public class ListOfObjectives extends ListOf
The ListOfObjectives
is a container for the Objective
elements of 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.
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 |
---|
ListOfObjectives()
Creates a new
ListOfObjectives with the given level, version, and package version. |
ListOfObjectives(FbcPkgNamespaces fbcns)
Creates a new
ListOfObjectives with the given FbcPkgNamespaces object. |
ListOfObjectives(long level)
Creates a new
ListOfObjectives with the given level, version, and package version. |
ListOfObjectives(long level,
long version)
Creates a new
ListOfObjectives with the given level, version, and package version. |
ListOfObjectives(long level,
long version,
long pkgVersion)
Creates a new
ListOfObjectives with the given level, version, and package version. |
Modifier and Type | Method and Description |
---|---|
int |
appendFrom(ListOf list)
Adds a clone of all items in the provided
ListOf to this object. |
ListOfObjectives |
cloneObject()
Creates and returns a deep copy of this
ListOfObjectives object. |
void |
delete()
Explicitly deletes the underlying native object.
|
Objective |
get(long n)
Get a
Objective from the ListOfObjectives . |
Objective |
get(java.lang.String sid)
Get a
Objective from the ListOfObjectives
based on its identifier. |
java.lang.String |
getActiveObjective()
Returns the value of the 'activeObjective' attribute of this
ListOfObjectives . |
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the objects contained in this
ListOf
(i.e., SBML_FBC_OBJECTIVE ). |
boolean |
isSetActiveObjective()
Predicate returning
true or false depending on whether this
ListOfObjective's 'activeObjective' attribute has been set. |
Objective |
remove(long n)
Removes the nth item from this
ListOfObjectives items and returns a pointer to
it. |
Objective |
remove(java.lang.String sid)
Removes item in this
ListOfObjectives items with the given identifier. |
void |
renameSIdRefs(java.lang.String oldid,
java.lang.String newid)
Renames all the SIdRef attributes on this element if they match
oldid , but not any found in child or plugin elements. |
int |
setActiveObjective(java.lang.String activeObjective)
Sets the value of the 'activeObjective' attribute of this
ListOfObjectives . |
int |
unsetActiveObjective()
Unsets the value of the 'activeObjective' attribute of this
ListOfObjectives . |
append, appendAndOwn, 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, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm
public ListOfObjectives() throws SBMLConstructorException
ListOfObjectives
with the given level, version, and package version.SBMLConstructorException
public ListOfObjectives(FbcPkgNamespaces fbcns) throws SBMLConstructorException
ListOfObjectives
with the given FbcPkgNamespaces
object.SBMLConstructorException
public ListOfObjectives(long level) throws SBMLConstructorException
ListOfObjectives
with the given level, version, and package version.SBMLConstructorException
public ListOfObjectives(long level, long version) throws SBMLConstructorException
ListOfObjectives
with the given level, version, and package version.SBMLConstructorException
public ListOfObjectives(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfObjectives
with the given level, version, and package version.SBMLConstructorException
public int appendFrom(ListOf list)
ListOf
to this object. This means that when this ListOf
is destroyed, the original items will not be destroyed. In addition, copy over the input ListOfObjectives
' 'activeObjective' attribute, if none is set for this element.
appendFrom
 in class ListOf
list
- A list of items to be added.
ListOf.append(SBase item)
public ListOfObjectives cloneObject()
ListOfObjectives
object.
cloneObject
 in class ListOf
ListOfObjectives
.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 ListOfObjectives.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 ListOfObjectives.delete()
themselves.
public Objective get(long n)
Objective
from the ListOfObjectives
.
get
 in class ListOf
n
- the index number of the Objective
to get.
Objective
in this ListOfObjectives
.
ListOf.size()
public Objective get(java.lang.String sid)
Objective
from the ListOfObjectives
based on its identifier.
sid
- a string representing the identifier
of the Objective
to get.
Objective
in this ListOfObjectives
with the given sid
or null
if no such
Objective
exists.
ListOfObjectives.get(long n)
,
ListOf.size()
public java.lang.String getActiveObjective()
ListOfObjectives
.
ListOfObjectives
.public java.lang.String getElementName()
getElementName
 in class ListOf
public int getItemTypeCode()
ListOf
(i.e., SBML_FBC_OBJECTIVE
).
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_OBJECTIVE
ListOfObjectives.getElementName()
,
SBase.getPackageName()
public boolean isSetActiveObjective()
true
or false
depending on whether this
ListOfObjective's 'activeObjective' attribute has been set.
true
if this ListOfObjective's 'activeObjective' attribute has been set,
otherwise false
is returned.public Objective remove(long n)
ListOfObjectives
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 Objective remove(java.lang.String sid)
ListOfObjectives
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
public void renameSIdRefs(java.lang.String oldid, java.lang.String newid)
oldid
, but not any found in child or plugin elements.renameSIdRefs
 in class SBase
oldid
- the old identifiernewid
- the new identifierpublic int setActiveObjective(java.lang.String activeObjective)
ListOfObjectives
.
public int unsetActiveObjective()
ListOfObjectives
.