public class ListOfDeletions extends ListOf
Deletion
objects.
The ListOfDeletions
is a container for the &ldquocomp&rdquo
Submodel
that defines elements to be removed before instantiation.
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
,
,
Deletion
,
ListOfExternalModelDefinitions
,
ListOfModelDefinitions
,
ListOfPorts
,
ListOfReplacedElements
,
ListOfSubmodels
Constructor and Description |
---|
ListOfDeletions()
Creates a new
ListOfDeletions with the given level, version, and package
version. |
ListOfDeletions(CompPkgNamespaces compns)
Creates a new
ListOfDeletions with the given CompPkgNamespaces object. |
ListOfDeletions(long level)
Creates a new
ListOfDeletions with the given level, version, and package
version. |
ListOfDeletions(long level,
long version)
Creates a new
ListOfDeletions with the given level, version, and package
version. |
ListOfDeletions(long level,
long version,
long pkgVersion)
Creates a new
ListOfDeletions with the given level, version, and package
version. |
Modifier and Type | Method and Description |
---|---|
ListOfDeletions |
cloneObject()
Creates and returns a deep copy of this
ListOfDeletions object. |
void |
delete()
Explicitly deletes the underlying native object.
|
SBase |
get(long n)
Get a
Deletion from the ListOfDeletions . |
Deletion |
get(String sid)
Get a
Deletion from the ListOfDeletions
based on its identifier. |
String |
getElementName()
Returns the XML element name of this SBML object.
|
int |
getItemTypeCode()
|
SBase |
remove(long n)
Removes the nth item from this
ListOfDeletions items and returns a
pointer to it. |
Deletion |
remove(String sid)
Removes an item from this
ListOfDeletions items based on its identifier
and returns a pointer to it. |
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, size
addCVTerm, 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, unsetUserData
public ListOfDeletions(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfDeletions
with the given level, version, and package
version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfDeletions(long level, long version) throws SBMLConstructorException
ListOfDeletions
with the given level, version, and package
version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfDeletions(long level) throws SBMLConstructorException
ListOfDeletions
with the given level, version, and package
version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfDeletions() throws SBMLConstructorException
ListOfDeletions
with the given level, version, and package
version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfDeletions(CompPkgNamespaces compns) throws SBMLConstructorException
ListOfDeletions
with the given CompPkgNamespaces
object.
compns
- the namespace to useSBMLConstructorException
public 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 ListOfDeletions.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 ListOfDeletions.delete()
themselves.
public ListOfDeletions cloneObject()
ListOfDeletions
object.
cloneObject
 in class ListOf
ListOfDeletions
.public SBase get(long n)
Deletion
from the ListOfDeletions
.
get
 in class ListOf
n
- the index number of the Deletion
to get.
Deletion
in this ListOfDeletions
.
ListOf.size()
public Deletion get(String sid)
Deletion
from the ListOfDeletions
based on its identifier.
sid
- a string representing the identifier
of the Deletion
to get.
Deletion
in this ListOfDeletions
with the given sid
or null
if no such
Member exists.
ListOfDeletions.get(long n)
,
ListOf.size()
public SBase remove(long n)
ListOfDeletions
items and returns a
pointer to it.
The caller owns the returned item and is responsible for deleting it.
remove
 in class ListOf
n
- the index of the item to remove
ListOf.size()
public Deletion remove(String sid)
ListOfDeletions
items based on its identifier
and returns a pointer to it.
The caller owns the returned item and is responsible for deleting it.
sid
- string representing the id of the item to remove
ListOf.size()
public int getItemTypeCode()
ListOf
(i.e., Deletion
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 ListOf
SBML_COMP_DELETION
(default).
ListOfDeletions.getElementName()
,
SBase.getPackageName()
public String getElementName()
getElementName
 in class ListOf