FluxObjective (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.FluxObjective

```
public class FluxObjective
extends SBase
```
fbc An objective function for a flux.
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>
```
See Also:

Objective, ListOfObjectives, ListOfFluxObjectives

Constructor Summary

Constructors
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.

Method Summary

All Methods Instance Methods Concrete Methods
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`.

Methods inherited from class org.sbml.libsbml.SBase
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

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - FluxObjective
```
public FluxObjective(long level,
                     long version,
                     long pkgVersion)
              throws SBMLConstructorException
```
    Creates a new FluxObjective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - FluxObjective
```
public FluxObjective(long level,
                     long version)
              throws SBMLConstructorException
```
    Creates a new FluxObjective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - FluxObjective
```
public FluxObjective(long level)
              throws SBMLConstructorException
```
    Creates a new FluxObjective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - FluxObjective
```
public FluxObjective()
              throws SBMLConstructorException
```
    Creates a new FluxObjective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - FluxObjective
```
public FluxObjective(FbcPkgNamespaces fbcns)
              throws SBMLConstructorException
```
    Creates a new FluxObjective with the given FbcPkgNamespaces object.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object
    
    Throws:
    
    SBMLConstructorException
  - FluxObjective
```
public FluxObjective(FluxObjective orig)
              throws SBMLConstructorException
```
    Copy constructor for FluxObjective.
    
    Parameters:
    
    orig - the FluxObjective instance to copy.
    
    Throws:
    
    SBMLConstructorException
- Method Detail
  - delete
```
public void delete()
```
    Explicitly deletes the underlying native object.
    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.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public FluxObjective cloneObject()
```
    Creates and returns a deep copy of this FluxObjective object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this FluxObjective object.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this FluxObjective.
    
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the value of the 'id' attribute of this FluxObjective as a string.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this FluxObjective.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the value of the 'name' attribute of this FluxObjective as a string.
  - getReaction
```
public java.lang.String getReaction()
```
    Returns the value of the 'reaction' attribute of this FluxObjective.
    
    Returns:
    
    the value of the 'reaction' attribute of this FluxObjective as a string.
  - getCoefficient
```
public double getCoefficient()
```
    Returns the value of the 'coefficient' attribute of this FluxObjective.
    
    Returns:
    
    the value of the 'coefficient' attribute of this FluxObjective as a double.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true if this FluxObjective's 'id' attribute is set.
    
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if this FluxObjective's 'id' attribute has been set, otherwise false is returned.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true if this FluxObjective's 'name' attribute is set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if this FluxObjective's 'name' attribute has been set, otherwise false is returned.
  - isSetReaction
```
public boolean isSetReaction()
```
    Predicate returning true if this FluxObjective's 'reaction' attribute is set.
    
    Returns:
    
    true if this FluxObjective's 'reaction' attribute has been set, otherwise false is returned.
  - isSetCoefficient
```
public boolean isSetCoefficient()
```
    Predicate returning true if this FluxObjective's 'coefficient' attribute is set.
    
    Returns:
    
    true if this FluxObjective's 'coefficient' attribute has been set, otherwise false is returned.
  - setId
```
public int setId(java.lang.String id)
```
    Sets the value of the 'id' attribute of this FluxObjective.
    Overrides:
    
    setId in class SBase
    
    Parameters:
    
    id - String value of the 'id' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this FluxObjective.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - String value of the 'name' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setReaction
```
public int setReaction(java.lang.String reaction)
```
    Sets the value of the 'reaction' attribute of this FluxObjective.
    Parameters:
    
    reaction - String value of the 'reaction' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setCoefficient
```
public int setCoefficient(double coefficient)
```
    Sets the value of the 'coefficient' attribute of this FluxObjective.
    Parameters:
    
    coefficient - double value of the 'coefficient' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetId
```
public int unsetId()
```
    Unsets the value of the 'id' attribute of this FluxObjective.
    Overrides:
    
    unsetId in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this FluxObjective.
    Overrides:
    
    unsetName in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetReaction
```
public int unsetReaction()
```
    Unsets the value of the 'reaction' attribute of this FluxObjective.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetCoefficient
```
public int unsetCoefficient()
```
    Unsets the value of the 'coefficient' attribute of this FluxObjective.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - renameSIdRefs
```
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 SIdRefin 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.
    
    Overrides:
    
    renameSIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    For FluxObjective, the XML element name is always 'fluxObjective'.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, i.e. 'fluxObjective'.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code for this SBML object.
    
    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.
    
    Overrides:
    
    getTypeCode in class SBase
    
    Returns:
    
    the SBML type code for this object: SBML_FBC_FLUXOBJECTIVE (default).
    
    See Also:
    
    FluxObjective.getElementName(), SBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required attributes for this FluxObjective object have been set.
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required attributes for this object have been defined.
    
    "Note:"
    The required attributes for a FluxObjective object are:
    
    'reaction'
    'coefficient'

Class FluxObjective

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

FluxObjective

FluxObjective

FluxObjective

FluxObjective

FluxObjective

FluxObjective

Method Detail

delete

cloneObject

getId

getName

getReaction

getCoefficient

isSetId

isSetName

isSetReaction

isSetCoefficient

setId

setName

setReaction

setCoefficient

unsetId

unsetName

unsetReaction

unsetCoefficient

renameSIdRefs

getElementName

getTypeCode

hasRequiredAttributes