public class ListOfFluxObjectives extends ListOf
FluxObjective
objects.
The ListOfFluxObjectives
is a container for the &ldquofbc&rdquo
Objective
that indicate which fluxes (and what ratios for those fluxes)
are to be used in maximizing or minimizing the Objective
.
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'.
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 |
---|---|
int |
addFluxObjective(FluxObjective fo)
Adds a copy the given 'FluxObjective' to this
ListOfFluxObjectives . |
ListOfFluxObjectives |
cloneObject()
Creates and returns a deep copy of this
ListOfFluxObjectives object. |
FluxObjective |
createFluxObjective()
Creates a new
FluxObjective object, adds it to the
ListOfFluxObjectives and returns the FluxObjective object created. |
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 object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the objects contained in this
ListOf . |
long |
getNumFluxObjectives()
Get the number of
FluxObjective objects in this ListOfFluxObjectives . |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
FluxObjective |
remove(long n)
Removes the nth
FluxObjective from this ListOfFluxObjectives
and returns a pointer to it. |
FluxObjective |
remove(java.lang.String sid)
Removes the
FluxObjective from this ListOfFluxObjectives with the given identifier
and returns a pointer to it. |
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, 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 ListOfFluxObjectives(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFluxObjectives
version
- a long integer, the SBML Version to assign to this ListOfFluxObjectives
pkgVersion
- a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
SBMLConstructorException
public ListOfFluxObjectives(long level, long version) throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFluxObjectives
version
- a long integer, the SBML Version to assign to this ListOfFluxObjectives
pkgVersion
- a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
SBMLConstructorException
public ListOfFluxObjectives(long level) throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFluxObjectives
version
- a long integer, the SBML Version to assign to this ListOfFluxObjectives
pkgVersion
- a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
SBMLConstructorException
public ListOfFluxObjectives() throws SBMLConstructorException
ListOfFluxObjectives
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFluxObjectives
version
- a long integer, the SBML Version to assign to this ListOfFluxObjectives
pkgVersion
- a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
SBMLConstructorException
public ListOfFluxObjectives(FbcPkgNamespaces fbcns) throws SBMLConstructorException
ListOfFluxObjectives
with the given FbcPkgNamespaces
object.
fbcns
- the FbcPkgNamespaces
objectSBMLConstructorException
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 ListOfFluxObjectives cloneObject()
ListOfFluxObjectives
object.
cloneObject
 in class ListOf
ListOfFluxObjectives
object.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 id or null if no such
FluxObjective
exists.
*
,
ListOf.size()
public int addFluxObjective(FluxObjective fo)
ListOfFluxObjectives
.
fo
- the FluxObjective
object to add
public long getNumFluxObjectives()
FluxObjective
objects in this ListOfFluxObjectives
.
FluxObjective
objects in this ListOfFluxObjectives
public FluxObjective createFluxObjective()
FluxObjective
object, adds it to the
ListOfFluxObjectives
and returns the FluxObjective
object created.
FluxObjective
object instance
ListOfFluxObjectives.addFluxObjective(FluxObjective fo)
public FluxObjective remove(long n)
FluxObjective
from this ListOfFluxObjectives
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 FluxObjective
to remove.
ListOf.size()
public FluxObjective remove(java.lang.String sid)
FluxObjective
from this ListOfFluxObjectives
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 FluxObjective
to remove.
FluxObjective
removed. As mentioned above, the caller owns the
returned item.public java.lang.String getElementName()
For ListOfFluxObjectives
, the XML element name is always 'listOfFluxObjectives'.
getElementName
 in class ListOf
'listOfFluxObjectives'.
public int getTypeCode()
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.
getTypeCode
 in class ListOf
SBML_LIST_OF
(default).
ListOfFluxObjectives.getElementName()
,
SBase.getPackageName()
public int getItemTypeCode()
ListOf
.
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
ListOf
instance: SBML_FBC_FLUXOBJECTIVE
(default).
ListOfFluxObjectives.getElementName()
,
SBase.getPackageName()