public class GeneAssociation extends SBase
This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
The GeneAssociation
class is a helper class for creating annotations to
store gene association information in Version 1 of the SBML
Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package. In
&ldquofbc&rdquo Version 2, the equivalent capability is handled by
the GeneProductAssociation
class and this class (GeneAssociation) is not used.
Constructor and Description |
---|
GeneAssociation()
|
GeneAssociation(FbcPkgNamespaces fbcns)
Creates a new
GeneAssociation with the given FbcPkgNamespaces object. |
GeneAssociation(GeneAssociation source)
Copy constructor.
|
GeneAssociation(long level)
|
GeneAssociation(long level,
long version)
|
GeneAssociation(long level,
long version,
long pkgVersion)
|
GeneAssociation(XMLNode node,
FbcPkgNamespaces fbcns)
|
Modifier and Type | Method and Description |
---|---|
GeneAssociation |
cloneObject()
Creates and returns a deep copy of this
GeneAssociation . |
Association |
createAssociation()
Creates a new association, sets it to this element and returns it.
|
void |
delete()
Explicitly deletes the underlying native object.
|
Association |
getAssociation()
Returns
Association object of this GeneAssociation . |
java.lang.String |
getElementName()
Returns the XML element name of this object.
|
java.lang.String |
getId()
Returns the string of the 'id' attribute of this
GeneAssociation . |
java.lang.String |
getReaction()
Returns the string of the 'reaction' attribute of this
GeneAssociation . |
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
boolean |
isSetAssociation()
Predicate returning
true if this GeneAssociation 's 'association'
element is set. |
boolean |
isSetId()
Predicate returning
true if this GeneAssociation 's 'id' attribute is
set. |
boolean |
isSetReaction()
Predicate returning
true if this GeneAssociation 's 'reaction'
attribute is set. |
int |
setAssociation(Association association)
Sets the
Association object of this GeneAssociation . |
int |
setId(java.lang.String id)
Sets the SIdRef string of the 'id' attribute of this
GeneAssociation . |
int |
setReaction(java.lang.String reaction)
Sets the SIdRef string of the 'reaction' attribute of this
GeneAssociation . |
XMLNode |
toXML()
Creates an
XMLNode object from this. |
int |
unsetAssociation()
Unsets the
Association object of this GeneAssociation . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
GeneAssociation . |
int |
unsetReaction()
Unsets the value of the 'id' attribute of this
GeneAssociation . |
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, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
public GeneAssociation(long level, long version, long pkgVersion) throws SBMLConstructorException
SBMLConstructorException
public GeneAssociation(long level, long version) throws SBMLConstructorException
SBMLConstructorException
public GeneAssociation(long level) throws SBMLConstructorException
SBMLConstructorException
public GeneAssociation() throws SBMLConstructorException
SBMLConstructorException
public GeneAssociation(XMLNode node, FbcPkgNamespaces fbcns) throws SBMLConstructorException
SBMLConstructorException
public GeneAssociation(FbcPkgNamespaces fbcns) throws SBMLConstructorException
GeneAssociation
with the given FbcPkgNamespaces
object.SBMLConstructorException
public GeneAssociation(GeneAssociation source) throws SBMLConstructorException
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 GeneAssociation.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 GeneAssociation.delete()
themselves.
public java.lang.String getId()
GeneAssociation
.
getId
 in class SBase
GeneAssociation
.public boolean isSetId()
true
if this GeneAssociation
's 'id' attribute is
set.
isSetId
 in class SBase
true
if this GeneAssociation
's 'id' attribute has been set,
otherwise false
is returned.public int setId(java.lang.String id)
GeneAssociation
.
public int unsetId()
GeneAssociation
.
public java.lang.String getReaction()
GeneAssociation
.
GeneAssociation
.public boolean isSetReaction()
true
if this GeneAssociation
's 'reaction'
attribute is set.
true
if this GeneAssociation
's 'reaction' attribute has been set,
otherwise false
is returned.public int setReaction(java.lang.String reaction)
GeneAssociation
.
reaction
- a SIdRef string to be set.
public int unsetReaction()
GeneAssociation
.
public Association createAssociation()
public Association getAssociation()
Association
object of this GeneAssociation
.
Association
object of this GeneAssociation
.public boolean isSetAssociation()
true
if this GeneAssociation
's 'association'
element is set.
true
if this GeneAssociation
's 'association' element has been set,
otherwise false
is returned.public int setAssociation(Association association)
Association
object of this GeneAssociation
.
association
- a Association
object to be set.
public int unsetAssociation()
public java.lang.String getElementName()
For GeneAssociation
, the XML element name is always 'geneAssociation'.
getElementName
 in class SBase
'geneAssociation'.
public GeneAssociation cloneObject()
GeneAssociation
.
cloneObject
 in class SBase
GeneAssociation
.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_GENEASSOCIATION
GeneAssociation.getElementName()
,
SBase.getPackageName()