public class GeneProduct extends SBase
Association
of a gene product with a Reaction
In the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package
representation format, a GeneProduct
object represents a single gene or
implied gene product. The gene or gene product is identified using the
required attribute 'label', which is a text string. (This attribute is
separate from the usual SBML 'id' attribute, which is used to
cross-reference entities within an SBML model.) A GeneProduct
object can
also possess an optional 'associatedSpecies' attribute if this a
attribute is defined, it should have a value of type SIdRef
and be the identifier of a Species
object defined in the enclosing Model
.
An 'associatedSpecies', if it exists, is interpreted to be a species
associated with the gene or gene product that is represented by the
GeneProduct
object.
Association
and
GeneAssociation
annotation classes. Please see the Version 1 and
Version 2 &ldquofbc&rdquo specifications for more details.Constructor and Description |
---|
GeneProduct()
Creates a new
GeneProduct with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
GeneProduct(FbcPkgNamespaces fbcns)
Creates a new
GeneProduct with the given FbcPkgNamespaces object. |
GeneProduct(GeneProduct orig)
Copy constructor for
GeneProduct . |
GeneProduct(long level)
Creates a new
GeneProduct with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
GeneProduct(long level,
long version)
Creates a new
GeneProduct with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
GeneProduct(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 |
---|---|
GeneProduct |
cloneObject()
Creates and returns a deep copy of this
GeneProduct object. |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getAssociatedSpecies()
Returns the value of the 'associatedSpecies' attribute of this
GeneProduct . |
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
GeneProduct . |
java.lang.String |
getLabel()
Returns the value of the 'label' attribute of this
GeneProduct . |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
GeneProduct . |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if all the required attributes
for this GeneProduct object have been set. |
boolean |
isSetAssociatedSpecies()
Predicate returning
true if this GeneProduct 's 'associatedSpecies'
attribute is set. |
boolean |
isSetId()
Predicate returning
true if this GeneProduct 's 'id' attribute is set. |
boolean |
isSetLabel()
Predicate returning
true if this GeneProduct 's 'label' attribute is
set. |
boolean |
isSetName()
Predicate returning
true if this GeneProduct 's 'name' attribute is
set. |
void |
renameSIdRefs(java.lang.String oldid,
java.lang.String newid)
Replaces all uses of a given
SIdRef type attribute value with another
value. |
int |
setAssociatedSpecies(java.lang.String associatedSpecies)
Sets the value of the 'associatedSpecies' attribute of this
GeneProduct . |
int |
setId(java.lang.String id)
Sets the value of the 'id' attribute of this
GeneProduct . |
int |
setLabel(java.lang.String label)
Sets the value of the 'label' attribute of this
GeneProduct . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
GeneProduct . |
int |
unsetAssociatedSpecies()
Unsets the value of the 'associatedSpecies' attribute of this
GeneProduct . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
GeneProduct . |
int |
unsetLabel()
Unsets the value of the 'label' attribute of this
GeneProduct . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
GeneProduct . |
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public GeneProduct(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 GeneProduct
version
- a long integer, the SBML Version to assign to this GeneProduct
pkgVersion
- a long integer, the SBML Fbc Version to assign to this GeneProduct
SBMLConstructorException
public GeneProduct(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 GeneProduct
version
- a long integer, the SBML Version to assign to this GeneProduct
pkgVersion
- a long integer, the SBML Fbc Version to assign to this GeneProduct
SBMLConstructorException
public GeneProduct(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 GeneProduct
version
- a long integer, the SBML Version to assign to this GeneProduct
pkgVersion
- a long integer, the SBML Fbc Version to assign to this GeneProduct
SBMLConstructorException
public GeneProduct() throws SBMLConstructorException
GeneProduct
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this GeneProduct
version
- a long integer, the SBML Version to assign to this GeneProduct
pkgVersion
- a long integer, the SBML Fbc Version to assign to this GeneProduct
SBMLConstructorException
public GeneProduct(FbcPkgNamespaces fbcns) throws SBMLConstructorException
GeneProduct
with the given FbcPkgNamespaces
object.
fbcns
- the FbcPkgNamespaces
objectSBMLConstructorException
public GeneProduct(GeneProduct orig) throws SBMLConstructorException
GeneProduct
.
orig
- the GeneProduct
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 GeneProduct.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 GeneProduct.delete()
themselves.
public GeneProduct cloneObject()
GeneProduct
object.
cloneObject
 in class SBase
GeneProduct
object.public java.lang.String getId()
GeneProduct
.
getId
 in class SBase
GeneProduct
as a string.public java.lang.String getName()
GeneProduct
.
getName
 in class SBase
GeneProduct
as a string.public java.lang.String getLabel()
GeneProduct
.
GeneProduct
as a
string.public java.lang.String getAssociatedSpecies()
GeneProduct
.
GeneProduct
as a string.public boolean isSetId()
true
if this GeneProduct
's 'id' attribute is set.
isSetId
 in class SBase
true
if this GeneProduct
's 'id' attribute has been set,
otherwise false
is returned.public boolean isSetName()
true
if this GeneProduct
's 'name' attribute is
set.
isSetName
 in class SBase
true
if this GeneProduct
's 'name' attribute has been set,
otherwise false
is returned.public boolean isSetLabel()
true
if this GeneProduct
's 'label' attribute is
set.
true
if this GeneProduct
's 'label' attribute has been set,
otherwise false
is returned.public boolean isSetAssociatedSpecies()
true
if this GeneProduct
's 'associatedSpecies'
attribute is set.
true
if this GeneProduct
's 'associatedSpecies' attribute has
been set, otherwise false
is returned.public int setId(java.lang.String id)
GeneProduct
.
public int setName(java.lang.String name)
GeneProduct
.
public int setLabel(java.lang.String label)
GeneProduct
.
label
- String value of the 'label' attribute to be
set
public int setAssociatedSpecies(java.lang.String associatedSpecies)
GeneProduct
.
associatedSpecies
- String value of the
'associatedSpecies' attribute to be set
public int unsetId()
GeneProduct
.
public int unsetName()
GeneProduct
.
public int unsetLabel()
GeneProduct
.
public int unsetAssociatedSpecies()
GeneProduct
.
public void renameSIdRefs(java.lang.String oldid, java.lang.String newid)
Replaces all uses of a given SIdRef
type attribute value with another
value.
In SBML, object identifiers are of a data type called SId
.
In SBML Level 3, an explicit data type called SIdRef
was
introduced for attribute values that refer to SId
values in
previous Levels of SBML, this data type did not exist and attributes were
simply described to as 'referring to an identifier', but the effective
data type was the same as SIdRef
in Level 3. These and
other methods of libSBML refer to the type SIdRef
for all
Levels of SBML, even if the corresponding SBML specification did not
explicitly name the data type.
This method works by looking at all attributes and (if appropriate)
mathematical formulas in MathML content, comparing the referenced
identifiers to the value of oldid
. If any matches are found, the
matching values are replaced with newid
. The method does not
descend into child elements.
renameSIdRefs
 in class SBase
oldid
- the old identifiernewid
- the new identifierpublic java.lang.String getElementName()
For GeneProduct
, the XML element name is always 'geneProduct'.
getElementName
 in class SBase
'geneProduct'.
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_GENEPRODUCT
(default).
GeneProduct.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes
for this GeneProduct
object have been set.
hasRequiredAttributes
 in class SBase
GeneProduct
object are: