public class ListOfPorts extends ListOf
Port
objects.
The ListOfPorts
is a container for the extended
Model
for Port
objects for that Model
.
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.
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
,
,
Port
,
ListOfDeletions
,
ListOfExternalModelDefinitions
,
ListOfModelDefinitions
,
ListOfReplacedElements
,
ListOfSubmodels
Constructor and Description |
---|
ListOfPorts()
Creates a new
ListOfPorts with the given level, version, and package version. |
ListOfPorts(CompPkgNamespaces compns)
Creates a new
ListOfPorts with the given CompPkgNamespaces object. |
ListOfPorts(long level)
Creates a new
ListOfPorts with the given level, version, and package version. |
ListOfPorts(long level,
long version)
Creates a new
ListOfPorts with the given level, version, and package version. |
ListOfPorts(long level,
long version,
long pkgVersion)
Creates a new
ListOfPorts with the given level, version, and package version. |
Modifier and Type | Method and Description |
---|---|
ListOfPorts |
cloneObject()
Creates and returns a deep copy of this
ListOfPorts object. |
void |
delete()
Explicitly deletes the underlying native object.
|
SBase |
get(long n)
Get a
Port from the ListOfPorts . |
Port |
get(java.lang.String sid)
Get a
Port from the ListOfPorts
based on its identifier. |
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. |
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
int |
getItemTypeCode()
|
SBase |
remove(long n)
Removes the nth item from this
ListOfPorts items and returns a pointer
to it. |
Port |
remove(java.lang.String sid)
Removes an item from this
ListOfPorts items based on the identifier and
returns a pointer to it. |
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, 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 ListOfPorts(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfPorts
with the given level, version, and package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfPorts(long level, long version) throws SBMLConstructorException
ListOfPorts
with the given level, version, and package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfPorts(long level) throws SBMLConstructorException
ListOfPorts
with the given level, version, and package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfPorts() throws SBMLConstructorException
ListOfPorts
with the given level, version, and package version.
level
- the SBML Levelversion
- the Version within the SBML LevelpkgVersion
- the version of the packageSBMLConstructorException
public ListOfPorts(CompPkgNamespaces compns) throws SBMLConstructorException
ListOfPorts
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 ListOfPorts.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 ListOfPorts.delete()
themselves.
public ListOfPorts cloneObject()
ListOfPorts
object.
cloneObject
 in class ListOf
ListOfPorts
.public SBase get(long n)
Port
from the ListOfPorts
.
get
 in class ListOf
n
- the index number of the Port
to get.
Port
in this ListOfPorts
.
ListOf.size()
public Port get(java.lang.String sid)
Port
from the ListOfPorts
based on its identifier.
sid
- a string representing the identifier
of the Port
to get.
Port
in this ListOfPorts
with the given sid
or null
if no such
Member
exists.
ListOfPorts.get(long n)
,
ListOf.size()
public Port remove(java.lang.String sid)
ListOfPorts
items based on the 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 Port
to remove
ListOf.size()
public SBase remove(long n)
ListOfPorts
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 int getItemTypeCode()
ListOf
(i.e., Port
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_PORT
(default).
ListOfPorts.getElementName()
,
SBase.getPackageName()
public java.lang.String getElementName()
getElementName
 in class ListOf
public SBase getElementBySId(java.lang.String id)
id
in the
model-wide SId namespace, or null
if no such object is found. Since the
id of Port
objects are in the PortSId namespace, no Port
object is
returned by this function.
getElementBySId
 in class ListOf
id
- string representing the id of objects to find
SBase
element with the given id
.