public class GeneProductAssociation extends SBase
Association
between gene products and reactions
In Version 2 of the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo)
package specification, GeneProductAssociation
is a class derived from
SBase
used to associate one more genes or gene products with reactions.
GeneProductAssociation
objects are essentially containers, with one such
container optionally attached as a subelement to a Reaction
object in a
model. The container can contain one of three kinds of objects, all of
which are subclasses of the libSBML parent class FbcAssociation
. (Note
that this class is named Association in the &ldquofbc&rdquo
Version 2 specification, but in libSBML is named FbcAssociation
to
avoid a name conflict with an existing class.)
One of the kinds of FbcAssociation
subclasses that can appear in a
GeneProductAssociation
is GeneProductRef
. This class of objects
references a GeneProduct
declared in a ListOfGeneProducts
attached to the
enclosing Model
object. In the &ldquofbc&rdquo approach, when more than
one gene (or gene product) is present in an association, they are written
as logical expressions using Boolean logical operators and and
or through the classes (in libSBML) FbcAnd
and FbcOr
. (In the
&ldquofbc&rdquo Version 2 specification, these are simply named
And and Or, respectively.) The FbcAnd
and FbcOr
objects
in turn can contain either GeneProductRef
objects or other FbcAnd
and/or
FbcOr
objects.
Here is a concrete example of what the XML representation of a simple or relationship might look like:
<reaction id = 'R_ABTA' ... rest of Reaction
declaration elided for this example ...>
<fbc:geneProductAssociation fbc:id='ga_16'>
<fbc:or>
<fbc:geneProductRef fbc:geneProduct='g_b2662'/>
<fbc:geneProductRef fbc:geneProduct='g_b1302'/>
</fbc:or>
</fbc:geneProductAssociationgt
</reaction>
Association
and
GeneAssociation
annotation classes. Please see the Version 1 and
Version 2 &ldquofbc&rdquo specifications for more details.Constructor and Description |
---|
GeneProductAssociation()
Creates a new
GeneProductAssociation with the given SBML Level, Version, and
&ldquofbc&rdquo package version. |
GeneProductAssociation(FbcPkgNamespaces fbcns)
Creates a new
GeneProductAssociation with the given FbcPkgNamespaces
object. |
GeneProductAssociation(GeneProductAssociation orig)
Copy constructor for
GeneProductAssociation . |
GeneProductAssociation(long level)
Creates a new
GeneProductAssociation with the given SBML Level, Version, and
&ldquofbc&rdquo package version. |
GeneProductAssociation(long level,
long version)
Creates a new
GeneProductAssociation with the given SBML Level, Version, and
&ldquofbc&rdquo package version. |
GeneProductAssociation(long level,
long version,
long pkgVersion)
Creates a new
GeneProductAssociation with the given SBML Level, Version, and
&ldquofbc&rdquo package version. |
Modifier and Type | Method and Description |
---|---|
GeneProductAssociation |
cloneObject()
Creates and returns a deep copy of this
GeneProductAssociation object. |
FbcAnd |
createAnd()
Creates a new 'association' and sets it for this
GeneProductAssociation . |
GeneProductRef |
createGeneProductRef()
Creates a new 'association' and sets it for this
GeneProductAssociation . |
FbcOr |
createOr()
Creates a new 'association' and sets it for this
GeneProductAssociation . |
void |
delete()
Explicitly deletes the underlying native object.
|
FbcAssociation |
getAssociation()
Returns the 'association' element of this
GeneProductAssociation . |
java.lang.String |
getElementName()
Returns the XML element name of this object.
|
java.lang.String |
getId()
Returns the value of the 'id' attribute of this
GeneProductAssociation . |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
GeneProductAssociation object. |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if all the required attributes for this
GeneProductAssociation object have been set. |
boolean |
hasRequiredElements()
Predicate returning
true if all the required elements for this
GeneProductAssociation object have been set. |
boolean |
isSetAssociation()
Predicate returning
true if this GeneProductAssociation 's
'association' element is set. |
boolean |
isSetId()
Predicate returning
true if this GeneProductAssociation 's 'id'
attribute is set. |
boolean |
isSetName()
Predicate returning
true if this GeneProductAssociation 's 'name'
attribute is set. |
int |
setAssociation(FbcAssociation association)
Sets the 'association' element of this
GeneProductAssociation . |
int |
setAssociation(java.lang.String association)
Sets the 'association' element of this
GeneProductAssociation . |
int |
setAssociation(java.lang.String association,
boolean usingId)
Sets the 'association' element of this
GeneProductAssociation . |
int |
setAssociation(java.lang.String association,
boolean usingId,
boolean addMissingGP)
Sets the 'association' element of this
GeneProductAssociation . |
int |
setId(java.lang.String sid)
Sets the value of the 'id' attribute of this
GeneProductAssociation . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
GeneProductAssociation . |
int |
unsetAssociation()
Unsets the 'association' element of this
GeneProductAssociation . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
GeneProductAssociation . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
GeneProductAssociation . |
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getObjectVersion, getPackageName, getPackageVersion, 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, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, 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 GeneProductAssociation(long level, long version, long pkgVersion) throws SBMLConstructorException
GeneProductAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquo package version.
level
- a long integer, the SBML Level to assign to this
GeneProductAssociation
.
version
- a long integer, the SBML Version to assign to this
GeneProductAssociation
.
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo Version to
assign to this GeneProductAssociation
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 GeneProductAssociation(long level, long version) throws SBMLConstructorException
GeneProductAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquo package version.
level
- a long integer, the SBML Level to assign to this
GeneProductAssociation
.
version
- a long integer, the SBML Version to assign to this
GeneProductAssociation
.
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo Version to
assign to this GeneProductAssociation
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 GeneProductAssociation(long level) throws SBMLConstructorException
GeneProductAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquo package version.
level
- a long integer, the SBML Level to assign to this
GeneProductAssociation
.
version
- a long integer, the SBML Version to assign to this
GeneProductAssociation
.
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo Version to
assign to this GeneProductAssociation
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 GeneProductAssociation() throws SBMLConstructorException
GeneProductAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquo package version.
level
- a long integer, the SBML Level to assign to this
GeneProductAssociation
.
version
- a long integer, the SBML Version to assign to this
GeneProductAssociation
.
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo Version to
assign to this GeneProductAssociation
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 GeneProductAssociation(FbcPkgNamespaces fbcns) throws SBMLConstructorException
GeneProductAssociation
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 GeneProductAssociation(GeneProductAssociation orig) throws SBMLConstructorException
GeneProductAssociation
.
orig
- the GeneProductAssociation
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 GeneProductAssociation.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 GeneProductAssociation.delete()
themselves.
public GeneProductAssociation cloneObject()
GeneProductAssociation
object.
cloneObject
 in class SBase
GeneProductAssociation
object.public java.lang.String getId()
GeneProductAssociation
.
getId
 in class SBase
GeneProductAssociation
.
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 java.lang.String getName()
GeneProductAssociation
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()
,
GeneProductAssociation.isSetName()
,
GeneProductAssociation.setName(String sid)
,
GeneProductAssociation.unsetName()
public FbcAssociation getAssociation()
GeneProductAssociation
.
GeneProductAssociation
.public FbcAnd createAnd()
GeneProductAssociation
.
FbcAnd
created.public FbcOr createOr()
GeneProductAssociation
.public GeneProductRef createGeneProductRef()
GeneProductAssociation
.public boolean isSetId()
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 boolean isSetName()
true
if this GeneProductAssociation
's 'name'
attribute is 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.
GeneProductAssociation.getName()
,
GeneProductAssociation.setName(String sid)
,
GeneProductAssociation.unsetName()
public boolean isSetAssociation()
true
if this GeneProductAssociation
's
'association' element is set.
true
if this GeneProductAssociation
's 'association' element has been set,
otherwise false
is returned.public int setId(java.lang.String sid)
GeneProductAssociation
.
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 int setName(java.lang.String name)
GeneProductAssociation
.
The string in name
is copied.
public int setAssociation(FbcAssociation association)
GeneProductAssociation
.
association
- FbcAssociation
to be set.
public int setAssociation(java.lang.String association, boolean usingId, boolean addMissingGP)
GeneProductAssociation
.
This is a helper method that allows a user to set the
GeneProductAssociation
via a string such as "a1 AND b1 OR
C2"
and have the method work out the correct XML structure.
association
- string representation of the association to be set.
usingId
- If true
, this method assumes that the infix
string association
uses the identifiers of GeneProduct
objects. If @c
false (the default), the method assumes that the string uses the label
attributes of GeneProduct
objects.
addMissingGP
- If true
(the default), then while
parsing the infix string in association
, any identifiers or labels
(depending on usingId
) found in the expression that do not correspond
to an existing GeneProduct
object will result in the addition of that
GeneProduct
. If false
, this method will not add a GeneProduct
in
that circumstance.
public int setAssociation(java.lang.String association, boolean usingId)
GeneProductAssociation
.
This is a helper method that allows a user to set the
GeneProductAssociation
via a string such as "a1 AND b1 OR
C2"
and have the method work out the correct XML structure.
association
- string representation of the association to be set.
usingId
- If true
, this method assumes that the infix
string association
uses the identifiers of GeneProduct
objects. If @c
false (the default), the method assumes that the string uses the label
attributes of GeneProduct
objects.
addMissingGP
- If true
(the default), then while
parsing the infix string in association
, any identifiers or labels
(depending on usingId
) found in the expression that do not correspond
to an existing GeneProduct
object will result in the addition of that
GeneProduct
. If false
, this method will not add a GeneProduct
in
that circumstance.
public int setAssociation(java.lang.String association)
GeneProductAssociation
.
This is a helper method that allows a user to set the
GeneProductAssociation
via a string such as "a1 AND b1 OR
C2"
and have the method work out the correct XML structure.
association
- string representation of the association to be set.
usingId
- If true
, this method assumes that the infix
string association
uses the identifiers of GeneProduct
objects. If @c
false (the default), the method assumes that the string uses the label
attributes of GeneProduct
objects.
addMissingGP
- If true
(the default), then while
parsing the infix string in association
, any identifiers or labels
(depending on usingId
) found in the expression that do not correspond
to an existing GeneProduct
object will result in the addition of that
GeneProduct
. If false
, this method will not add a GeneProduct
in
that circumstance.
public int unsetId()
GeneProductAssociation
.
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 unsetName()
GeneProductAssociation
.
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
GeneProductAssociation.getName()
,
GeneProductAssociation.setName(String sid)
,
GeneProductAssociation.isSetName()
public int unsetAssociation()
GeneProductAssociation
.
public java.lang.String getElementName()
For GeneProductAssociation
, the XML element name is always 'geneProductAssociation'.
getElementName
 in class SBase
'geneProductAssociation'.
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 SBase
SBML_FBC_GENEPRODUCTASSOCIATION
(default).
GeneProductAssociation.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes for this
GeneProductAssociation
object have been set.
hasRequiredAttributes
 in class SBase
GeneProductAssociation
object are:
public boolean hasRequiredElements()
true
if all the required elements for this
GeneProductAssociation
object have been set.
hasRequiredElements
 in class SBase
GeneProductAssociation
object are: