public class ListOfGeneProducts extends ListOf
GeneProduct
objects.
The ListOfGeneProducts
is a container for the SBML extended Model
that lists all the possible GeneProduct
elements in the model. These
GeneProduct
elements are referenced in the GeneProductAssociation
child
of an extended Reaction
.
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):
SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.
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'.
ListOfFunctionDefinitions
,
ListOfUnitDefinitions
,
ListOfCompartmentTypes
,
ListOfSpeciesTypes
,
ListOfCompartments
,
ListOfSpecies
,
ListOfParameters
,
ListOfInitialAssignments
,
ListOfRules
,
ListOfConstraints
,
ListOfReactions
,
,
GeneProduct
,
FbcModelPlugin
Association
and
GeneAssociation
annotation classes. Please see the Version 1 and
Version 2 &ldquofbc&rdquo specifications for more details.
Constructor and Description |
---|
ListOfGeneProducts()
Creates a new
GeneProduct with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
ListOfGeneProducts(FbcPkgNamespaces fbcns)
Creates a new
ListOfGeneProducts with the given FbcPkgNamespaces object. |
ListOfGeneProducts(long level)
Creates a new
GeneProduct with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
ListOfGeneProducts(long level,
long version)
Creates a new
GeneProduct with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
ListOfGeneProducts(long level,
long version,
long pkgVersion)
Creates a new
GeneProduct with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
Modifier and Type | Method and Description |
---|---|
int |
addGeneProduct(GeneProduct gp)
Adds a copy the given
GeneProduct to this ListOfGeneProducts . |
ListOfGeneProducts |
cloneObject()
Creates and returns a deep copy of this
ListOfGeneProducts object. |
GeneProduct |
createGeneProduct()
Creates a new
GeneProduct object, adds it to the ListOfGeneProducts and
returns the GeneProduct object created. |
void |
delete()
Explicitly deletes the underlying native object.
|
GeneProduct |
get(long n)
Get a
GeneProduct from the ListOfGeneProducts . |
GeneProduct |
get(java.lang.String sid)
Get a
GeneProduct from the ListOfGeneProducts 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 |
getNumGeneProducts()
Get the number of
GeneProduct objects in this ListOfGeneProducts . |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
GeneProduct |
remove(long n)
Removes the nth
GeneProduct from this ListOfGeneProducts
and returns a pointer to it. |
GeneProduct |
remove(java.lang.String sid)
Removes the
GeneProduct from this ListOfGeneProducts 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, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
public ListOfGeneProducts(long level, long version, long pkgVersion) throws SBMLConstructorException
GeneProduct
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfGeneProducts
.
version
- a long integer, the SBML Version to assign to this
ListOfGeneProducts
.
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this ListOfGeneProducts
.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public ListOfGeneProducts(long level, long version) throws SBMLConstructorException
GeneProduct
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfGeneProducts
.
version
- a long integer, the SBML Version to assign to this
ListOfGeneProducts
.
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this ListOfGeneProducts
.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public ListOfGeneProducts(long level) throws SBMLConstructorException
GeneProduct
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfGeneProducts
.
version
- a long integer, the SBML Version to assign to this
ListOfGeneProducts
.
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this ListOfGeneProducts
.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public ListOfGeneProducts() throws SBMLConstructorException
GeneProduct
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
ListOfGeneProducts
.
version
- a long integer, the SBML Version to assign to this
ListOfGeneProducts
.
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this ListOfGeneProducts
.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public ListOfGeneProducts(FbcPkgNamespaces fbcns) throws SBMLConstructorException
ListOfGeneProducts
with the given FbcPkgNamespaces
object.
The package namespaces object used in this constructor is derived from a
SBMLNamespaces
object, which encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and
package version and name information used in addition to SBML Level 3 Core. A
common approach to using libSBML's SBMLNamespaces
facilities is to create an
package namespace object somewhere in a program once, then hand that object
as needed to object constructors of that package that accept it as and
argument, such as this one.
fbcns
- the FbcPkgNamespaces
object.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.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 ListOfGeneProducts.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 ListOfGeneProducts.delete()
themselves.
public ListOfGeneProducts cloneObject()
ListOfGeneProducts
object.
cloneObject
 in class ListOf
ListOfGeneProducts
object.public GeneProduct get(long n)
GeneProduct
from the ListOfGeneProducts
.
get
 in class ListOf
n
- the index number of the GeneProduct
to get.
GeneProduct
in this ListOfGeneProducts
.
ListOf.size()
public GeneProduct get(java.lang.String sid)
GeneProduct
from the ListOfGeneProducts
based on its identifier.
sid
- a string representing the identifier of the GeneProduct
to
get.
GeneProduct
in this ListOfGeneProducts
with the given id or null
if no such GeneProduct
exists.
ListOfGeneProducts.get(long n)
,
ListOf.size()
public int addGeneProduct(GeneProduct gp)
GeneProduct
to this ListOfGeneProducts
.
gp
- the GeneProduct
object to add.
public long getNumGeneProducts()
GeneProduct
objects in this ListOfGeneProducts
.
GeneProduct
objects in this ListOfGeneProducts
.public GeneProduct createGeneProduct()
GeneProduct
object, adds it to the ListOfGeneProducts
and
returns the GeneProduct
object created.
GeneProduct
object instance.
ListOfGeneProducts.addGeneProduct(GeneProduct gp)
public GeneProduct remove(long n)
GeneProduct
from this ListOfGeneProducts
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 GeneProduct
to remove.
ListOf.size()
public GeneProduct remove(java.lang.String sid)
GeneProduct
from this ListOfGeneProducts
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 GeneProduct
to remove.
GeneProduct
removed. As mentioned above, the caller owns the
returned item.public java.lang.String getElementName()
For ListOfGeneProducts
, the XML element name is always
'listOfGeneProducts'.
getElementName
 in class ListOf
'listOfGeneProducts'.
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
method on the object.
SBase.getPackageName()
getTypeCode
 in class ListOf
SBML_LIST_OF
(default).
ListOfGeneProducts.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
method on the object.
SBase.getPackageName()
getItemTypeCode
 in class ListOf
ListOf
instance: SBML_FBC_GENEPRODUCT
(default).
ListOfGeneProducts.getElementName()
,
SBase.getPackageName()