public class ListOfSpeciesReferences extends ListOf
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'.
Constructor and Description |
---|
ListOfSpeciesReferences(long level,
long version)
Creates a new, empty
ListOfSpeciesReferences object. |
ListOfSpeciesReferences(SBMLNamespaces sbmlns)
Creates a new
ListOfSpeciesReferences object. |
Modifier and Type | Method and Description |
---|---|
ListOfSpeciesReferences |
cloneObject()
Creates and returns a deep copy of this
ListOfSpeciesReferences
instance. |
void |
delete()
Explicitly deletes the underlying native object.
|
SimpleSpeciesReference |
get(long n)
Get a
SpeciesReference from the ListOfSpeciesReferences . |
SimpleSpeciesReference |
get(java.lang.String sid)
Get a
SpeciesReference from the ListOfSpeciesReferences
based on its identifier. |
java.lang.String |
getElementName()
Returns the XML element name of this object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the objects contained in this
ListOf
(i.e., SpeciesReference objects, if the list is non-empty). |
SimpleSpeciesReference |
remove(long n)
Removes the nth item from this
ListOfSpeciesReferences items and returns a pointer to
it. |
SimpleSpeciesReference |
remove(java.lang.String sid)
Removes item in this
ListOfSpeciesReferences items with the given identifier. |
append, appendAndOwn, appendFrom, clear, clear, getElementByMetaId, getElementBySId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, size
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, getPackageName, getPackageVersion, 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, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm
public ListOfSpeciesReferences(long level, long version) throws SBMLConstructorException
ListOfSpeciesReferences
object.
The object is constructed such that it is valid for the given SBML Level and Version combination.
level
- the SBML Level
version
- the Version within the SBML LevelSBMLConstructorException
public ListOfSpeciesReferences(SBMLNamespaces sbmlns) throws SBMLConstructorException
ListOfSpeciesReferences
object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces
object in
sbmlns
.
sbmlns
- an SBMLNamespaces
object that is used to determine the
characteristics of the ListOfSpeciesReferences
object to be created.SBMLConstructorException
public ListOfSpeciesReferences cloneObject()
ListOfSpeciesReferences
instance.
cloneObject
 in class ListOf
ListOfSpeciesReferences
.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 ListOfSpeciesReferences.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 ListOfSpeciesReferences.delete()
themselves.
public SimpleSpeciesReference get(long n)
SpeciesReference
from the ListOfSpeciesReferences
.
get
 in class ListOf
n
- the index number of the SpeciesReference
to get.
SpeciesReference
in this ListOfSpeciesReferences
.
ListOf.size()
public SimpleSpeciesReference get(java.lang.String sid)
SpeciesReference
from the ListOfSpeciesReferences
based on its identifier.
sid
- a string representing the identifier
of the SpeciesReference
to get.
SpeciesReference
in this ListOfSpeciesReferences
with the given sid
or null
if no such
SpeciesReference
exists.
ListOfSpeciesReferences.get(long n)
,
ListOf.size()
public java.lang.String getElementName()
For ListOfSpeciesReferences
, the XML element name is
'listOfSpeciesReferences'.
getElementName
 in class ListOf
'listOfSpeciesReferences'.
public int getItemTypeCode()
ListOf
(i.e., SpeciesReference
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 &ldquoSBML_
&rdquo.
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_SPECIES_REFERENCE
(default).
ListOfSpeciesReferences.getElementName()
,
SBase.getPackageName()
public SimpleSpeciesReference remove(long n)
ListOfSpeciesReferences
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 SimpleSpeciesReference remove(java.lang.String sid)
ListOfSpeciesReferences
items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier sid
, then
null
is returned.
sid
- the identifier of the item to remove