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` object.
`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 sid)` 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, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setIdAttribute, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetIdAttribute, 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
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - 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
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - 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
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - 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
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - FluxObjective
```
public FluxObjective(FbcPkgNamespaces fbcns)
              throws SBMLConstructorException
```
    Creates a new FluxObjective with the given FbcPkgNamespaces object.
    
    The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - 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 id of this FluxObjective.
    
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.isSetIdAttribute(), SBase.unsetIdAttribute()
    
    "Note:"
    Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the getIdAttribute() function instead.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
    letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
    
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this FluxObjective object.
    
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
    The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
    As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
    An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the name of this SBML object, or the empty string if not set or unsettable.
    
    See Also:
    
    SBase.getIdAttribute(), FluxObjective.isSetName(), FluxObjective.setName(String sid), FluxObjective.unsetName()
  - 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 the 'id' attribute of this SBML object is set, false otherwise.
    
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.unsetIdAttribute(), SBase.isSetIdAttribute()
    
    "Note:"
    Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the isSetIdAttribute() function instead.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
    letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
    
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true if this FluxObjective's 'name' attribute is set.
    
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
    The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
    As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
    An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if the 'name' attribute of this SBML object is set, false otherwise.
    
    See Also:
    
    FluxObjective.getName(), FluxObjective.setName(String sid), FluxObjective.unsetName()
  - 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 sid)
```
    Sets the value of the 'id' attribute of this FluxObjective.
    
    The string sid is copied.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
```
   letter .= 'a'..'z','A'..'Z'
   digit  .= '0'..'9'
   idChar .= letter | digit | '_'
   SId    .= ( letter | '_' ) idChar*
 
```
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
    Overrides:
    
    setId in class SBase
    
    Parameters:
    
    sid - the string to use as the identifier of this object.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    LIBSBML_UNEXPECTED_ATTRIBUTE
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.isSetIdAttribute(), SBase.unsetIdAttribute()
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this FluxObjective.
    
    The string in name is copied.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - the new name for the SBML object.
    
    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 - the 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 - the 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.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
```
   letter .= 'a'..'z','A'..'Z'
   digit  .= '0'..'9'
   idChar .= letter | digit | '_'
   SId    .= ( letter | '_' ) idChar*
 
```
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
    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
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.isSetIdAttribute(), SBase.unsetIdAttribute()
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this FluxObjective.
    
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
    The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
    As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
    An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
    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
    See Also:
    
    FluxObjective.getName(), FluxObjective.setName(String sid), FluxObjective.isSetName()
  - 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 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.
    
    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 SBase.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 libSBML plug-ins for SBML Level 3. packages, To fully identify 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