public class ListOfFluxBounds extends ListOf
FluxBound
objects.
The ListOfFluxBounds
is a container for the FluxBound
elements of a Model
.
Note that this class is only defined for Version 1 of the fbc specification,
and was replaced in Version 2 by Parameter
elements referenced by the
upperFluxBound or lowerFluxBound attributes on an FbcReactionPlugin
.
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 |
---|
ListOfFluxBounds()
Creates a new
ListOfFluxBounds with the given level, version, and package version. |
ListOfFluxBounds(FbcPkgNamespaces fbcns)
Creates a new
ListOfFluxBounds with the given FbcPkgNamespaces object. |
ListOfFluxBounds(long level)
Creates a new
ListOfFluxBounds with the given level, version, and package version. |
ListOfFluxBounds(long level,
long version)
Creates a new
ListOfFluxBounds with the given level, version, and package version. |
ListOfFluxBounds(long level,
long version,
long pkgVersion)
Creates a new
ListOfFluxBounds with the given level, version, and package version. |
Modifier and Type | Method and Description |
---|---|
ListOfFluxBounds |
cloneObject()
Creates and returns a deep copy of this
ListOfFluxBounds . |
void |
delete()
Explicitly deletes the underlying native object.
|
FluxBound |
get(long n)
Get a
FluxBound from the ListOfFluxBounds . |
FluxBound |
get(String sid)
Get a
FluxBound from the ListOfFluxBounds
based on its identifier. |
String |
getElementName()
Returns the XML element name of this object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the SBML objects
contained in this
ListOf object. |
FluxBound |
remove(long n)
Removes the nth item from this
ListOfFluxBounds items and returns a pointer to
it. |
FluxBound |
remove(String sid)
Removes item in this
ListOfFluxBounds items with the given identifier. |
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, 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 ListOfFluxBounds(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfFluxBounds
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxBounds(long level, long version) throws SBMLConstructorException
ListOfFluxBounds
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxBounds(long level) throws SBMLConstructorException
ListOfFluxBounds
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxBounds() throws SBMLConstructorException
ListOfFluxBounds
with the given level, version, and package version.SBMLConstructorException
public ListOfFluxBounds(FbcPkgNamespaces fbcns) throws SBMLConstructorException
ListOfFluxBounds
with the given FbcPkgNamespaces
object.SBMLConstructorException
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 ListOfFluxBounds.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 ListOfFluxBounds.delete()
themselves.
public ListOfFluxBounds cloneObject()
ListOfFluxBounds
.
cloneObject
 in class ListOf
ListOfFluxBounds
.public FluxBound get(long n)
FluxBound
from the ListOfFluxBounds
.
get
 in class ListOf
n
- the index number of the FluxBound
to get.
FluxBound
in this ListOfFluxBounds
.
ListOf.size()
public FluxBound get(String sid)
FluxBound
from the ListOfFluxBounds
based on its identifier.
sid
- a string representing the identifier
of the FluxBound
to get.
FluxBound
in this ListOfFluxBounds
with the given sid
or null
if no such
FluxBound
exists.
ListOfFluxBounds.get(long n)
,
ListOf.size()
public FluxBound remove(long n)
ListOfFluxBounds
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 remove
ListOf.size()
public FluxBound remove(String sid)
ListOfFluxBounds
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 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_FBC_FLUXBOUND
(default).
ListOfFluxBounds.getElementName()
,
SBase.getPackageName()
public String getElementName()
For ListOfFluxBounds
, the XML element name is always 'listOfFluxBounds'.
getElementName
 in class ListOf
'listOfFluxBounds'.