public class FbcReactionPlugin extends SBasePlugin
Reaction
by the &ldquofbc&rdquo package.
The FbcReactionPlugin
class inherits from the SBasePlugin
class, and
codifies the extentions to the Reaction
class defined in the Flux Balance Constraints
package (&ldquofbc&rdquo). This extention allows the modeler to define
(in Version 2 of the &ldquofbc&rdquo package) an upper and lower
flux bound, with the 'upperFluxBound' and 'lowerFluxBound' attributes,
as well as a way to reference any GeneProduct
associated with
this Reaction
, through the GeneProductAssociation
child.
FluxBound
element is
used instead of the 'upperFluxBound' and 'lowerFluxBound' attributes.
There is no equivalent of the GeneProductAssociation
, which was added
in Version 2.Constructor and Description |
---|
FbcReactionPlugin(FbcReactionPlugin orig)
Copy constructor for
FbcReactionPlugin . |
FbcReactionPlugin(java.lang.String uri,
java.lang.String prefix,
FbcPkgNamespaces fbcns)
Creates a new
FbcReactionPlugin object using the given parameters. |
Modifier and Type | Method and Description |
---|---|
SBasePlugin |
cloneObject()
Creates and returns a deep copy of this
FbcReactionPlugin object. |
GeneProductAssociation |
createGeneProductAssociation()
Creates a new
GeneProductAssociation object and adds it to the FbcReactionPlugin object. |
void |
delete()
Explicitly deletes the underlying native object.
|
GeneProductAssociation |
getGeneProductAssociation()
Returns the
GeneProductAssociation from this FbcReactionPlugin object. |
java.lang.String |
getLowerFluxBound()
Returns the value of the 'lowerFluxBound' attribute of this
FbcReactionPlugin . |
java.lang.String |
getUpperFluxBound()
Returns the value of the 'upperFluxBound' attribute of this
FbcReactionPlugin . |
boolean |
isSetGeneProductAssociation()
Predicate returning
true if this FbcReactionPlugin 's
'GeneProductAssociation' element has been set. |
boolean |
isSetLowerFluxBound()
Predicate returning
true if this FbcReactionPlugin 's 'lowerFluxBound'
attribute is set. |
boolean |
isSetUpperFluxBound()
Predicate returning
true if this FbcReactionPlugin 's 'upperFluxBound'
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 |
setGeneProductAssociation(GeneProductAssociation geneProductAssociation)
Sets the
GeneProductAssociation element in this FbcReactionPlugin object. |
int |
setLowerFluxBound(java.lang.String lowerFluxBound)
Sets the value of the 'lowerFluxBound' attribute of this
FbcReactionPlugin . |
int |
setUpperFluxBound(java.lang.String upperFluxBound)
Sets the value of the 'upperFluxBound' attribute of this
FbcReactionPlugin . |
int |
unsetGeneProductAssociation()
Unsets the the 'geneProduct' element of this
FbcReactionPlugin . |
int |
unsetLowerFluxBound()
Unsets the value of the 'lowerFluxBound' attribute of this
FbcReactionPlugin . |
int |
unsetUpperFluxBound()
Unsets the value of the 'upperFluxBound' attribute of this
FbcReactionPlugin . |
getElementByMetaId, getElementBySId, getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameUnitSIdRefs, setElementNamespace
public FbcReactionPlugin(java.lang.String uri, java.lang.String prefix, FbcPkgNamespaces fbcns)
FbcReactionPlugin
object using the given parameters.
In the XML representation of an SBML document, XML namespaces are used to
identify the origin of each XML construct used. XML namespaces are
identified by their unique resource identifiers (URIs). The core SBML
specifications stipulate the namespaces that must be used for core SBML
constructs for example, all XML elements that belong to SBML Level 3
Version 1 Core must be placed in the XML namespace identified by the URI
'http://www.sbml.org/sbml/level3/version1/core'
. Individual
SBML Level 3 packages define their own XML namespaces for example,
all elements belonging to the SBML Level 3 Layout Version 1
package must be placed in the XML namespace
'http://www.sbml.org/sbml/level3/version1/layout/version1/'
.
The SBMLNamespaces
object encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and (in
Level 3) packages used in addition to SBML Level 3 Core. A
common approach to using libSBML's SBMLNamespaces
facilities is to create an
SBMLNamespaces
object somewhere in a program once, then hand that object
as needed to object constructors that accept SBMLNamespaces
as arguments.
uri
- the URI of the SBML Level 3 package implemented by
this libSBML package extension.
prefix
- the XML namespace prefix being used for the package.
fbcns
- the namespaces object for the package.public FbcReactionPlugin(FbcReactionPlugin orig)
FbcReactionPlugin
.
orig
- the FbcReactionPlugin
instance to copy.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 FbcReactionPlugin.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 FbcReactionPlugin.delete()
themselves.
delete
 in class SBasePlugin
public SBasePlugin cloneObject()
FbcReactionPlugin
object.
cloneObject
 in class SBasePlugin
FbcReactionPlugin
object.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 SBasePlugin
oldid
- the old identifier.newid
- the new identifier.public GeneProductAssociation getGeneProductAssociation()
GeneProductAssociation
from object in this FbcReactionPlugin
object.GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public boolean isSetGeneProductAssociation()
true
if the 'GeneProductAssociation' element has been set,
otherwise false
is returned.GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public int setGeneProductAssociation(GeneProductAssociation geneProductAssociation)
geneProductAssociation
- the geneProductAssociation to be set.
GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public GeneProductAssociation createGeneProductAssociation()
GeneProductAssociation
object.GeneProduct
objects are only defined for version 2
of the 'Flux Balance Constraints' specification, and have no
equivalent in version 1 of the specification.
public java.lang.String getLowerFluxBound()
FbcReactionPlugin
.
FbcReactionPlugin
as a string.FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public java.lang.String getUpperFluxBound()
FbcReactionPlugin
.
FbcReactionPlugin
as a string.FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public boolean isSetLowerFluxBound()
true
if this FbcReactionPlugin
's 'lowerFluxBound' attribute has been set,
otherwise false
is returned.FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public boolean isSetUpperFluxBound()
true
if this FbcReactionPlugin
's 'upperFluxBound' attribute has been set,
otherwise false
is returned.FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public int setLowerFluxBound(java.lang.String lowerFluxBound)
FbcReactionPlugin
.
lowerFluxBound
- the value of the 'lowerFluxBound' attribute to be set.
FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public int setUpperFluxBound(java.lang.String upperFluxBound)
FbcReactionPlugin
.
upperFluxBound
- the value of the 'upperFluxBound' attribute to be set.
FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public int unsetLowerFluxBound()
FbcReactionPlugin
.
FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public int unsetUpperFluxBound()
FbcReactionPlugin
.
FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.
public int unsetGeneProductAssociation()
FbcReactionPlugin
.
FbcReactionPlugin
are only defined for version 2 of the 'Flux
Balance Constraints' specification. In version 1, this information
was encoded in the FluxBound
children of the FbcModelPlugin
.