Objective (LibSBML Java API)

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

```
public class Objective
extends SBase
```
fbc An objective function.
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.
The Objective class is derived from the normal SBML SBase class and inherits the 'metaid' and 'sboTerm' attributes, as well as the subcomponents for Annotation and Notes. To these, the Objective class adds an optional attribute named 'type'. The type attribute can take one of two literal values: 'maximize' or 'minimize. The values represent the sense of the optimality constraint for the FBC model.
The &ldquofbc&rdquo package allows for the definition of multiple model objectives, with one being designated as active. Here is an example of the XML encoding of a model with a list of objective functions:
```
<fbc:listOfObjectives fbc:activeObjective='obj1'>
 <fbc:objective fbc:id='obj1' fbc:type='maximize'>
  <fbc:listOfFluxObjectives>
   <fbc:fluxObjective fbc:reaction='R101' fbc:coefficient='1'/>
  </fbc:listOfFluxObjectives>
 </fbc:objective>
 <fbc:objective fbc:id='obj2' fbc:type='minimize'>
  <fbc:listOfFluxObjectives>
   <fbc:fluxObjective fbc:reaction='R102' fbc:coefficient='-2.5'/>
   <fbc:fluxObjective fbc:reaction='R103' fbc:coefficient='1'/>
  </fbc:listOfFluxObjectives>
 </fbc:objective>
</fbc:listOfObjectives>
```
See Also:

FluxObjective

Constructor Summary

Constructors
Constructor and Description
`Objective()` Creates a new `Objective` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`Objective(FbcPkgNamespaces fbcns)` Creates a new `Objective` with the given `FbcPkgNamespaces` object.
`Objective(long level)` Creates a new `Objective` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`Objective(long level, long version)` Creates a new `Objective` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`Objective(long level, long version, long pkgVersion)` Creates a new `Objective` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`Objective(Objective orig)` Copy constructor for `Objective`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addFluxObjective(FluxObjective fo)` Adds a copy the given 'FluxObjective' to this `Objective`.
`Objective`	`cloneObject()` Creates and returns a deep copy of this `Objective` object.
`FluxObjective`	`createFluxObjective()` Creates a new `FluxObjective` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`FluxObjective`	`getFluxObjective(long n)` Get a `FluxObjective` from the `ListOfFluxObjectives`.
`FluxObjective`	`getFluxObjective(java.lang.String sid)` Get a `FluxObjective` from the `ListOfFluxObjectives` based on its identifier.
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `Objective`.
`ListOfFluxObjectives`	`getListOfFluxObjectives()` Returns the 'ListOfFluxObjectives' in this `Objective` object.
`java.lang.String`	`getName()` Returns the value of the 'name' attribute of this `Objective`.
`long`	`getNumFluxObjectives()` Get the number of `FluxObjective` objects in this `Objective`.
`int`	`getObjectiveType()` Returns the enumeration value of the 'type' attribute of this `Objective`.
`java.lang.String`	`getType()` Returns the string of the 'type' attribute of this `Objective`.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`boolean`	`hasRequiredAttributes()` Predicate returning `true` if all the required attributes for this `Objective` object have been set.
`boolean`	`hasRequiredElements()` Predicate returning `true` if all the required elements for this `Objective` object have been set.
`boolean`	`isSetId()` Predicate returning `true` if this `Objective`'s 'id' attribute is set.
`boolean`	`isSetName()` Predicate returning `true` if this `Objective`'s 'name' attribute is set.
`boolean`	`isSetType()` Predicate returning `true` if this `Objective`'s 'type' attribute is set.
`FluxObjective`	`removeFluxObjective(long n)` Removes the nth `FluxObjective` from the `ListOfFluxObjectives`.
`FluxObjective`	`removeFluxObjective(java.lang.String sid)` Removes the `FluxObjective` with the given identifier from the `ListOfFluxObjectives`.
`int`	`setId(java.lang.String id)` Sets the value of the 'id' attribute of this `Objective`.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `Objective`.
`int`	`setType(int type)` Sets the SIdRef string of the 'type' attribute of this `Objective`.
`int`	`setType(java.lang.String type)` Sets the value of the 'type' attribute of this `Objective`.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `Objective`.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `Objective`.
`int`	`unsetType()` Unsets the value of the 'type' attribute of this `Objective`.

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, renameSIdRefs, 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
  - Objective
```
public Objective(long level,
                 long version,
                 long pkgVersion)
          throws SBMLConstructorException
```
    Creates a new Objective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Objective
    
    version - a long integer, the SBML Version to assign to this Objective
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this Objective
    
    Throws:
    
    SBMLConstructorException
  - Objective
```
public Objective(long level,
                 long version)
          throws SBMLConstructorException
```
    Creates a new Objective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Objective
    
    version - a long integer, the SBML Version to assign to this Objective
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this Objective
    
    Throws:
    
    SBMLConstructorException
  - Objective
```
public Objective(long level)
          throws SBMLConstructorException
```
    Creates a new Objective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Objective
    
    version - a long integer, the SBML Version to assign to this Objective
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this Objective
    
    Throws:
    
    SBMLConstructorException
  - Objective
```
public Objective()
          throws SBMLConstructorException
```
    Creates a new Objective with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Objective
    
    version - a long integer, the SBML Version to assign to this Objective
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this Objective
    
    Throws:
    
    SBMLConstructorException
  - Objective
```
public Objective(FbcPkgNamespaces fbcns)
          throws SBMLConstructorException
```
    Creates a new Objective with the given FbcPkgNamespaces object.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object
    
    Throws:
    
    SBMLConstructorException
  - Objective
```
public Objective(Objective orig)
          throws SBMLConstructorException
```
    Copy constructor for Objective.
    
    Parameters:
    
    orig - the Objective 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 Objective.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 Objective.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public Objective cloneObject()
```
    Creates and returns a deep copy of this Objective object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this Objective object.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this Objective.
    
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the value of the 'id' attribute of this Objective as a string.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this Objective.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the value of the 'name' attribute of this Objective as a string.
  - getObjectiveType
```
public int getObjectiveType()
```
    Returns the enumeration value of the 'type' attribute of this Objective.
    
    Returns:
    
    the enumeration value of the 'type' attribute of this Objective.
  - getType
```
public java.lang.String getType()
```
    Returns the string of the 'type' attribute of this Objective.
    
    Returns:
    
    the string of the 'type' attribute of this Objective.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true if this Objective's 'id' attribute is set.
    
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if this Objective's 'id' attribute has been set, otherwise false is returned.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true if this Objective's 'name' attribute is set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if this Objective's 'name' attribute has been set, otherwise false is returned.
  - isSetType
```
public boolean isSetType()
```
    Predicate returning true if this Objective's 'type' attribute is set.
    
    Returns:
    
    true if this Objective's 'type' 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 Objective.
    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 Objective.
    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
  - setType
```
public int setType(int type)
```
    Sets the SIdRef string of the 'type' attribute of this Objective.
    Parameters:
    
    type - a SIdRef string 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
  - setType
```
public int setType(java.lang.String type)
```
    Sets the value of the 'type' attribute of this Objective.
    Parameters:
    
    type - string value of the 'type' 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 Objective.
    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 Objective.
    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
  - unsetType
```
public int unsetType()
```
    Unsets the value of the 'type' attribute of this Objective.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getListOfFluxObjectives
```
public ListOfFluxObjectives getListOfFluxObjectives()
```
    Returns the 'ListOfFluxObjectives' in this Objective object.
    
    Returns:
    
    the 'ListOfFluxObjectives' attribute of this Objective.
  - getFluxObjective
```
public FluxObjective getFluxObjective(long n)
```
    Get a FluxObjective from the ListOfFluxObjectives.
    
    Parameters:
    
    n - the index number of the FluxObjective to get.
    
    Returns:
    
    the nth FluxObjective in the ListOfFluxObjectives within this Objective.
    
    See Also:
    
    Objective.getNumFluxObjectives()
  - getFluxObjective
```
public FluxObjective getFluxObjective(java.lang.String sid)
```
    Get a FluxObjective from the ListOfFluxObjectives based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the FluxObjective to get.
    
    Returns:
    
    the FluxObjective in the ListOfFluxObjectives with the given id or null if no such FluxObjective exists.
    
    See Also:
    
    , Objective.getFluxObjective(long n)
  - addFluxObjective
```
public int addFluxObjective(FluxObjective fo)
```
    Adds a copy the given 'FluxObjective' to this Objective.
    Parameters:
    
    fo - the FluxObjective object to add
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - getNumFluxObjectives
```
public long getNumFluxObjectives()
```
    Get the number of FluxObjective objects in this Objective.
    
    Returns:
    
    the number of FluxObjective objects in this Objective
  - createFluxObjective
```
public FluxObjective createFluxObjective()
```
    Creates a new FluxObjective object.
    This method creates the FluxObjective object, adds it to this Objective object's ListOfFluxObjectives, and returns the FluxObjective object created.
    
    Returns:
    
    a new FluxObjective object instance
    
    See Also:
    
    Objective.addFluxObjective(FluxObjective fo)
  - removeFluxObjective
```
public FluxObjective removeFluxObjective(long n)
```
    Removes the nth FluxObjective from the ListOfFluxObjectives.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the FluxObjective to remove.
    
    See Also:
    
    Objective.getNumFluxObjectives()
  - removeFluxObjective
```
public FluxObjective removeFluxObjective(java.lang.String sid)
```
    Removes the FluxObjective with the given identifier from the ListOfFluxObjectives.
    The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.
    
    Parameters:
    
    sid - the identifier of the FluxObjective to remove.
    
    Returns:
    
    the FluxObjective removed. As mentioned above, the caller owns the returned item.
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    For Objective, the XML element name is always 'objective'.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, i.e. 'objective'.
  - 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_OBJECTIVE (default).
    
    See Also:
    
    Objective.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 Objective 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 Objective object are:
    
    'id'
    'type'
  - hasRequiredElements
```
public boolean hasRequiredElements()
```
    Predicate returning true if all the required elements for this Objective object have been set.
    
    Overrides:
    
    hasRequiredElements in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required elements for this object have been defined.
    
    "Note:"
    
    The required elements for a Objective object are:

Class Objective

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

Objective

Objective

Objective

Objective

Objective

Objective

Method Detail

delete

cloneObject

getId

getName

getObjectiveType

getType

isSetId

isSetName

isSetType

setId

setName

setType

setType

unsetId

unsetName

unsetType

getListOfFluxObjectives

getFluxObjective

getFluxObjective

addFluxObjective

getNumFluxObjectives

createFluxObjective

removeFluxObjective

removeFluxObjective

getElementName

getTypeCode

hasRequiredAttributes

hasRequiredElements