SBaseRef (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.CompBase
  - - org.sbml.libsbml.SBaseRef

Direct Known Subclasses:

Deletion, Port, Replacing
```
public class SBaseRef
extends CompBase
```
comp Base class for references to objects.
The SBaseRef class was introduced by the SBML Level 3 Hierarchical Model Composition (&ldquocomp&rdquo) package as the principle way by which submodel elements may be referenced. The SBaseRef class is usually found as the base class of a Port, Deletion, ReplacedElement, or ReplacedBy class, but may appear as an child of one of the above classes if the parent object references a Submodel.
An SBaseRef object must reference an element using exactly one of the optional attributes of the class. Subclasses of SBaseRef may define additional optional attributes that are legal ways to reference an element.
SBaseRef objects may reference elements that do not live in the Model parent of the SBaseRef object. However, the SBaseRef class itself does not provide a method of determining which Model or Submodel is being referenced. The subclasses of SBaseRef provide methods for this instead.
Once the Model to which the SBaseRef object is referencing has been established, there are four optional attributes defined in the SBaseRef class that are each methods of referencing an element:
- 'portRef' (type PortSIdRef): As its name implies, this attribute is used to refer to a port identifier, in the case when the reference being constructed with the SBaseRef is intended to refer to a port on a submodel. The namespace of the PortSIdRef value is the set of identifiers of type PortSId defined in the submodel, not the parent model.
- 'idRef' (type SIdRef): As its name implies, this attribute is used to refer to a regular identifier (i.e., the value of an 'id' attribute on some other object), in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace of the SIdRef value is the set of identifiers of type SId defined in the submodel, not the parent model.
- 'unitRef' (type UnitSIdRef): This attribute is used to refer to the identifier of a UnitDefinition object. The namespace of the UnitSIdRef value is the set of unit identifiers defined in the submodel, not the parent model. (Note that even though this attribute is of type UnitSIdRef, the reserved unit identifiers that are defined by SBML Level 3 (see Section 3.1.10 of the core specification) are *not* permitted as values of 'unitRef'. Reserved unit identifiers may not be replaced or deleted.)
- 'metaIdRef' (type IDREF): This attribute is used to refer to a 'metaid' attribute value on some other object, in the case when the reference being constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace of the 'metaIdRef' value is the entire document in which the referenced model resides, but must refer to a subelement of the referenced model. Since meta identifiers are optional attributes of SBase, all SBML objects have the potential to have a meta identifier value.
An SBaseRef object may have up to one subcomponent named 'sBaseRef', of type SBaseRef. This permits recursive structures to be constructed so that objects inside submodels can be referenced.
The form of such recursive references must be as follows. The highest-level SBaseRef object of such a chain (which will necessarily be an object of class Port, Deletion, ReplacedElement or ReplacedBy, because they are the only classes derived from the class SBaseRef) must refer to a Submodel object in the containing model. All child SBaseRef objects in the chain must refer to components inside the Model instance to which the Submodel refers.

Constructor Summary

Constructors
Constructor and Description
`SBaseRef()` Creates a new `SBaseRef` with the given level, version, and package version.
`SBaseRef(CompPkgNamespaces compns)` Creates a new `SBaseRef` with the given `CompPkgNamespaces` object.
`SBaseRef(long level)` Creates a new `SBaseRef` with the given level, version, and package version.
`SBaseRef(long level, long version)` Creates a new `SBaseRef` with the given level, version, and package version.
`SBaseRef(long level, long version, long pkgVersion)` Creates a new `SBaseRef` with the given level, version, and package version.
`SBaseRef(SBaseRef source)` Copy constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clearReferencedElement()` Removes the saved referenced element, if it had been saved earlier.
`SBase`	`cloneObject()` Creates and returns a deep copy of this `SBaseRef` object.
`void`	`connectToChild()`
`SBaseRef`	`createSBaseRef()` Creates a new, empty `SBaseRef`, adds it to this `SBaseRef` and returns the created `SBaseRef`.
`void`	`delete()` Explicitly deletes the underlying native object.
`SBase`	`getElementByMetaId(java.lang.String metaid)` Returns the first child element it can find with the given `metaid`, or itself if it has 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 SBML object.
`java.lang.String`	`getIdRef()` Returns the value of the 'idRef' attribute of this `SBaseRef`.
`java.lang.String`	`getMetaIdRef()` Returns the value of the 'metaIdRef' attribute of this `SBaseRef`.
`int`	`getNumReferents()` Returns how many elements are being referred to by this `SBaseRef`.
`java.lang.String`	`getPortRef()` Returns the value of the 'portRef' attribute of this `SBaseRef`.
`SBase`	`getReferencedElement()` Returns the object pointed to by this element.
`SBase`	`getReferencedElementFrom(Model model)` Examines the referenced `Model` for the referenced object, and returns it, if found.
`SBaseRef`	`getSBaseRef()` Get the child sBaseRef of this sBaseRef.
`int`	`getTypeCode()` Returns the libSBML type code of this object instance.
`java.lang.String`	`getUnitRef()` Returns the value of the 'unitRef' attribute of this `SBaseRef`.
`boolean`	`hasRequiredAttributes()` Returns `true` if getNumReferents() is exactly 1.
`boolean`	`isSetIdRef()` Predicate returning `true` or `false` depending on whether this `SBaseRef`'s 'idRef' attribute has been set.
`boolean`	`isSetMetaIdRef()` Predicate returning `true` or `false` depending on whether this `SBaseRef`'s 'metaIdRef' attribute has been set.
`boolean`	`isSetPortRef()` Predicate returning `true` or `false` depending on whether this `SBaseRef`'s 'portRef' attribute has been set.
`boolean`	`isSetSBaseRef()` Predicate for testing whether the sBaseRef for this `SBaseRef` is set.
`boolean`	`isSetUnitRef()` Predicate returning `true` or `false` depending on whether this `SBaseRef`'s 'unitRef' attribute has been set.
`int`	`performDeletion()` DEPRECATED FUNCTION: DO NOT USE
`int`	`removeFromParentAndDelete()` Finds this `SBaseRef`'s parent, which can either be a List or can be another `SBaseRef`, and tells it to remove this.
`void`	`renameSIdRefs(java.lang.String oldid, java.lang.String newid)` Replaces all uses of a given `SIdRef` type attribute value with another value.
`int`	`saveReferencedElement()` Finds and stores the referenced object by finding the `Model` it needs to point to, calling 'saveReferencedElement' on its parent (which will also be a `SBaseRef` or one of its subclasses), and the storing the result.
`int`	`setIdRef(java.lang.String id)` Sets the value of the 'idRef' attribute of this `SBaseRef`.
`int`	`setMetaIdRef(java.lang.String id)` Sets the value of the 'metaIdRef' attribute of this `SBaseRef`.
`int`	`setPortRef(java.lang.String id)` Sets the value of the 'portRef' attribute of this `SBaseRef`.
`int`	`setSBaseRef(SBaseRef sBaseRef)` Sets the sBaseRef definition of this `SBaseRef` to a copy of the given `SBaseRef` object instance.
`int`	`setUnitRef(java.lang.String id)` Sets the value of the 'unitRef' attribute of this `SBaseRef`.
`int`	`unsetIdRef()` Unsets the value of the 'idRef' attribute of this `SBaseRef`.
`int`	`unsetMetaIdRef()` Unsets the value of the 'metaIdRef' attribute of this `SBaseRef`.
`int`	`unsetPortRef()` Unsets the value of the 'portRef' attribute of this `SBaseRef`.
`int`	`unsetSBaseRef()` Unsets the child `SBaseRef` of this `SBaseRef`.
`int`	`unsetUnitRef()` Unsets the value of the 'unitRef' attribute of this `SBaseRef`.

Methods inherited from class org.sbml.libsbml.CompBase
getPackageName, getPackageURI, getPackageVersion, getParentModel

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, 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, 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
  - SBaseRef
```
public SBaseRef(long level,
                long version,
                long pkgVersion)
         throws SBMLConstructorException
```
    Creates a new SBaseRef with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - SBaseRef
```
public SBaseRef(long level,
                long version)
         throws SBMLConstructorException
```
    Creates a new SBaseRef with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - SBaseRef
```
public SBaseRef(long level)
         throws SBMLConstructorException
```
    Creates a new SBaseRef with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - SBaseRef
```
public SBaseRef()
         throws SBMLConstructorException
```
    Creates a new SBaseRef with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - SBaseRef
```
public SBaseRef(CompPkgNamespaces compns)
         throws SBMLConstructorException
```
    Creates a new SBaseRef with the given CompPkgNamespaces object.
    
    The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
    
    Parameters:
    
    compns - the CompPkgNamespaces object.
    
    Throws:
    
    SBMLConstructorException
    
    "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. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - SBaseRef
```
public SBaseRef(SBaseRef source)
         throws SBMLConstructorException
```
    Copy constructor.
    
    Parameters:
    
    source - the instance 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 SBaseRef.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 SBaseRef.delete() themselves.
    
    Overrides:
    
    delete in class CompBase
  - cloneObject
```
public SBase cloneObject()
```
    Creates and returns a deep copy of this SBaseRef object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this SBaseRef 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 the object to find.
    
    Returns:
    
    a pointer to the SBase element 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 itself if it has the given metaid, or null if no such object is found.
    
    Overrides:
    
    getElementByMetaId in class SBase
    
    Parameters:
    
    metaid - string representing the metaid of the object to find.
    
    Returns:
    
    a pointer to the SBase element with the given metaid.
  - getMetaIdRef
```
public java.lang.String getMetaIdRef()
```
    Returns the value of the 'metaIdRef' attribute of this SBaseRef.
    
    Returns:
    
    the value of the 'metaIdRef' attribute of this SBaseRef.
  - isSetMetaIdRef
```
public boolean isSetMetaIdRef()
```
    Predicate returning true or false depending on whether this SBaseRef's 'metaIdRef' attribute has been set.
    
    Returns:
    
    true if this SBaseRef's 'metaIdRef' attribute has been set, otherwise false is returned.
  - setMetaIdRef
```
public int setMetaIdRef(java.lang.String id)
```
    Sets the value of the 'metaIdRef' attribute of this SBaseRef.
    This method fails if the id is not a valid syntax for an IDREF (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). An sBaseRef must use exactly one method to point to a submodel element.
    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_OPERATION_FAILED
  - unsetMetaIdRef
```
public int unsetMetaIdRef()
```
    Unsets the value of the 'metaIdRef' attribute of this SBaseRef.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getPortRef
```
public java.lang.String getPortRef()
```
    Returns the value of the 'portRef' attribute of this SBaseRef.
    
    Returns:
    
    the value of the 'portRef' attribute of this SBaseRef.
  - isSetPortRef
```
public boolean isSetPortRef()
```
    Predicate returning true or false depending on whether this SBaseRef's 'portRef' attribute has been set.
    
    Returns:
    
    true if this SBaseRef's 'portRef' attribute has been set, otherwise false is returned.
  - setPortRef
```
public int setPortRef(java.lang.String id)
```
    Sets the value of the 'portRef' attribute of this SBaseRef. Fails if the id is not a valid syntax for a PortSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). An SBaseRef must use exactly one method to point to a submodel element.
    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_OPERATION_FAILED
  - unsetPortRef
```
public int unsetPortRef()
```
    Unsets the value of the 'portRef' attribute of this SBaseRef.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getIdRef
```
public java.lang.String getIdRef()
```
    Returns the value of the 'idRef' attribute of this SBaseRef.
    
    Returns:
    
    the value of the 'idRef' attribute of this SBaseRef.
  - isSetIdRef
```
public boolean isSetIdRef()
```
    Predicate returning true or false depending on whether this SBaseRef's 'idRef' attribute has been set.
    
    Returns:
    
    true if this SBaseRef's 'idRef' attribute has been set, otherwise false is returned.
  - setIdRef
```
public int setIdRef(java.lang.String id)
```
    Sets the value of the 'idRef' attribute of this SBaseRef.
    This method fails if the id is not a valid syntax for an SIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). A sBaseRef must use exactly one method to point to a submodel element.
    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_OPERATION_FAILED
  - unsetIdRef
```
public int unsetIdRef()
```
    Unsets the value of the 'idRef' attribute of this SBaseRef.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
```
   letter .= 'a'..'z','A'..'Z'
   digit  .= '0'..'9'
   idChar .= letter | digit | '_'
   SId    .= ( letter | '_' ) idChar*
 
```
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.isSetIdAttribute(), SBase.unsetIdAttribute()
  - getUnitRef
```
public java.lang.String getUnitRef()
```
    Returns the value of the 'unitRef' attribute of this SBaseRef.
    
    Returns:
    
    the value of the 'unitRef' attribute of this SBaseRef.
  - isSetUnitRef
```
public boolean isSetUnitRef()
```
    Predicate returning true or false depending on whether this SBaseRef's 'unitRef' attribute has been set.
    
    Returns:
    
    true if this SBaseRef's 'unitRef' attribute has been set, otherwise false is returned.
  - setUnitRef
```
public int setUnitRef(java.lang.String id)
```
    Sets the value of the 'unitRef' attribute of this SBaseRef.
    This method fails if the id is not a valid syntax for a UnitSIdRef (LIBSBML_INVALID_ATTRIBUTE_VALUE), or if the SBaseRef already points to an element of the submodel using a different interface (LIBSBML_OPERATION_FAILED). A sBaseRef must use exactly one method to point to a submodel element.
    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_OPERATION_FAILED
  - unsetUnitRef
```
public int unsetUnitRef()
```
    Unsets the value of the 'unitRef' attribute of this SBaseRef.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getSBaseRef
```
public SBaseRef getSBaseRef()
```
    Get the child sBaseRef of this sBaseRef.
    
    Returns:
    
    the SBaseRef child of this SBaseRef, or null if none exists.
  - isSetSBaseRef
```
public boolean isSetSBaseRef()
```
    Predicate for testing whether the sBaseRef for this SBaseRef is set.
    
    Returns:
    
    true if the sBaseRef of this SBaseRef is set, false otherwise.
  - setSBaseRef
```
public int setSBaseRef(SBaseRef sBaseRef)
```
    Sets the sBaseRef definition of this SBaseRef to a copy of the given SBaseRef object instance.
    This method fails if the added sBaseRef does not match the level/version/package of the parent object or if the added sBaseRef cannot be copied.
    Parameters:
    
    sBaseRef - the SBaseRef object instance to use.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
  - createSBaseRef
```
public SBaseRef createSBaseRef()
```
    Creates a new, empty SBaseRef, adds it to this SBaseRef and returns the created SBaseRef.
    
    Returns:
    
    the newly created SBaseRef object instance.
  - unsetSBaseRef
```
public int unsetSBaseRef()
```
    Unsets the child SBaseRef of this SBaseRef. Deletes the former SBaseRef child, if one existed.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getNumReferents
```
public int getNumReferents()
```
    Returns how many elements are being referred to by this SBaseRef. A valid SBaseRef will have exactly one. Possible referents are portRef, idRef, unitRef, and metaIdRef.
    
    Returns:
    
    integer value between 0 and 4: the number of different ways this element points to its referent.
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Returns true if getNumReferents() is exactly 1.
    
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    boolean: 'true' if the attributes are correctly set 'false' if not.
  - 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 SIdRef in 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.
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this SBML object.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, as a text string.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code of this object instance.
    
    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:
    
    getTypeCode in class SBase
    
    Returns:
    
    the SBML type code for this object: SBML_COMP_SBASEREF.
    
    See Also:
    
    SBaseRef.getElementName(), CompBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - connectToChild
```
public void connectToChild()
```
    Overrides:
    
    connectToChild in class SBase
  - getReferencedElementFrom
```
public SBase getReferencedElementFrom(Model model)
```
    Examines the referenced Model for the referenced object, and returns it, if found.
    
    Parameters:
    
    model - the Model in which to look for the object referenced by this SBaseRef.
    
    Returns:
    
    the element in the referenced Model to which this SBaseRef refers. If this object references an object in a Submodel, the returned object will be in the instantiated Model in that Submodel.
  - saveReferencedElement
```
public int saveReferencedElement()
```
    Finds and stores the referenced object by finding the Model it needs to point to, calling 'saveReferencedElement' on its parent (which will also be a SBaseRef or one of its subclasses), and the storing the result.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getReferencedElement
```
public SBase getReferencedElement()
```
    Returns the object pointed to by this element. If that element was previously found and set with 'saveReferencedElement', that element is returned otherwise, 'saveReferencedElement' is called first, and the found element is returned.
  - clearReferencedElement
```
public void clearReferencedElement()
```
    Removes the saved referenced element, if it had been saved earlier.
  - performDeletion
```
public int performDeletion()
```
    DEPRECATED FUNCTION: DO NOT USE
    Deletes the referenced object, plus any other elements that element points to through ReplacedElement or ReplacedBy children. Instead of calling this function directly, use 'CompModelPlugin.instantiateSubmodels' instead, which deals with all the intricacies of replacements and deletions, and gives you access to the non-flattened hierarchical form of the model.
  - removeFromParentAndDelete
```
public int removeFromParentAndDelete()
```
    Finds this SBaseRef's parent, which can either be a List or can be another SBaseRef, and tells it to remove this.
    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

Class SBaseRef

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.CompBase

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

SBaseRef

SBaseRef

SBaseRef

SBaseRef

SBaseRef

SBaseRef

Method Detail

delete

cloneObject

getElementBySId

getElementByMetaId

getMetaIdRef

isSetMetaIdRef

setMetaIdRef

unsetMetaIdRef

getPortRef

isSetPortRef

setPortRef

unsetPortRef

getIdRef

isSetIdRef

setIdRef

unsetIdRef

getUnitRef

isSetUnitRef

setUnitRef

unsetUnitRef

getSBaseRef

isSetSBaseRef

setSBaseRef

createSBaseRef

unsetSBaseRef

getNumReferents

hasRequiredAttributes

renameSIdRefs

getElementName

getTypeCode

connectToChild

getReferencedElementFrom

saveReferencedElement

getReferencedElement

clearReferencedElement

performDeletion

removeFromParentAndDelete