public class ListOfOutputs extends ListOf
Output
objects.
The ListOfOutputs
is a container for the Output
elements of a Transition
.
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 |
---|
ListOfOutputs()
Creates a new
ListOfOutputs with the given level, version, and package version. |
ListOfOutputs(long level)
Creates a new
ListOfOutputs with the given level, version, and package version. |
ListOfOutputs(long level,
long version)
Creates a new
ListOfOutputs with the given level, version, and package version. |
ListOfOutputs(long level,
long version,
long pkgVersion)
Creates a new
ListOfOutputs with the given level, version, and package version. |
ListOfOutputs(QualPkgNamespaces qualns)
Creates a new
ListOfOutputs with the given QualPkgNamespaces object. |
Modifier and Type | Method and Description |
---|---|
ListOfOutputs |
cloneObject()
Creates and returns a deep copy of this
ListOfOutputs object. |
void |
delete()
Explicitly deletes the underlying native object.
|
Output |
get(long n)
Get a
Output from the ListOfOutputs . |
Output |
get(java.lang.String sid)
Get a
Output from the ListOfOutputs
based on its identifier. |
Output |
getBySpecies(java.lang.String sid)
Get a
Output from the ListOfOutputs
based on the qualitativeSpecies to which it refers. |
java.lang.String |
getElementName()
Returns the XML name of this object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the SBML objects
contained in this
ListOf object. |
Output |
remove(long n)
Removes the nth
Output from this ListOfOutputs
and returns a pointer to it. |
Output |
remove(java.lang.String sid)
Removes the
Output from this ListOfOutputs with the given 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, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getObjectVersion, 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, unsetUserData
public ListOfOutputs(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfOutputs
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfOutputs
.
version
- a long integer, the SBML Version to assign to this ListOfOutputs
.
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfOutputs
.
SBMLConstructorException
SBMLDocument
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 ListOfOutputs(long level, long version) throws SBMLConstructorException
ListOfOutputs
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfOutputs
.
version
- a long integer, the SBML Version to assign to this ListOfOutputs
.
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfOutputs
.
SBMLConstructorException
SBMLDocument
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 ListOfOutputs(long level) throws SBMLConstructorException
ListOfOutputs
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfOutputs
.
version
- a long integer, the SBML Version to assign to this ListOfOutputs
.
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfOutputs
.
SBMLConstructorException
SBMLDocument
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 ListOfOutputs() throws SBMLConstructorException
ListOfOutputs
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfOutputs
.
version
- a long integer, the SBML Version to assign to this ListOfOutputs
.
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfOutputs
.
SBMLConstructorException
SBMLDocument
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 ListOfOutputs(QualPkgNamespaces qualns) throws SBMLConstructorException
ListOfOutputs
with the given QualPkgNamespaces
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.
qualns
- the QualPkgNamespaces
object.
SBMLConstructorException
SBMLDocument
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 ListOfOutputs.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 ListOfOutputs.delete()
themselves.
public ListOfOutputs cloneObject()
ListOfOutputs
object.
cloneObject
 in class ListOf
ListOfOutputs
object.public Output get(long n)
Output
from the ListOfOutputs
.
get
 in class ListOf
n
- the index number of the Output
to get.
Output
in this ListOfOutputs
.
ListOf.size()
public Output get(java.lang.String sid)
Output
from the ListOfOutputs
based on its identifier.
sid
- a string representing the identifier
of the Output
to get.
Output
in this ListOfOutputs
with the given id or null if no such
Output
exists.
*
,
ListOf.size()
public Output getBySpecies(java.lang.String sid)
Output
from the ListOfOutputs
based on the qualitativeSpecies to which it refers.
sid
- a string representing the qualitativeSpecies attribute
of the Output
to get.
Output
in this ListOfOutputs
with the given qualitativeSpecies or null if no such
Output
exists.
*
,
ListOf.size()
public Output remove(long n)
Output
from this ListOfOutputs
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 Output
to remove.
ListOf.size()
public Output remove(java.lang.String sid)
Output
from this ListOfOutputs
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.
public java.lang.String getElementName()
getElementName
 in class ListOf
public int getItemTypeCode()
ListOf
object.
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_QUAL_OUTPUT
(default).
ListOfOutputs.getElementName()
,
SBase.getPackageName()