public class FluxObjective extends SBase
An integral component in a complete description of a steady-state model is
the so-called objective function, which generally consists of a
linear combination of model variables (fluxes) and a sense (direction). In
the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package, this concept
is succinctly captured in the Objective
class. An Objective
object
includes a list of flux objectives, each in the form of a FluxObjective
object.
The FluxObjective
class is a relatively simple container for a model
variable weighted by a signed linear coefficient. In addition to the
common SBML object attributes of 'id' and 'name' (both of which are
optional), it adds two required attributes: 'reaction' and 'coefficient'.
The 'reaction' attribute must have a value of type SIdRef
,
and its value is restricted to the identifier of a Reaction
object in the
model. The 'reaction' attribute identifiers the reaction to which the
FluxObjective
applies. The 'coefficient' attribute must have a value of
type double
, and refers to the coefficient that this
FluxObjective
takes in the enclosing Objective
. Its unit of measurement
is dimensionless
. The meaning of these two attributes
together is given by the formula coefficient ×
reaction-flux. Since reactions in SBML Level 3 are in units of
extent, the units of a flux objective are thus extent per
time.
The following example * illustrates the use of these attributes in an example of a * ListOfObjectives:
<fbc:listOfObjectives fbc:activeObjective='obj1'> <fbc:objective fbc:id='obj1' fbc:type='maximize'> <fbc:listOfFluxObjectives> <fbc:fluxObjective fbc:reaction='R1' fbc:coefficient='1'/> <fbc:fluxObjective fbc:reaction='R2' fbc:coefficient='2'/> </fbc:listOfFluxObjectives> </fbc:objective> </fbc:listOfObjectives>
Objective
,
ListOfObjectives
,
ListOfFluxObjectives
Constructor and Description |
---|
FluxObjective()
Creates a new
FluxObjective with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FluxObjective(FbcPkgNamespaces fbcns)
Creates a new
FluxObjective with the given FbcPkgNamespaces object. |
FluxObjective(FluxObjective orig)
Copy constructor for
FluxObjective . |
FluxObjective(long level)
Creates a new
FluxObjective with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FluxObjective(long level,
long version)
Creates a new
FluxObjective with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
FluxObjective(long level,
long version,
long pkgVersion)
Creates a new
FluxObjective with the given SBML Level, Version, and
&ldquofbc&rdquopackage version. |
Modifier and Type | Method and Description |
---|---|
FluxObjective |
cloneObject()
Creates and returns a deep copy of this
FluxObjective object. |
void |
delete()
Explicitly deletes the underlying native object.
|
double |
getCoefficient()
Returns the value of the 'coefficient' attribute of this
FluxObjective . |
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
FluxObjective . |
java.lang.String |
getName()
Returns the value of the 'name' attribute of this
FluxObjective . |
java.lang.String |
getReaction()
Returns the value of the 'reaction' attribute of this
FluxObjective . |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if all the required attributes
for this FluxObjective object have been set. |
boolean |
isSetCoefficient()
Predicate returning
true if this FluxObjective 's 'coefficient'
attribute is set. |
boolean |
isSetId()
Predicate returning
true if this FluxObjective 's 'id' attribute is
set. |
boolean |
isSetName()
Predicate returning
true if this FluxObjective 's 'name' attribute is
set. |
boolean |
isSetReaction()
Predicate returning
true if this FluxObjective 's 'reaction' 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 |
setCoefficient(double coefficient)
Sets the value of the 'coefficient' attribute of this
FluxObjective . |
int |
setId(java.lang.String id)
Sets the value of the 'id' attribute of this
FluxObjective . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
FluxObjective . |
int |
setReaction(java.lang.String reaction)
Sets the value of the 'reaction' attribute of this
FluxObjective . |
int |
unsetCoefficient()
Unsets the value of the 'coefficient' attribute of this
FluxObjective . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
FluxObjective . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
FluxObjective . |
int |
unsetReaction()
Unsets the value of the 'reaction' attribute of this
FluxObjective . |
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 FluxObjective(long level, long version, long pkgVersion) throws SBMLConstructorException
FluxObjective
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxObjective(long level, long version) throws SBMLConstructorException
FluxObjective
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxObjective(long level) throws SBMLConstructorException
FluxObjective
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxObjective() throws SBMLConstructorException
FluxObjective
with the given SBML Level, Version, and
&ldquofbc&rdquopackage version.
level
- a long integer, the SBML Level to assign to this
FluxObjective
version
- a long integer, the SBML Version to assign to this
FluxObjective
pkgVersion
- a long integer, the SBML Fbc Version to assign to
this FluxObjective
SBMLConstructorException
public FluxObjective(FbcPkgNamespaces fbcns) throws SBMLConstructorException
FluxObjective
with the given FbcPkgNamespaces
object.
fbcns
- the FbcPkgNamespaces
objectSBMLConstructorException
public FluxObjective(FluxObjective orig) throws SBMLConstructorException
FluxObjective
.
orig
- the FluxObjective
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 FluxObjective.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 FluxObjective.delete()
themselves.
public FluxObjective cloneObject()
FluxObjective
object.
cloneObject
 in class SBase
FluxObjective
object.public java.lang.String getId()
FluxObjective
.
getId
 in class SBase
FluxObjective
as a string.public java.lang.String getName()
FluxObjective
.
getName
 in class SBase
FluxObjective
as a
string.public java.lang.String getReaction()
FluxObjective
.
FluxObjective
as a
string.public double getCoefficient()
FluxObjective
.
FluxObjective
as a double.public boolean isSetId()
true
if this FluxObjective
's 'id' attribute is
set.
isSetId
 in class SBase
true
if this FluxObjective
's 'id' attribute has been set,
otherwise false
is returned.public boolean isSetName()
true
if this FluxObjective
's 'name' attribute is
set.
isSetName
 in class SBase
true
if this FluxObjective
's 'name' attribute has been set,
otherwise false
is returned.public boolean isSetReaction()
true
if this FluxObjective
's 'reaction' attribute
is set.
true
if this FluxObjective
's 'reaction' attribute has been set,
otherwise false
is returned.public boolean isSetCoefficient()
true
if this FluxObjective
's 'coefficient'
attribute is set.
true
if this FluxObjective
's 'coefficient' attribute has been
set, otherwise false
is returned.public int setId(java.lang.String id)
FluxObjective
.
public int setName(java.lang.String name)
FluxObjective
.
public int setReaction(java.lang.String reaction)
FluxObjective
.
reaction
- String value of the 'reaction' attribute to be set
public int setCoefficient(double coefficient)
FluxObjective
.
coefficient
- double value of the 'coefficient' attribute to be set
public int unsetId()
FluxObjective
.
public int unsetName()
FluxObjective
.
public int unsetReaction()
FluxObjective
.
public int unsetCoefficient()
FluxObjective
.
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 FluxObjective
, the XML element name is always 'fluxObjective'.
getElementName
 in class SBase
'fluxObjective'.
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_FLUXOBJECTIVE
(default).
FluxObjective.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes
for this FluxObjective
object have been set.
hasRequiredAttributes
 in class SBase
FluxObjective
object are: