public class ListOfFbcAssociations extends ListOf
FbcAssociation
objects.
The ListOfFbcAssociations
is a container of FbcAssociation
objects
for the FbcAnd
and FbcOr
classes. Unlike the ListOf___ classes in
SBML, the ListOfFbcAssociations
is not a class that appears in the
&ldquofbc&rdquo specification, and instead is used in libsbml
as a convenience class to store arbitrary numbers of FbcAssociation
objects. Also unlike other ListOf___ classes, the FbcAnd
and FbcOr
classes require at least two child FbcAssociation
objects, so valid
ListOfFbcAssociations
libsbml objects will always contain two or more
children.
In addition, these children will have element names associated with
their derived class, not the base FbcAssociation
class:
&ldquofbc:and&rdquo, &ldquofbc:or&rdquo, and &ldquofbc:geneProductRef&rdquo.
FbcAssociation
,
FbcAnd
,
FbcOr
,
GeneProductRef
Association
and
GeneAssociation
annotation classes. Please see the Version 1 and
Version 2 &ldquofbc&rdquo specifications for more details.
Constructor and Description |
---|
ListOfFbcAssociations()
Creates a new
ListOfFbcAssociations with the given SBML Level, Version,
and &ldquofbc&rdquopackage version. |
ListOfFbcAssociations(FbcPkgNamespaces fbcns)
Creates a new
ListOfFbcAssociations with the given FbcPkgNamespaces
object. |
ListOfFbcAssociations(long level)
Creates a new
ListOfFbcAssociations with the given SBML Level, Version,
and &ldquofbc&rdquopackage version. |
ListOfFbcAssociations(long level,
long version)
Creates a new
ListOfFbcAssociations with the given SBML Level, Version,
and &ldquofbc&rdquopackage version. |
ListOfFbcAssociations(long level,
long version,
long pkgVersion)
Creates a new
ListOfFbcAssociations with the given SBML Level, Version,
and &ldquofbc&rdquopackage version. |
Modifier and Type | Method and Description |
---|---|
int |
addFbcAssociation(FbcAssociation fa)
Adds a copy the given
FbcAssociation object to this
ListOfFbcAssociations . |
ListOfFbcAssociations |
cloneObject()
Creates and returns a deep copy of this
ListOfFbcAssociations object. |
FbcAnd |
createAnd()
Creates a new
FbcAnd object. |
GeneProductRef |
createGeneProductRef()
Creates a new
GeneProductRef object. |
FbcOr |
createOr()
Creates a new
FbcOr object. |
void |
delete()
Explicitly deletes the underlying native object.
|
FbcAssociation |
get(long n)
Get a
FbcAssociation from the ListOfFbcAssociations . |
FbcAssociation |
get(String sid)
Get a
FbcAssociation from the ListOfFbcAssociations based on its
identifier. |
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 |
getNumFbcAssociations()
Get the number of
FbcAssociation objects in this ListOfFbcAssociations . |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
FbcAssociation |
remove(long n)
Removes the nth
FbcAssociation |
FbcAssociation |
remove(String sid)
Removes the
FbcAssociation with the given identifier |
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 ListOfFbcAssociations(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfFbcAssociations
with the given SBML Level, Version,
and &ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfFbcAssociations
version
- a long integer, the SBML Version to assign to this
ListOfFbcAssociations
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this ListOfFbcAssociations
SBMLConstructorException
public ListOfFbcAssociations(long level, long version) throws SBMLConstructorException
ListOfFbcAssociations
with the given SBML Level, Version,
and &ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfFbcAssociations
version
- a long integer, the SBML Version to assign to this
ListOfFbcAssociations
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this ListOfFbcAssociations
SBMLConstructorException
public ListOfFbcAssociations(long level) throws SBMLConstructorException
ListOfFbcAssociations
with the given SBML Level, Version,
and &ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfFbcAssociations
version
- a long integer, the SBML Version to assign to this
ListOfFbcAssociations
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this ListOfFbcAssociations
SBMLConstructorException
public ListOfFbcAssociations() throws SBMLConstructorException
ListOfFbcAssociations
with the given SBML Level, Version,
and &ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfFbcAssociations
version
- a long integer, the SBML Version to assign to this
ListOfFbcAssociations
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this ListOfFbcAssociations
SBMLConstructorException
public ListOfFbcAssociations(FbcPkgNamespaces fbcns) throws SBMLConstructorException
ListOfFbcAssociations
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 ListOfFbcAssociations.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 ListOfFbcAssociations.delete()
themselves.
public ListOfFbcAssociations cloneObject()
ListOfFbcAssociations
object.
cloneObject
 in class ListOf
ListOfFbcAssociations
object.public FbcAssociation get(long n)
FbcAssociation
from the ListOfFbcAssociations
.
get
 in class ListOf
n
- the index number of the FbcAssociation
to get.
FbcAssociation
in this ListOfFbcAssociations
.
ListOf.size()
,
ListOfFbcAssociations.getNumFbcAssociations()
public FbcAssociation get(String sid)
FbcAssociation
from the ListOfFbcAssociations
based on its
identifier.
sid
- a string representing the identifier of the FbcAssociation
to
get.
FbcAssociation
in this ListOfFbcAssociations
with the given id
or null if no such FbcAssociation
exists.
ListOfFbcAssociations.get(long n)
,
ListOf.size()
public int addFbcAssociation(FbcAssociation fa)
FbcAssociation
object to this
ListOfFbcAssociations
.
fa
- the FbcAssociation
object to add
public long getNumFbcAssociations()
FbcAssociation
objects in this ListOfFbcAssociations
.
FbcAssociation
objects in this
ListOfFbcAssociations
public FbcAnd createAnd()
FbcAnd
object.
This method creates a new FbcAssociation
object of subclass FbcAnd
, adds
it to the ListOfFbcAssociations
, and returns the FbcAssociation
object
created.
FbcAssociation
object instance
ListOfFbcAssociations.createOr()
,
ListOfFbcAssociations.createGeneProductRef()
,
ListOfFbcAssociations.addFbcAssociation(FbcAssociation fa)
public FbcOr createOr()
FbcOr
object.
This method creates a new FbcAssociation
object of subclass FbcOr
, adds
it to the ListOfFbcAssociations
, and returns the FbcAssociation
object
created.
FbcAssociation
object instance
ListOfFbcAssociations.createAnd()
,
ListOfFbcAssociations.createGeneProductRef()
,
ListOfFbcAssociations.addFbcAssociation(FbcAssociation fa)
public GeneProductRef createGeneProductRef()
GeneProductRef
object.
This method creates a new FbcAssociation
object of subclass
GeneProductRef
, adds it to the ListOfFbcAssociations
, and returns the
FbcAssociation
object created.
FbcAssociation
object instance
ListOfFbcAssociations.createOr()
,
ListOfFbcAssociations.createAnd()
,
ListOfFbcAssociations.addFbcAssociation(FbcAssociation fa)
public FbcAssociation remove(long n)
FbcAssociation
This method removes the nth object from this ListOfFbcAssociations
and
returns a pointer to it.
remove
 in class ListOf
n
- the index of the FbcAssociation
to remove.
ListOf.size()
public FbcAssociation remove(String sid)
FbcAssociation
with the given identifier
This method searches for and removes the FbcAssociation
object with the
given identifier sid
, 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 FbcAssociation
to remove.
FbcAssociation
removed. As mentioned above, the caller owns
the returned item.public String getElementName()
For ListOfFbcAssociations
, the XML element name is always
'listOfFbcAssociations'.
getElementName
 in class ListOf
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).
ListOfFbcAssociations.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_ASSOCIATION
(default).
ListOfFbcAssociations.getElementName()
,
SBase.getPackageName()