ListOfRules (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.ListOf
  - - org.sbml.libsbml.ListOfRules

```
public class ListOfRules
extends ListOf
```
A list of Rule objects.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.
Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See Also:

ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions, ListOfEvents

Constructor Summary

Constructors
Constructor and Description
`ListOfRules(long level, long version)` Creates a new `ListOfRules` object.
`ListOfRules(SBMLNamespaces sbmlns)` Creates a new `ListOfRules` object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ListOfRules`	`cloneObject()` Creates and returns a deep copy of this `ListOfRules` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`Rule`	`get(long n)` Get a `Rule` from the `ListOfRules`.
`Rule`	`get(java.lang.String sid)` Get a `Rule` from the `ListOfRules` based on its identifier.
`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.
`int`	`getItemTypeCode()` Returns the libSBML type code for the objects contained in this `ListOf` (i.e., `Rule` objects, if the list is non-empty).
`Rule`	`remove(long n)` Removes the nth item from this `ListOfRules` items and returns a pointer to it.
`Rule`	`remove(java.lang.String sid)` Removes item in this `ListOfRules` items with the given identifier.

Methods inherited from class org.sbml.libsbml.ListOf
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, size

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, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - ListOfRules
```
public ListOfRules(long level,
                   long version)
            throws SBMLConstructorException
```
    Creates a new ListOfRules object.
    The object is constructed such that it is valid for the given SBML Level and Version combination.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    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.
  - ListOfRules
```
public ListOfRules(SBMLNamespaces sbmlns)
            throws SBMLConstructorException
```
    Creates a new ListOfRules object.
    The object is constructed such that it is valid for the SBML Level and Version combination determined by the SBMLNamespaces object in sbmlns.
    
    Parameters:
    
    sbmlns - an SBMLNamespaces object that is used to determine the characteristics of the ListOfRules object to be created.
    
    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.
- 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 ListOfRules.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 ListOfRules.delete() themselves.
    
    Overrides:
    
    delete in class ListOf
  - cloneObject
```
public ListOfRules cloneObject()
```
    Creates and returns a deep copy of this ListOfRules object.
    
    Overrides:
    
    cloneObject in class ListOf
    
    Returns:
    
    the (deep) copy of this ListOfRules object.
  - getItemTypeCode
```
public int getItemTypeCode()
```
    Returns the libSBML type code for the objects contained in this ListOf (i.e., Rule objects, if the list is non-empty).
    
    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 SBase.getPackageName() method on the object.
    
    Overrides:
    
    getItemTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for objects contained in this list: SBML_RULE (default).
    
    See Also:
    
    ListOfRules.getElementName(), SBase.getPackageName()
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    For ListOfRules, the XML element name is 'listOfRules'.
    
    Overrides:
    
    getElementName in class ListOf
    
    Returns:
    
    the name of this element, i.e., 'listOfRules'.
  - get
```
public Rule get(long n)
```
    Get a Rule from the ListOfRules.
    
    Overrides:
    
    get in class ListOf
    
    Parameters:
    
    n - the index number of the Rule to get.
    
    Returns:
    
    the nth Rule in this ListOfRules.
    
    See Also:
    
    ListOf.size()
  - get
```
public Rule get(java.lang.String sid)
```
    Get a Rule from the ListOfRules based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the Rule to get.
    
    Returns:
    
    Rule in this ListOfRules with the given id or null if no such Rule exists.
    
    See Also:
    
    ListOfRules.get(long n), ListOf.size()
  - remove
```
public Rule remove(long n)
```
    Removes the nth item from this ListOfRules items and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Overrides:
    
    remove in class ListOf
    
    Parameters:
    
    n - the index of the item to remove.
    
    See Also:
    
    ListOf.size()
  - 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.
    Note that AssignmentRules and RateRules do not actually have IDs, but the libsbml interface pretends that they do: no assignment rule or rate rule is returned by this function.
    
    Overrides:
    
    getElementBySId in class ListOf
    
    Parameters:
    
    id - string representing the id of the object to find.
    
    Returns:
    
    pointer to the first element found with the given id.
  - remove
```
public Rule remove(java.lang.String sid)
```
    Removes item in this ListOfRules items with the given identifier.
    The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.
    
    Parameters:
    
    sid - the identifier of the item to remove.
    
    Returns:
    
    the item removed. As mentioned above, the caller owns the returned item.

Class ListOfRules

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.ListOf

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

ListOfRules

ListOfRules

Method Detail

delete

cloneObject

getItemTypeCode

getElementName

get

get

remove

getElementBySId

remove