public class FbcAssociation extends SBase
FbcAnd
, FbcOr
, and GeneProductRef
The FbcAssociation
class is the abstract base class for the classes that
can be used as children of the GeneProductAssociation
child of a Reaction
.
The FbcAnd
class is used when all of its children are definitely associated
with the Reaction
the FbcOr
class is used when at least one of its children
are associated with the Reaction
and the GeneProductRef
class is used to
denote a particular GeneProduct
.
Association
and
GeneAssociation
annotation classes. Please see the Version 1 and
Version 2 &ldquofbc&rdquo specifications for more details.Constructor and Description |
---|
FbcAssociation()
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FbcAssociation(FbcAssociation orig)
Copy constructor for
FbcAssociation . |
FbcAssociation(FbcPkgNamespaces fbcns)
Creates a new
FbcAssociation with the given FbcPkgNamespaces object. |
FbcAssociation(long level)
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FbcAssociation(long level,
long version)
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FbcAssociation(long level,
long version,
long pkgVersion)
Creates a new
FbcAssociation with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
Modifier and Type | Method and Description |
---|---|
FbcAssociation |
cloneObject()
Creates and returns a deep copy of this
FbcAssociation object. |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getElementName()
Returns the XML element name of this object.
|
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if all the required attributes
for this FbcAssociation object have been set. |
boolean |
isFbcAnd()
Returns
true , if this abstract 'FbcAssociation' is of type FbcAnd . |
boolean |
isFbcOr()
Returns
true , if this abstract 'FbcAssociation' is of type FbcOr . |
boolean |
isGeneProductRef()
Returns
true , if this abstract 'FbcAssociation' is of type
GeneProductRef . |
static FbcAssociation |
parseFbcInfixAssociation(java.lang.String association,
FbcModelPlugin plugin)
Parses a gene association in infix format and returns a corresponding
Association object. |
void |
setElementName(java.lang.String name)   |
java.lang.String |
toInfix()
Converts this
FbcAssociation object into an infix string representation. |
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, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
public FbcAssociation(long level, long version, long pkgVersion) throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FbcAssociation
version
- a long integer, the SBML Version to assign to this
FbcAssociation
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this FbcAssociation
SBMLConstructorException
public FbcAssociation(long level, long version) throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FbcAssociation
version
- a long integer, the SBML Version to assign to this
FbcAssociation
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this FbcAssociation
SBMLConstructorException
public FbcAssociation(long level) throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FbcAssociation
version
- a long integer, the SBML Version to assign to this
FbcAssociation
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this FbcAssociation
SBMLConstructorException
public FbcAssociation() throws SBMLConstructorException
FbcAssociation
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FbcAssociation
version
- a long integer, the SBML Version to assign to this
FbcAssociation
pkgVersion
- a long integer, the SBML &ldquofbc&rdquo package
Version to assign to this FbcAssociation
SBMLConstructorException
public FbcAssociation(FbcPkgNamespaces fbcns) throws SBMLConstructorException
FbcAssociation
with the given FbcPkgNamespaces
object.
fbcns
- the FbcPkgNamespaces
objectSBMLConstructorException
public FbcAssociation(FbcAssociation orig) throws SBMLConstructorException
FbcAssociation
.
orig
- the FbcAssociation
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 FbcAssociation.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 FbcAssociation.delete()
themselves.
public FbcAssociation cloneObject()
FbcAssociation
object.
cloneObject
 in class SBase
FbcAssociation
object.public boolean isFbcAnd()
true
, if this abstract 'FbcAssociation' is of type FbcAnd
.
true
, if this abstract 'FbcAssociation' is of type FbcAnd
.public boolean isFbcOr()
true
, if this abstract 'FbcAssociation' is of type FbcOr
.
true
, if this abstract 'FbcAssociation' is of type FbcOr
.public boolean isGeneProductRef()
true
, if this abstract 'FbcAssociation' is of type
GeneProductRef
.
true
, if this abstract 'FbcAssociation' is of type
GeneProductRef
.public java.lang.String getElementName()
For FbcAssociation
, the XML element name is always 'fbcAssociation'.
getElementName
 in class SBase
'fbcAssociation'.
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_ASSOCIATION
(default).
FbcAssociation.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes
for this FbcAssociation
object have been set.
hasRequiredAttributes
 in class SBase
FbcAssociation
has no required attributes, so this
method always returns true.
public static FbcAssociation parseFbcInfixAssociation(java.lang.String association, FbcModelPlugin plugin)
Association
object.
This parses a string that has a list of gene names and conjunctions or disjunctions. For example:
(b2422) and (b2425) and (b2423) and (b2424) or (b2422) and (b2423) and (b2424) and (b2413) and (b3917)
This method also creates missing GeneProduct
objects, in case the unique
reference does not yet exist.
association
- the string to parse.plugin
- the FbcModelPlugin
on which to add the geneProduct elements
null
in case of an error.
public java.lang.String toInfix()
FbcAssociation
object into an infix string representation.
public void setElementName(java.lang.String name)