LibSBML %%version%%, an application programming interface (API) library for SBML.
 | SBML Team http://www.sbml.org/ sbml-team@caltech.edu |
public class ListOfReplacedElements extends ListOf
ReplacedElement objects.
The ListOfReplacedElements is a container for any SBase object. It
contains ReplacedElement objects, which point to elements the parent
SBase object is to replace.
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):
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'.
ListOfFunctionDefinitions,
ListOfUnitDefinitions,
ListOfCompartmentTypes,
ListOfSpeciesTypes,
ListOfCompartments,
ListOfSpecies,
ListOfParameters,
ListOfInitialAssignments,
ListOfRules,
ListOfConstraints,
ListOfReactions,
ReplacedElement,
ListOfDeletions,
ListOfExternalModelDefinitions,
ListOfModelDefinitions,
ListOfPorts,
ListOfSubmodels| Constructor and Description |
|---|
ListOfReplacedElements()
Creates a new
ListOfReplacedElements with the given level, version, and
package version. |
ListOfReplacedElements(CompPkgNamespaces compns)
Creates a new
ListOfReplacedElements with the given CompPkgNamespaces
object. |
ListOfReplacedElements(long level)
Creates a new
ListOfReplacedElements with the given level, version, and
package version. |
ListOfReplacedElements(long level,
long version)
Creates a new
ListOfReplacedElements with the given level, version, and
package version. |
ListOfReplacedElements(long level,
long version,
long pkgVersion)
Creates a new
ListOfReplacedElements with the given level, version, and
package version. |
| Modifier and Type | Method and Description |
|---|---|
ListOfReplacedElements |
cloneObject()
Creates and returns a deep copy of this
ListOfReplacedElements object. |
void |
delete()
Explicitly deletes the underlying native object.
|
SBase |
get(long n)
Get a
ReplacedElement from the ListOfReplacedElements. |
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the objects contained in this
ListOf
(i.e., ReplacedElements objects, if the list is non-empty). |
SBase |
remove(long n)
Removes the nth item from this
ListOfReplacedElements items and returns
a pointer to it. |
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, sizeaddCVTerm, 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, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserDatapublic ListOfReplacedElements(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfReplacedElements with the given level, version, and
package version.
level - the SBML Levelversion - the Version within the SBML LevelpkgVersion - the version of the packageSBMLConstructorExceptionpublic ListOfReplacedElements(long level, long version) throws SBMLConstructorException
ListOfReplacedElements with the given level, version, and
package version.
level - the SBML Levelversion - the Version within the SBML LevelpkgVersion - the version of the packageSBMLConstructorExceptionpublic ListOfReplacedElements(long level) throws SBMLConstructorException
ListOfReplacedElements with the given level, version, and
package version.
level - the SBML Levelversion - the Version within the SBML LevelpkgVersion - the version of the packageSBMLConstructorExceptionpublic ListOfReplacedElements() throws SBMLConstructorException
ListOfReplacedElements with the given level, version, and
package version.
level - the SBML Levelversion - the Version within the SBML LevelpkgVersion - the version of the packageSBMLConstructorExceptionpublic ListOfReplacedElements(CompPkgNamespaces compns) throws SBMLConstructorException
ListOfReplacedElements with the given CompPkgNamespaces
object.
compns - the namespace to useSBMLConstructorExceptionpublic void delete()
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 ListOfReplacedElements.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 ListOfReplacedElements.delete() themselves.
public ListOfReplacedElements cloneObject()
ListOfReplacedElements object.
cloneObject in class ListOfListOfReplacedElements.public SBase get(long n)
ReplacedElement from the ListOfReplacedElements.
get in class ListOfn - the index number of the ReplacedElement to get.
ReplacedElement in this ListOfReplacedElements.
ListOf.size()public SBase remove(long n)
ListOfReplacedElements items and returns
a pointer to it.
The caller owns the returned item and is responsible for deleting it.
remove in class ListOfn - the index of the item to remove
ListOf.size()public int getItemTypeCode()
ListOf
(i.e., ReplacedElements 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 getPackageName()
method on the object.
getItemTypeCode in class ListOfSBML_COMP_REPLACEDELEMENT (default).
ListOfReplacedElements.getElementName(),
SBase.getPackageName()public java.lang.String getElementName()
getElementName in class ListOf
LibSBML %%version%%, an application programming interface (API) library for SBML.
SBML Team
http://www.sbml.org/
sbml-team@caltech.edu