of this KineticLaw object.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_UNEXPECTED_ATTRIBUTE
    "Note:"
    
    The attributes 'timeUnits' and 'substanceUnits' are present only in SBML Level 2 Version 1. In SBML Level 2 Version 2, the 'timeUnits' and 'substanceUnits' attributes were removed. For compatibility with new versions of SBML, users are cautioned to avoid these attributes.
  - addParameter
```
public int addParameter(Parameter p)
```
    Adds a copy of the given Parameter object to the list of local parameters in this KineticLaw.
    Parameters:
    
    p - the Parameter to add
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_DUPLICATE_OBJECT_ID
    LIBSBML_INVALID_OBJECT
    LIBSBML_OPERATION_FAILED
    See Also:
    
    KineticLaw.createParameter()
    
    "Note:"
    
    This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
  - addLocalParameter
```
public int addLocalParameter(LocalParameter p)
```
    Adds a copy of the given LocalParameter object to the list of local parameters in this KineticLaw.
    Parameters:
    
    p - the LocalParameter to add
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_DUPLICATE_OBJECT_ID
    LIBSBML_INVALID_OBJECT
    LIBSBML_OPERATION_FAILED
    See Also:
    
    KineticLaw.createLocalParameter()
    
    "Note:"
    
    This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.
  - createParameter
```
public Parameter createParameter()
```
    Creates a new Parameter object, adds it to this KineticLaw's list of local parameters, and returns the Parameter object created.
    
    Returns:
    
    a new Parameter object instance
    
    See Also:
    
    KineticLaw.addParameter(Parameter p)
  - createLocalParameter
```
public LocalParameter createLocalParameter()
```
    Creates a new LocalParameter object, adds it to this KineticLaw's list of local parameters, and returns the LocalParameter object created.
    
    Returns:
    
    a new LocalParameter object instance
    
    See Also:
    
    KineticLaw.addLocalParameter(LocalParameter p)
  - getListOfParameters
```
public ListOfParameters getListOfParameters()
```
    Returns the list of local parameters in this KineticLaw object.
    
    Returns:
    
    the list of Parameters for this KineticLaw.
  - getListOfLocalParameters
```
public ListOfLocalParameters getListOfLocalParameters()
```
    Returns the list of local parameters in this KineticLaw object.
    
    Returns:
    
    the list of LocalParameters for this KineticLaw.
  - getParameter
```
public Parameter getParameter(long n)
```
    Returns the nth Parameter object in the list of local parameters in this KineticLaw instance.
    
    Parameters:
    
    n - the index of the Parameter object sought
    
    Returns:
    
    the nth Parameter of this KineticLaw.
  - getLocalParameter
```
public LocalParameter getLocalParameter(long n)
```
    Returns the nth LocalParameter object in the list of local parameters in this KineticLaw instance.
    
    Parameters:
    
    n - the index of the LocalParameter object sought
    
    Returns:
    
    the nth LocalParameter of this KineticLaw.
  - getParameter
```
public Parameter getParameter(java.lang.String sid)
```
    Returns a local parameter based on its identifier.
    
    Parameters:
    
    sid - the identifier of the Parameter being sought.
    
    Returns:
    
    the Parameter object in this KineticLaw instace having the given 'id', or null if no such Parameter exists.
  - getLocalParameter
```
public LocalParameter getLocalParameter(java.lang.String sid)
```
    Returns a local parameter based on its identifier.
    
    Parameters:
    
    sid - the identifier of the LocalParameter being sought.
    
    Returns:
    
    the LocalParameter object in this KineticLaw instace having the given 'id', or null if no such LocalParameter exists.
  - getNumParameters
```
public long getNumParameters()
```
    Returns the number of local parameters in this KineticLaw instance.
    
    Returns:
    
    the number of Parameters in this KineticLaw.
  - getNumLocalParameters
```
public long getNumLocalParameters()
```
    Returns the number of local parameters in this KineticLaw instance.
    
    Returns:
    
    the number of LocalParameters in this KineticLaw.
  - getDerivedUnitDefinition
```
public UnitDefinition getDerivedUnitDefinition()
```
    Calculates and returns a UnitDefinition that expresses the units of measurement assumed for the 'math' expression of this KineticLaw.
    
    The units are calculated based on the mathematical expression in the KineticLaw and the model quantities referenced by <ci> elements used within that expression. The KineticLaw.getDerivedUnitDefinition() method returns the calculated units.
    
    Overrides:
    
    getDerivedUnitDefinition in class SBase
    
    Returns:
    
    a UnitDefinition that expresses the units of the math expression of this KineticLaw, or null if one cannot be constructed.
    
    See Also:
    
    KineticLaw.containsUndeclaredUnits()
    
    "Note:"
    
    The functionality that facilitates unit analysis depends on the model as a whole. Thus, in cases where the object has not been added to a model or the model itself is incomplete, unit analysis is not possible and this method will return null.
    
    "Warning:"
    
    Note that it is possible the 'math' expression in the KineticLaw contains pure numbers or parameters with undeclared units. In those cases, it is not possible to calculate the units of the overall expression without making assumptions. LibSBML does not make assumptions about the units, and KineticLaw.getDerivedUnitDefinition() returns the units as far as it is able to determine them. For example, in an expression X + Y, if X has unambiguously-defined units and Y does not, it will return the units of X. It is important that callers also invoke the method KineticLaw.containsUndeclaredUnits()to determine whether this situation holds. Callers may wish to take suitable actions in those scenarios.
  - containsUndeclaredUnits
```
public boolean containsUndeclaredUnits()
```
    Predicate returning true if the math expression of this KineticLaw contains parameters/numbers with undeclared units.
    
    Overrides:
    
    containsUndeclaredUnits in class SBase
    
    Returns:
    
    true if the math expression of this KineticLaw includes parameters/numbers with undeclared units, false otherwise.
    
    See Also:
    
    KineticLaw.getDerivedUnitDefinition()
    
    "Note:"
    
    A return value of true indicates that the UnitDefinition returned by KineticLaw.getDerivedUnitDefinition() may not accurately represent the units of the expression.
  - removeParameter
```
public Parameter removeParameter(long n)
```
    Removes the nth Parameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the Parameter object to remove
    
    Returns:
    
    the Parameter object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
  - removeLocalParameter
```
public LocalParameter removeLocalParameter(long n)
```
    Removes the nth LocalParameter object in the list of local parameters in this KineticLaw instance and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the LocalParameter object to remove
    
    Returns:
    
    the LocalParameter object removed. As mentioned above, the caller owns the returned item. null is returned if the given index is out of range.
  - removeParameter
```
public Parameter removeParameter(java.lang.String sid)
```
    Removes a Parameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    sid - the identifier of the Parameter to remove
    
    Returns:
    
    the Parameter object removed. As mentioned above, the caller owns the returned object. null is returned if no Parameter object with the identifier exists in this KineticLaw instance.
  - removeLocalParameter
```
public LocalParameter removeLocalParameter(java.lang.String sid)
```
    Removes a LocalParameter object with the given identifier in the list of local parameters in this KineticLaw instance and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    sid - the identifier of the LocalParameter to remove
    
    Returns:
    
    the LocalParameter object removed. As mentioned above, the caller owns the returned object. null is returned if no LocalParameter object with the identifier exists in this KineticLaw instance.
  - connectToChild
```
public void connectToChild()
```
    Overrides:
    
    connectToChild in class SBase
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code for this SBML object.
    
    LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. In the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. Note that different Level 3 package plug-ins may use overlapping type codes to identify the package to which a given object belongs, call the getPackageName() method on the object.
    
    Overrides:
    
    getTypeCode in class SBase
    
    Returns:
    
    the SBML type code for this object: SBML_KINETIC_LAW (default).
    
    See Also:
    
    KineticLaw.getElementName(), SBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object, which for Species, is always 'kineticLaw'.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, i.e., 'kineticLaw'.
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required attributes for this KineticLaw object have been set.
    The required attributes for a KineticLaw object are:
    - 'formula' (SBML Level 1 only)
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    true if the required attributes have been set, false otherwise.
  - hasRequiredElements
```
public boolean hasRequiredElements()
```
    Predicate returning true if all the required elements for this KineticLaw object have been set.
    Overrides:
    
    hasRequiredElements in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required elements for this object have been defined.
    
    "Note:"
    The required elements for a KineticLaw object are:
    
    'math'
  - removeFromParentAndDelete
```
public int removeFromParentAndDelete()
```
    Finds this KineticLaw's Reaction parent and calls unsetKineticLaw() on it, indirectly deleting itself.
    Overridden from the SBase function since the parent is not a ListOf.
    Overrides:
    
    removeFromParentAndDelete in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - renameSIdRefs
```
public void renameSIdRefs(java.lang.String oldid,
                          java.lang.String newid)
```
    Replaces all uses of a given SIdRef type attribute value with another value.
    
    In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRefin Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
    This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
    
    Overrides:
    
    renameSIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - renameUnitSIdRefs
```
public void renameUnitSIdRefs(java.lang.String oldid,
                              java.lang.String newid)
```
    Replaces all uses of a given UnitSIdRef type attribute value with another value.
    
    In SBML, unit definitions have identifiers of type UnitSId. In SBML Level 3, an explicit data type called UnitSIdRef was introduced for attribute values that refer to UnitSId values in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to a unit identifier', but the effective data type was the same as UnitSIdRef in Level 3. These and other methods of libSBML refer to the type UnitSIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
    This method works by looking at all unit identifier attribute values (including, if appropriate, inside mathematical formulas), comparing the referenced unit identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
    
    Overrides:
    
    renameUnitSIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier

Class KineticLaw

A warning about identifier shadowing

SBML Level/Version differences

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

KineticLaw

KineticLaw

KineticLaw

Method Detail

delete

cloneObject

getElementBySId

getElementByMetaId

getFormula

getMath

getTimeUnits

getSubstanceUnits

isSetFormula

isSetMath

isSetTimeUnits

isSetSubstanceUnits

setFormula

setMath

setTimeUnits

setSubstanceUnits

unsetTimeUnits

unsetSubstanceUnits

addParameter

addLocalParameter

createParameter

createLocalParameter

getListOfParameters

getListOfLocalParameters

getParameter

getLocalParameter

getParameter

getLocalParameter

getNumParameters

getNumLocalParameters

getDerivedUnitDefinition

containsUndeclaredUnits

removeParameter

removeLocalParameter

removeParameter

removeLocalParameter

connectToChild

getTypeCode

getElementName

hasRequiredAttributes

hasRequiredElements

removeFromParentAndDelete

renameSIdRefs

renameUnitSIdRefs