org.sbml.libsbml

Class CompSBasePlugin

java.lang.Object

org.sbml.libsbml.SBasePlugin

org.sbml.libsbml.CompSBasePlugin

Direct Known Subclasses:

CompModelPlugin

public class CompSBasePlugin
extends SBasePlugin

comp Extension of SBase.

The CompSBasePlugin class inherits from the SBasePlugin class, and codifies the extensions to the SBase class defined in the Hierarchical Model Composition (“comp”) package. This extension allows the modeler to define one or more submodel elements which the parent SBase object replaces, and/or a single submodel element which replaces the parent SBase object.

This is accomplished through the addition of an optional ListOfReplacedElements child, which may contain one or more ReplacedElement objects, each of which references a submodel object to be replaced by the containing SBase object, and through the addition of a single optional ReplacedBy child, which references a submodel object which is to replace the containing SBase object.

If a single SBase element both contains a ListOfReplacedElements and has a ReplacedBy child, it and all the referenced ReplacedElement objects are to be replaced by the object referenced by the ReplacedBy element.

See Also:

ReplacedElement, ReplacedBy

Constructor Summary

Constructors

Constructor and Description
CompSBasePlugin(CompSBasePlugin orig) Copy constructor.
CompSBasePlugin(java.lang.String uri, java.lang.String prefix, CompPkgNamespaces compns) Creates a new CompSBasePlugin object using the given parameters.

Method Summary

Modifier and Type	Method and Description
int	addReplacedElement(ReplacedElement replacedElement) Adds a copy of the given ReplacedElement object to the list of ReplacedElements.
void	clearReplacedElements() Remove all ReplacedElements, if any exist.
SBasePlugin	cloneObject() Creates and returns a deep copy of this CompSBasePlugin object.
ReplacedBy	createReplacedBy() Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.
ReplacedElement	createReplacedElement() Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.
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.
ListOfReplacedElements	getListOfReplacedElements() Returns the ListOf object that holds all replacedElements.
long	getNumReplacedElements() Returns the number of ReplacedElements for this CompSBasePlugin.
ReplacedBy	getReplacedBy() Get the child ReplacedBy of this SBase.
ReplacedElement	getReplacedElement(long n) Returns the ReplacedElement with the given index.
boolean	isSetReplacedBy() Predicate for testing whether the ReplacedBy for this SBase is set.
void	logInvalidId(java.lang.String attribute, java.lang.String wrongattribute) Helper to log a common type of error.
ReplacedElement	removeReplacedElement(long index) Removes the ReplacedElement with the given index.
int	setReplacedBy(ReplacedBy replacedBy) Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.
int	unsetReplacedBy() Unsets the child ReplacedBy of this SBase.

Methods inherited from class org.sbml.libsbml.SBasePlugin

getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, setElementNamespace

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CompSBasePlugin

public CompSBasePlugin(java.lang.String uri,
                       java.lang.String prefix,
                       CompPkgNamespaces compns)

Creates a new CompSBasePlugin object using the given parameters.

In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs; for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces; for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.

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:

uri - the URI of the SBML Level 3 package implemented by this libSBML package extension.

prefix - the XML namespace prefix being used for the package.

compns - the namespaces object for the package.

CompSBasePlugin

public CompSBasePlugin(CompSBasePlugin orig)

Copy constructor. Creates a copy of this CompSBasePlugin object.

Parameters:

orig - the instance to copy.

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 CompSBasePlugin.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 CompSBasePlugin.delete() themselves.

Overrides:

delete in class SBasePlugin

cloneObject

public SBasePlugin cloneObject()

Creates and returns a deep copy of this CompSBasePlugin object.

Overrides:

cloneObject in class SBasePlugin

Returns:

a (deep) copy of this CompSBasePlugin 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 SBasePlugin

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 SBasePlugin

Parameters:

metaid - string representing the metaid of the object to find.

Returns:

a pointer to the SBase element with the given metaid.

getListOfReplacedElements

public ListOfReplacedElements getListOfReplacedElements()

Returns the ListOf object that holds all replacedElements.

Returns:

the ListOf object that holds all replacedElements.

getReplacedElement

public ReplacedElement getReplacedElement(long n)

Returns the ReplacedElement with the given index.

Parameters:

n - the index number of the ReplacedElement to get.

Returns:

the nth ReplacedElement in the ListOfReplacedElements. If the index is invalid, null is returned.

addReplacedElement

public int addReplacedElement(ReplacedElement replacedElement)

Adds a copy of the given ReplacedElement object to the list of ReplacedElements.

Parameters:

replacedElement - the ReplacedElement object to be added to the list of ReplacedElements. Fails if the added ReplacedElement is null, does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_INVALID_OBJECT
• LIBSBML_LEVEL_MISMATCH
• LIBSBML_VERSION_MISMATCH
• LIBSBML_PKG_VERSION_MISMATCH

getNumReplacedElements

public long getNumReplacedElements()

Returns the number of ReplacedElements for this CompSBasePlugin.

Returns:

the number of ReplacedElements for this CompSBasePlugin.

clearReplacedElements

public void clearReplacedElements()

Remove all ReplacedElements, if any exist.

createReplacedElement

public ReplacedElement createReplacedElement()

Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.

Returns:

a newly created ReplacedElement object.

removeReplacedElement

public ReplacedElement removeReplacedElement(long index)

Removes the ReplacedElement with the given index.

A pointer to the ReplacedElement that was removed is returned. If no ReplacedElement has been removed, null is returned.

Parameters:

index - the index of the ReplacedElement object to remove.

Returns:

the ReplacedElement object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

getReplacedBy

public ReplacedBy getReplacedBy()

Get the child ReplacedBy of this SBase.

Returns:

the ReplacedBy child of this SBase.

isSetReplacedBy

public boolean isSetReplacedBy()

Predicate for testing whether the ReplacedBy for this SBase is set.

Returns:

true if the ReplacedBy of this SBase is set, false otherwise.

setReplacedBy

public int setReplacedBy(ReplacedBy replacedBy)

Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.

This method fails if the added ReplacedBy does not match the level/version/package of the parent object or if the added ReplacedBy cannot be copied.

Parameters:

replacedBy - the ReplacedBy 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

createReplacedBy

public ReplacedBy createReplacedBy()

Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.

Returns:

the newly created ReplacedBy object instance.

unsetReplacedBy

public int unsetReplacedBy()

Unsets the child ReplacedBy of this SBase.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED

logInvalidId

public void logInvalidId(java.lang.String attribute,
                         java.lang.String wrongattribute)

Helper to log a common type of error.