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 . |
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 |
setId(java.lang.String id)
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, 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, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, 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
objectSBMLConstructorException
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
objectSBMLConstructorException
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
objectSBMLConstructorException
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
objectSBMLConstructorException
public GeneProductAssociation(FbcPkgNamespaces fbcns) throws SBMLConstructorException
GeneProductAssociation
with the given FbcPkgNamespaces
object.
fbcns
- the FbcPkgNamespaces
objectSBMLConstructorException
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
as a string.public java.lang.String getName()
GeneProductAssociation
.
getName
 in class SBase
GeneProductAssociation
as a string.public FbcAssociation getAssociation()
GeneProductAssociation
.
GeneProductAssociation
.public FbcAnd createAnd()
GeneProductAssociation
.
public FbcOr createOr()
GeneProductAssociation
.public GeneProductRef createGeneProductRef()
GeneProductAssociation
.public boolean isSetId()
true
if this GeneProductAssociation
's 'id'
attribute is set.
isSetId
 in class SBase
true
if this GeneProductAssociation
's 'id' attribute has been set,
otherwise false
is returned.public boolean isSetName()
true
if this GeneProductAssociation
's 'name'
attribute is set.
isSetName
 in class SBase
true
if this GeneProductAssociation
's 'name' attribute has been set,
otherwise false
is returned.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 id)
GeneProductAssociation
.
public int setName(java.lang.String name)
GeneProductAssociation
.
public int setAssociation(FbcAssociation association)
GeneProductAssociation
.
association
- FbcAssociation
to be set.
public int setAssociation(java.lang.String association)
GeneProductAssociation
.
association
- string representation of the association to be set
public int unsetId()
GeneProductAssociation
.
public int unsetName()
GeneProductAssociation
.
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: