public class ListOfFluxObjectives extends ListOf
The ListOfFluxObjectives
is a container for the FluxObjective
elements of a Model
annotation.
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 |
---|
ListOfFluxObjectives()
Creates a new
ListOfFluxObjectives with the given level, version, and package version. |
ListOfFluxObjectives(FbcPkgNamespaces fbcns)
Creates a new
ListOfFluxObjectives with the given FbcPkgNamespaces object. |
ListOfFluxObjectives(long level)
Creates a new
ListOfFluxObjectives with the given level, version, and package version. |
ListOfFluxObjectives(long level,
long version)
Creates a new
ListOfFluxObjectives with the given level, version, and package version. |
ListOfFluxObjectives(long level,
long version,
long pkgVersion)
Creates a new
ListOfFluxObjectives with the given level, version, and package version. |
Modifier and Type | Method and Description |
---|---|
ListOfFluxObjectives |
cloneObject()
Creates and returns a deep copy of this
ListOfFluxObjectives . |
void |
delete()
Explicitly deletes the underlying native object.
|
FluxObjective |
get(long n)
Get a
FluxObjective from the ListOfFluxObjectives . |
FluxObjective |
get(java.lang.String sid)
Get a
FluxObjective from the ListOfFluxObjectives
based on its identifier. |
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the SBML objects
contained in this
ListOf object. |
FluxObjective |
remove(long n)
Removes the nth item from this
ListOfFluxObjectives items and returns a pointer to
it. |
FluxObjective |
remove(java.lang.String sid)
Removes item in this
ListOfFluxObjectives 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 ListOfFluxObjectives() throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxObjectives(FbcPkgNamespaces fbcns) throws SBMLConstructorException
ListOfFluxObjectives
with the given FbcPkgNamespaces
object.SBMLConstructorException
public ListOfFluxObjectives(long level) throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxObjectives(long level, long version) throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxObjectives(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxObjectives cloneObject()
ListOfFluxObjectives
.
cloneObject
 in class ListOf
ListOfFluxObjectives
.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 ListOfFluxObjectives.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 ListOfFluxObjectives.delete()
themselves.
public FluxObjective get(long n)
FluxObjective
from the ListOfFluxObjectives
.
get
 in class ListOf
n
- the index number of the FluxObjective
to get.
FluxObjective
in this ListOfFluxObjectives
.
ListOf.size()
public FluxObjective get(java.lang.String sid)
FluxObjective
from the ListOfFluxObjectives
based on its identifier.
sid
- a string representing the identifier
of the FluxObjective
to get.
FluxObjective
in this ListOfFluxObjectives
with the given sid
or null
if no such
FluxObjective
exists.
ListOfFluxObjectives.get(long n)
,
ListOf.size()
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 &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_FBC_FLUXOBJECTIVE
(default).
ListOfFluxObjectives.getElementName()
,
SBase.getPackageName()
public FluxObjective remove(long n)
ListOfFluxObjectives
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 removeListOf.size()
public FluxObjective remove(java.lang.String sid)
ListOfFluxObjectives
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 @c
null is returned.
sid
- the identifier of the item to remove