public class ListOfOutwardBindingSites extends ListOf
OutwardBindingSite objects.
The ListOfOutwardBindingSites is a container for OutwardBindingSite objects.
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):
SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.
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 |
|---|
ListOfOutwardBindingSites()
Creates a new
ListOfOutwardBindingSites with the given level, version, and package version. |
ListOfOutwardBindingSites(long level)
Creates a new
ListOfOutwardBindingSites with the given level, version, and package version. |
ListOfOutwardBindingSites(long level,
long version)
Creates a new
ListOfOutwardBindingSites with the given level, version, and package version. |
ListOfOutwardBindingSites(long level,
long version,
long pkgVersion)
Creates a new
ListOfOutwardBindingSites with the given level, version, and package version. |
ListOfOutwardBindingSites(MultiPkgNamespaces multins)
Creates a new
ListOfOutwardBindingSites with the given
MultiPkgNamespaces object. |
| Modifier and Type | Method and Description |
|---|---|
ListOfOutwardBindingSites |
cloneObject()
Creates and returns a deep copy of this
ListOfOutwardBindingSites
object. |
void |
delete()
Explicitly deletes the underlying native object.
|
OutwardBindingSite |
get(long n)
Get a
OutwardBindingSite from the ListOfOutwardBindingSites. |
OutwardBindingSite |
get(java.lang.String sid)
Get a
OutwardBindingSite from the ListOfOutwardBindingSites
based on its identifier. |
java.lang.String |
getElementName()
Returns the XML element name of this object, which for
ListOfOutwardBindingSites, is
always 'listOfOutwardBindingSites'. |
int |
getItemTypeCode()
Returns the libSBML type code for the SBML objects
contained in this
ListOf object |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
OutwardBindingSite |
remove(long n)
Removes the nth
OutwardBindingSite from this ListOfOutwardBindingSites
and returns a pointer to it. |
OutwardBindingSite |
remove(java.lang.String sid)
Removes the
OutwardBindingSite from this ListOfOutwardBindingSites with the given identifier
and returns a pointer to it. |
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, insert, insertAndOwn, removeFromParentAndDelete, sizeaddCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserDatapublic ListOfOutwardBindingSites(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfOutwardBindingSites with the given level, version, and package version.
level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites
version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites
pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSitesSBMLConstructorExceptionpublic ListOfOutwardBindingSites(long level, long version) throws SBMLConstructorException
ListOfOutwardBindingSites with the given level, version, and package version.
level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites
version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites
pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSitesSBMLConstructorExceptionpublic ListOfOutwardBindingSites(long level) throws SBMLConstructorException
ListOfOutwardBindingSites with the given level, version, and package version.
level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites
version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites
pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSitesSBMLConstructorExceptionpublic ListOfOutwardBindingSites() throws SBMLConstructorException
ListOfOutwardBindingSites with the given level, version, and package version.
level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites
version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites
pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSitesSBMLConstructorExceptionpublic ListOfOutwardBindingSites(MultiPkgNamespaces multins) throws SBMLConstructorException
ListOfOutwardBindingSites with the given
MultiPkgNamespaces object.
The package namespaces object used in this constructor is derived from a
SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and
package version and name information used in addition to SBML Level 3 Core. A
common approach to using libSBML's SBMLNamespaces facilities is to create an
package namespace object somewhere in a program once, then hand that object
as needed to object constructors of that package that accept it as and
argument, such as this one.
multins - the MultiPkgNamespaces object
SBMLConstructorExceptionSBMLDocument having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.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 ListOfOutwardBindingSites.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 ListOfOutwardBindingSites.delete() themselves.
public ListOfOutwardBindingSites cloneObject()
ListOfOutwardBindingSites
object.
cloneObject in class ListOfListOfOutwardBindingSites object.public OutwardBindingSite get(long n)
OutwardBindingSite from the ListOfOutwardBindingSites.
get in class ListOfn - the index number of the OutwardBindingSite to get.
OutwardBindingSite in this ListOfOutwardBindingSites.
If the index n is invalid, null is returned.
ListOf.size()public OutwardBindingSite get(java.lang.String sid)
OutwardBindingSite from the ListOfOutwardBindingSites
based on its identifier.
sid - a string representing the identifier
of the OutwardBindingSite to get.
OutwardBindingSite in this ListOfOutwardBindingSites
with the given id or null if no such
OutwardBindingSite exists.
*,
ListOf.size()public OutwardBindingSite remove(long n)
OutwardBindingSite from this ListOfOutwardBindingSites
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 OutwardBindingSite to remove.
ListOf.size()public OutwardBindingSite remove(java.lang.String sid)
OutwardBindingSite from this ListOfOutwardBindingSites with the given identifier
and returns a pointer to it.
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 OutwardBindingSite to remove.
OutwardBindingSite removed. As mentioned above, the caller owns the
returned item.public java.lang.String getElementName()
ListOfOutwardBindingSites, is
always 'listOfOutwardBindingSites'.
getElementName in class ListOf'listOfOutwardBindingSites'.public int getTypeCode()
LibSBML attaches an identifying code to every
kind of SBML object. These are known as SBML type codes. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class libsbmlConstants. The names of the type codes all begin with the
characters SBML_.
getTypeCode in class ListOfSBML_UNKNOWN (default).
ListOfOutwardBindingSites.getElementName()public int getItemTypeCode()
ListOf object
LibSBML attaches an identifying code to every
kind of SBML object. These are known as SBML type codes. In
other languages, the set of type codes is stored in an enumeration; in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class libsbmlConstants. The names of the type codes all begin with the
characters SBML_.
getItemTypeCode in class ListOfListOf instance, or
SBML_UNKNOWN (default).
ListOfOutwardBindingSites.getElementName()