public class Deletion extends SBaseRef
The Deletion
class was introduced by the SBML Level 3 Hierarchical Model Composition
(&ldquocomp&rdquo) package to allow elements of submodels to be removed
before instantiation.
The Deletion
object class is used to define a deletion operation
to be applied when a submodel instantiates a model definition.
Deletions may be useful in hierarchical model composition scenarios for
various reasons. For example, some components in a submodel may be
redundant in the composed model, perhaps because the same features are
implemented in a different way in the new model.
Deletions function as follows. When the Model
to which the Submodel
object refers (via the 'modelRef' attribute) is read and processed for
inclusion into the composed model, each Deletion
object identifies an
object to remove from that Model
instance. The resulting submodel
instance consists of everything in the Model
object instance minus the
entities referenced by the list of Deletion
objects.
As might be expected, deletions can have wide-ranging implications, especially when the object deleted has substantial substructure, as in the case of reactions. The following are rules regarding deletions and their effects.
SBaseRef
object.
The Deletion
object class is subclassed from SBaseRef
, and reuses all the
machinery provided by SBaseRef
. In addition, it defines two optional
attributes, 'id' and 'name'. The 'id' attribute can be used to give an
identifier to a given deletion operation. The identifier has no
mathematical meaning, but it may be useful for creating submodels that
can be manipulated more directly by other submodels. (Indeed, it is
legitimate for an enclosing model definition to delete a deletion!)
The optional 'name' attribute is provided on Deletion
for the
same reason it is provided on other elements that have identifiers
viz., to provide for the possibility of giving a human-readable name to
the object. The name may be useful in situations when deletions are
displayed to modelers.
Constructor and Description |
---|
Deletion()
Creates a new
Deletion with the given level, version, and package version. |
Deletion(CompPkgNamespaces compns)
Creates a new
Deletion with the given CompPkgNamespaces object. |
Deletion(Deletion source)
Copy constructor.
|
Deletion(long level)
Creates a new
Deletion with the given level, version, and package version. |
Deletion(long level,
long version)
Creates a new
Deletion with the given level, version, and package version. |
Deletion(long level,
long version,
long pkgVersion)
Creates a new
Deletion with the given level, version, and package version. |
Modifier and Type | Method and Description |
---|---|
SBase |
cloneObject()
Creates and returns a deep copy of this
Deletion object. |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getElementName()
Returns the XML element name of this SBML object.
|
java.lang.String |
getId()
Returns the value of the 'id' attribute of this
Deletion . |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
Deletion object. |
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
boolean |
isSetId()
Predicate returning
true or false depending on whether this
object's 'id' attribute has been set. |
boolean |
isSetName()
Predicate returning
true or false depending on whether this
object's 'name' attribute has been set. |
int |
saveReferencedElement()
Finds and stores the referenced object.
|
int |
setId(java.lang.String sid)
Sets the value of the 'id' attribute of this
Deletion . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
Deletion . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
Deletion . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
Deletion . |
clearReferencedElement, connectToChild, createSBaseRef, getElementByMetaId, getElementBySId, getIdRef, getMetaIdRef, getNumReferents, getPortRef, getReferencedElement, getReferencedElementFrom, getSBaseRef, getUnitRef, hasRequiredAttributes, isSetIdRef, isSetMetaIdRef, isSetPortRef, isSetSBaseRef, isSetUnitRef, performDeletion, removeFromParentAndDelete, renameSIdRefs, setIdRef, setMetaIdRef, setPortRef, setSBaseRef, setUnitRef, unsetIdRef, unsetMetaIdRef, unsetPortRef, unsetSBaseRef, unsetUnitRef
getPackageName, getPackageURI, getPackageVersion, getParentModel
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setIdAttribute, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public Deletion(long level, long version, long pkgVersion) throws SBMLConstructorException
Deletion
with the given level, version, and package version.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
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 Deletion(long level, long version) throws SBMLConstructorException
Deletion
with the given level, version, and package version.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
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 Deletion(long level) throws SBMLConstructorException
Deletion
with the given level, version, and package version.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
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 Deletion() throws SBMLConstructorException
Deletion
with the given level, version, and package version.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
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 Deletion(CompPkgNamespaces compns) throws SBMLConstructorException
Deletion
with the given CompPkgNamespaces
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.
compns
- the CompPkgNamespaces
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 Deletion(Deletion source) throws SBMLConstructorException
source
- the Deletion
instance to copy.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 Deletion.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 Deletion.delete()
themselves.
public SBase cloneObject()
Deletion
object.
cloneObject
 in class SBaseRef
Deletion
object.public int setId(java.lang.String sid)
Deletion
.
The string sid
is copied.
The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always SId
or a type derived
from that, such as UnitSId
, depending on the object in
question. All data types are defined as follows:
letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
The characters (
and )
are used for grouping, the
character *
'zero or more times', and the character
|
indicates logical 'or'. The equality of SBML identifiers is
determined by an exact character sequence match i.e., comparisons must be
performed in a case-sensitive manner. This applies to all uses of SId
,
SIdRef
, and derived types.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, check, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The exception to this rule is that for InitialAssignment
, EventAssignment
,
AssignmentRule
, and RateRule
objects, the getId() function and the isSetId()
functions (though not the setId() or unsetId() functions) would instead
reference the value of the 'variable' attribute (for the rules and event
assignments) or the 'symbol' attribute (for initial assignments).
The AlgebraicRule
fell into this category as well, though because it
contained neither a 'variable' nor a 'symbol' attribute, getId() would
always return an empty string, and isSetId() would always return false.
For this reason, four new functions are now provided
(getIdAttribute(), setIdAttribute(String),
isSetIdAttribute(), and unsetIdAttribute()) that will always
act on the actual 'id' attribute, regardless of the object's type. The
new functions should be used instead of the old ones unless the old behavior
is somehow necessary.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
setId
 in class SBase
sid
- the string to use as the identifier of this object.
SBase.getIdAttribute()
,
SBase.setIdAttribute(String sid)
,
SBase.isSetIdAttribute()
,
SBase.unsetIdAttribute()
public java.lang.String getId()
Deletion
.
getId
 in class SBase
Deletion
.
SBase.getIdAttribute()
,
SBase.setIdAttribute(String sid)
,
SBase.isSetIdAttribute()
,
SBase.unsetIdAttribute()
The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always SId
or a type derived
from that, such as UnitSId
, depending on the object in
question. All data types are defined as follows:
letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
The characters (
and )
are used for grouping, the
character *
'zero or more times', and the character
|
indicates logical 'or'. The equality of SBML identifiers is
determined by an exact character sequence match i.e., comparisons must be
performed in a case-sensitive manner. This applies to all uses of SId
,
SIdRef
, and derived types.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, check, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The exception to this rule is that for InitialAssignment
, EventAssignment
,
AssignmentRule
, and RateRule
objects, the getId() function and the isSetId()
functions (though not the setId() or unsetId() functions) would instead
reference the value of the 'variable' attribute (for the rules and event
assignments) or the 'symbol' attribute (for initial assignments).
The AlgebraicRule
fell into this category as well, though because it
contained neither a 'variable' nor a 'symbol' attribute, getId() would
always return an empty string, and isSetId() would always return false.
For this reason, four new functions are now provided
(getIdAttribute(), setIdAttribute(String),
isSetIdAttribute(), and unsetIdAttribute()) that will always
act on the actual 'id' attribute, regardless of the object's type. The
new functions should be used instead of the old ones unless the old behavior
is somehow necessary.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
public boolean isSetId()
true
or false
depending on whether this
object's 'id' attribute has been set.
isSetId
 in class SBase
true
if the 'id' attribute of this SBML object is
set, false
otherwise.
SBase.getIdAttribute()
,
SBase.setIdAttribute(String sid)
,
SBase.unsetIdAttribute()
,
SBase.isSetIdAttribute()
The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always SId
or a type derived
from that, such as UnitSId
, depending on the object in
question. All data types are defined as follows:
letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
The characters (
and )
are used for grouping, the
character *
'zero or more times', and the character
|
indicates logical 'or'. The equality of SBML identifiers is
determined by an exact character sequence match i.e., comparisons must be
performed in a case-sensitive manner. This applies to all uses of SId
,
SIdRef
, and derived types.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, check, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The exception to this rule is that for InitialAssignment
, EventAssignment
,
AssignmentRule
, and RateRule
objects, the getId() function and the isSetId()
functions (though not the setId() or unsetId() functions) would instead
reference the value of the 'variable' attribute (for the rules and event
assignments) or the 'symbol' attribute (for initial assignments).
The AlgebraicRule
fell into this category as well, though because it
contained neither a 'variable' nor a 'symbol' attribute, getId() would
always return an empty string, and isSetId() would always return false.
For this reason, four new functions are now provided
(getIdAttribute(), setIdAttribute(String),
isSetIdAttribute(), and unsetIdAttribute()) that will always
act on the actual 'id' attribute, regardless of the object's type. The
new functions should be used instead of the old ones unless the old behavior
is somehow necessary.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
public int unsetId()
Deletion
.
The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always SId
or a type derived
from that, such as UnitSId
, depending on the object in
question. All data types are defined as follows:
letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
The characters (
and )
are used for grouping, the
character *
'zero or more times', and the character
|
indicates logical 'or'. The equality of SBML identifiers is
determined by an exact character sequence match i.e., comparisons must be
performed in a case-sensitive manner. This applies to all uses of SId
,
SIdRef
, and derived types.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, check, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The exception to this rule is that for InitialAssignment
, EventAssignment
,
AssignmentRule
, and RateRule
objects, the getId() function and the isSetId()
functions (though not the setId() or unsetId() functions) would instead
reference the value of the 'variable' attribute (for the rules and event
assignments) or the 'symbol' attribute (for initial assignments).
The AlgebraicRule
fell into this category as well, though because it
contained neither a 'variable' nor a 'symbol' attribute, getId() would
always return an empty string, and isSetId() would always return false.
For this reason, four new functions are now provided
(getIdAttribute(), setIdAttribute(String),
isSetIdAttribute(), and unsetIdAttribute()) that will always
act on the actual 'id' attribute, regardless of the object's type. The
new functions should be used instead of the old ones unless the old behavior
is somehow necessary.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
unsetId
 in class SBase
SBase.getIdAttribute()
,
SBase.setIdAttribute(String sid)
,
SBase.isSetIdAttribute()
,
SBase.unsetIdAttribute()
public int setName(java.lang.String name)
public java.lang.String getName()
Deletion
object.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The 'name' attribute is
optional and is not intended to be used for cross-referencing purposes
within a model. Its purpose instead is to provide a human-readable
label for the component. The data type of 'name' is the type
string
defined in XML Schema. SBML imposes no
restrictions as to the content of 'name' attributes beyond those
restrictions defined by the string
type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
getName
 in class SBase
SBase.getIdAttribute()
,
Deletion.isSetName()
,
Deletion.setName(String sid)
,
Deletion.unsetName()
public boolean isSetName()
true
or false
depending on whether this
object's 'name' attribute has been set.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The 'name' attribute is
optional and is not intended to be used for cross-referencing purposes
within a model. Its purpose instead is to provide a human-readable
label for the component. The data type of 'name' is the type
string
defined in XML Schema. SBML imposes no
restrictions as to the content of 'name' attributes beyond those
restrictions defined by the string
type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
isSetName
 in class SBase
true
if the 'name' attribute of this SBML object is
set, false
otherwise.
Deletion.getName()
,
Deletion.setName(String sid)
,
Deletion.unsetName()
public int unsetName()
Deletion
.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The 'name' attribute is
optional and is not intended to be used for cross-referencing purposes
within a model. Its purpose instead is to provide a human-readable
label for the component. The data type of 'name' is the type
string
defined in XML Schema. SBML imposes no
restrictions as to the content of 'name' attributes beyond those
restrictions defined by the string
type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
unsetName
 in class SBase
Deletion.getName()
,
Deletion.setName(String sid)
,
Deletion.isSetName()
public java.lang.String getElementName()
getElementName
 in class SBaseRef
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 SBaseRef
SBML_COMP_DELETION
.
Deletion.getElementName()
,
CompBase.getPackageName()
public int saveReferencedElement()
Submodel
parent,
gets its instantiated Model
object, calls
'getReferencedElementFrom()' using that model, and stores the result.
saveReferencedElement
 in class SBaseRef