org.sbml.libsbml

Class Replacing

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.CompBase

org.sbml.libsbml.SBaseRef

org.sbml.libsbml.Replacing

Direct Known Subclasses:

ReplacedBy, ReplacedElement

public class Replacing
extends SBaseRef

comp A convenience subclass of the ReplacedElement and ReplacedBy constructs from the &ldquocomp&rdquo package.

The Replacing class does not exist officialy in the the 'Hierarchical Model Composition' package (&ldquocomp&rdquo), but is implemented here as a convenience subclass of the ReplacedElement and ReplacedBy classes, since both of those classes define a 'submodelRef' attribute.

The required attribute 'submodelRef' takes a value of type SIdRef, which must be the identifier of a Submodel object in the containing model. The model referenced by the Submodel object establishes the object namespaces for the 'portRef', 'idRef', 'unitRef' and 'metaIdRef' attributes: only objects within the Model object may be referenced by those attributes.

Method Summary

Methods

Modifier and Type	Method and Description
void	delete() Explicitly deletes the underlying native object.
java.lang.String	getSubmodelRef() Returns the value of the 'submodelRef' attribute of this SBaseRef.
boolean	hasRequiredAttributes() Returns true if getNumReferents() is exactly 1 and if the submodelRef is set.
boolean	isSetSubmodelRef() Predicate returning true or false depending on whether this SBaseRef's 'submodelRef' attribute has been set.
int	performReplacement() DEPRECATED FUNCTION: DO NOT USE
void	renameSIdRefs(java.lang.String oldid, java.lang.String newid) Renames all the SIdRef attributes on this element if they match oldid, but not any found in child or plugin elements.
int	saveReferencedElement() Finds and stores the referenced object.
int	setSubmodelRef(java.lang.String id) Sets the value of the 'submodelRef' attribute of this SBaseRef.
int	unsetSubmodelRef() Unsets the value of the 'SubmodelRef' attribute of this SBaseRef.

Methods inherited from class org.sbml.libsbml.SBaseRef

clearReferencedElement, cloneObject, createSBaseRef, getElementByMetaId, getElementBySId, getElementName, getIdRef, getMetaIdRef, getNumReferents, getPortRef, getReferencedElement, getReferencedElementFrom, getSBaseRef, getTypeCode, getUnitRef, isSetIdRef, isSetMetaIdRef, isSetPortRef, isSetSBaseRef, isSetUnitRef, performDeletion, removeFromParentAndDelete, setIdRef, setMetaIdRef, setPortRef, setSBaseRef, setUnitRef, unsetIdRef, unsetMetaIdRef, unsetPortRef, unsetSBaseRef, unsetUnitRef

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, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

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 Replacing.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 Replacing.delete() themselves.

Overrides:

delete in class SBaseRef

getSubmodelRef

public java.lang.String getSubmodelRef()

Returns the value of the 'submodelRef' attribute of this SBaseRef.

Returns:

the value of the 'submodelRef' attribute of this SBaseRef.

hasRequiredAttributes

public boolean hasRequiredAttributes()

Returns true if getNumReferents() is exactly 1 and if the submodelRef is set.

Overrides:

hasRequiredAttributes in class SBaseRef

Returns:

boolean: 'true' if the attributes are correctly set 'false' if not.

isSetSubmodelRef

public boolean isSetSubmodelRef()

Predicate returning true or false depending on whether this SBaseRef's 'submodelRef' attribute has been set.

Returns:

true if this SBaseRef's 'submodelRef' attribute has been set, otherwise false is returned.

performReplacement

public int performReplacement()

DEPRECATED FUNCTION: DO NOT USE

To retain old functionality, this function calls performReplacementAndCollect, and then actually removes the now-redundant element. However, this can lead to doubly-deleted elements, as well as the incorrect interpretation of some models. The replacement function performReplacementAndCollect has been marked protected, in the hopes that people will instead simply use CompModelPlugin.instantiateSubmodels, which hides all the complexity while still allowing access to a non-flattened version of a hierarchical model.

renameSIdRefs

public void renameSIdRefs(java.lang.String oldid,
                 java.lang.String newid)

Renames all the SIdRef attributes on this element if they match oldid, but not any found in child or plugin elements.

Overrides:

renameSIdRefs in class SBaseRef

Parameters:

oldid - the old identifier

newid - the new identifier

saveReferencedElement

public int saveReferencedElement()

Finds and stores the referenced object. Finds the Submodel to which it refers, getting the instantiated Model inside that Submodel, calling 'getReferencedElementFrom' on that model, and storing the result.

Overrides:

saveReferencedElement in class SBaseRef

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_INVALID_ATTRIBUTE_VALUE
• LIBSBML_OPERATION_FAILED

setSubmodelRef

public int setSubmodelRef(java.lang.String id)

Sets the value of the 'submodelRef' attribute of this SBaseRef. Fails if the id is not a valid syntax for an SIdRef.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_ATTRIBUTE_VALUE

unsetSubmodelRef

public int unsetSubmodelRef()

Unsets the value of the 'SubmodelRef' attribute of this SBaseRef.

Returns:

integer value indicating success/failure of the operation. The possible return values are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED