public class ListOfFunctionTerms extends ListOf
FunctionTerm
objects.
The ListOfFunctionTerms
is a container for the FunctionTerms 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):
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 |
---|
ListOfFunctionTerms()
Creates a new
ListOfFunctionTerms with the given level, version, and package version. |
ListOfFunctionTerms(ListOfFunctionTerms orig)   |
ListOfFunctionTerms(long level)
Creates a new
ListOfFunctionTerms with the given level, version, and package version. |
ListOfFunctionTerms(long level,
long version)
Creates a new
ListOfFunctionTerms with the given level, version, and package version. |
ListOfFunctionTerms(long level,
long version,
long pkgVersion)
Creates a new
ListOfFunctionTerms with the given level, version, and package version. |
ListOfFunctionTerms(QualPkgNamespaces qualns)
Creates a new
ListOfFunctionTerms with the given QualPkgNamespaces object. |
Modifier and Type | Method and Description |
---|---|
ListOfFunctionTerms |
cloneObject()
Creates and returns a deep copy of this
ListOfFunctionTerms object. |
DefaultTerm |
createDefaultTerm()
Creates a new
DefaultTerm object, adds it to this
ListOfFunctionTerms and returns the DefaultTerm object created. |
void |
delete()
Explicitly deletes the underlying native object.
|
FunctionTerm |
get(long n)
Get a
FunctionTerm from the ListOfFunctionTerms . |
FunctionTerm |
get(String sid)
Get a
FunctionTerm from the ListOfFunctionTerms
based on its identifier. |
DefaultTerm |
getDefaultTerm()
Get the
DefaultTerm from this ListOfFunctionTerms . |
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. |
boolean |
isSetDefaultTerm()
Predicate returning
true if the defaultTerm
for this ListOfFunctionTerms object has been set. |
FunctionTerm |
remove(long n)
Removes the nth
FunctionTerm from this ListOfFunctionTerms
and returns a pointer to it. |
FunctionTerm |
remove(String sid)
Removes the
FunctionTerm from this ListOfFunctionTerms with the given identifier
and returns a pointer to it. |
int |
setDefaultTerm(DefaultTerm dt)
Sets the given
DefaultTerm to this Transition . |
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 ListOfFunctionTerms(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfFunctionTerms
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFunctionTerms
version
- a long integer, the SBML Version to assign to this ListOfFunctionTerms
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfFunctionTerms
SBMLConstructorException
public ListOfFunctionTerms(long level, long version) throws SBMLConstructorException
ListOfFunctionTerms
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFunctionTerms
version
- a long integer, the SBML Version to assign to this ListOfFunctionTerms
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfFunctionTerms
SBMLConstructorException
public ListOfFunctionTerms(long level) throws SBMLConstructorException
ListOfFunctionTerms
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFunctionTerms
version
- a long integer, the SBML Version to assign to this ListOfFunctionTerms
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfFunctionTerms
SBMLConstructorException
public ListOfFunctionTerms() throws SBMLConstructorException
ListOfFunctionTerms
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfFunctionTerms
version
- a long integer, the SBML Version to assign to this ListOfFunctionTerms
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfFunctionTerms
SBMLConstructorException
public ListOfFunctionTerms(QualPkgNamespaces qualns) throws SBMLConstructorException
ListOfFunctionTerms
with the given QualPkgNamespaces
object.
qualns
- the QualPkgNamespaces
objectSBMLConstructorException
public ListOfFunctionTerms(ListOfFunctionTerms orig) throws SBMLConstructorException
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 ListOfFunctionTerms.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 ListOfFunctionTerms.delete()
themselves.
public ListOfFunctionTerms cloneObject()
ListOfFunctionTerms
object.
cloneObject
 in class ListOf
ListOfFunctionTerms
object.public FunctionTerm get(long n)
FunctionTerm
from the ListOfFunctionTerms
.
get
 in class ListOf
n
- the index number of the FunctionTerm
to get.
FunctionTerm
in this ListOfFunctionTerms
.
ListOf.size()
public FunctionTerm get(String sid)
FunctionTerm
from the ListOfFunctionTerms
based on its identifier.
sid
- a string representing the identifier
of the FunctionTerm
to get.
FunctionTerm
in this ListOfFunctionTerms
with the given id or null if no such
FunctionTerm
exists.
*
,
ListOf.size()
public FunctionTerm remove(long n)
FunctionTerm
from this ListOfFunctionTerms
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 FunctionTerm
to remove.
ListOf.size()
public FunctionTerm remove(String sid)
FunctionTerm
from this ListOfFunctionTerms
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 FunctionTerm
to remove.
FunctionTerm
removed. As mentioned above, the caller owns the
returned item.public 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_FUNCTION_TERM
(default).
ListOfFunctionTerms.getElementName()
,
SBase.getPackageName()
public DefaultTerm getDefaultTerm()
DefaultTerm
from this ListOfFunctionTerms
.
DefaultTerm
in this ListOfFunctionTerms
, or null if no such value is set.
Transition.getDefaultTerm()
public int setDefaultTerm(DefaultTerm dt)
DefaultTerm
to this Transition
.
dt
- the DefaultTerm
object to add
public boolean isSetDefaultTerm()
true
if the defaultTerm
for this ListOfFunctionTerms
object has been set.
public DefaultTerm createDefaultTerm()
DefaultTerm
object, adds it to this
ListOfFunctionTerms
and returns the DefaultTerm
object created.
DefaultTerm
object instance
ListOfFunctionTerms.setDefaultTerm(DefaultTerm ft)