ListOfFluxObjectives (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.ListOf
  - - org.sbml.libsbml.ListOfFluxObjectives

```
public class ListOfFluxObjectives
extends ListOf
```
fbc A list of FluxObjective objects.
The ListOfFluxObjectives is a container for the &ldquofbc&rdquo Objective that indicate which fluxes (and what ratios for those fluxes) are to be used in maximizing or minimizing the Objective.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See Also:

ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions,
, Objective, FluxObjective

Constructor Summary

Constructors
Constructor and Description
`ListOfFluxObjectives()` Creates a new `ListOfFluxObjectives` with the given level, version, and package version.
`ListOfFluxObjectives(FbcPkgNamespaces fbcns)` Creates a new `ListOfFluxObjectives` with the given `FbcPkgNamespaces` object.
`ListOfFluxObjectives(long level)` Creates a new `ListOfFluxObjectives` with the given level, version, and package version.
`ListOfFluxObjectives(long level, long version)` Creates a new `ListOfFluxObjectives` with the given level, version, and package version.
`ListOfFluxObjectives(long level, long version, long pkgVersion)` Creates a new `ListOfFluxObjectives` with the given level, version, and package version.

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 `ListOfFluxObjectives`.
`ListOfFluxObjectives`	`cloneObject()` Creates and returns a deep copy of this `ListOfFluxObjectives` object.
`FluxObjective`	`createFluxObjective()` Creates a new `FluxObjective` object, adds it to the `ListOfFluxObjectives` and returns the `FluxObjective` object created.
`void`	`delete()` Explicitly deletes the underlying native object.
`FluxObjective`	`get(long n)` Get a `FluxObjective` from the `ListOfFluxObjectives`.
`FluxObjective`	`get(java.lang.String sid)` Get a `FluxObjective` from the `ListOfFluxObjectives` based on its identifier.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`int`	`getItemTypeCode()` Returns the libSBML type code for the objects contained in this `ListOf`.
`long`	`getNumFluxObjectives()` Get the number of `FluxObjective` objects in this `ListOfFluxObjectives`.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`FluxObjective`	`remove(long n)` Removes the nth `FluxObjective` from this `ListOfFluxObjectives` and returns a pointer to it.
`FluxObjective`	`remove(java.lang.String sid)` Removes the `FluxObjective` from this `ListOfFluxObjectives` with the given identifier and returns a pointer to it.

Methods inherited from class org.sbml.libsbml.ListOf
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, insert, insertAndOwn, removeFromParentAndDelete, size

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, 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, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - ListOfFluxObjectives
```
public ListOfFluxObjectives(long level,
                            long version,
                            long pkgVersion)
                     throws SBMLConstructorException
```
    Creates a new ListOfFluxObjectives with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFluxObjectives
    
    version - a long integer, the SBML Version to assign to this ListOfFluxObjectives
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
    
    Throws:
    
    SBMLConstructorException
  - ListOfFluxObjectives
```
public ListOfFluxObjectives(long level,
                            long version)
                     throws SBMLConstructorException
```
    Creates a new ListOfFluxObjectives with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFluxObjectives
    
    version - a long integer, the SBML Version to assign to this ListOfFluxObjectives
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
    
    Throws:
    
    SBMLConstructorException
  - ListOfFluxObjectives
```
public ListOfFluxObjectives(long level)
                     throws SBMLConstructorException
```
    Creates a new ListOfFluxObjectives with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFluxObjectives
    
    version - a long integer, the SBML Version to assign to this ListOfFluxObjectives
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
    
    Throws:
    
    SBMLConstructorException
  - ListOfFluxObjectives
```
public ListOfFluxObjectives()
                     throws SBMLConstructorException
```
    Creates a new ListOfFluxObjectives with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this ListOfFluxObjectives
    
    version - a long integer, the SBML Version to assign to this ListOfFluxObjectives
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this ListOfFluxObjectives
    
    Throws:
    
    SBMLConstructorException
  - ListOfFluxObjectives
```
public ListOfFluxObjectives(FbcPkgNamespaces fbcns)
                     throws SBMLConstructorException
```
    Creates a new ListOfFluxObjectives with the given FbcPkgNamespaces object.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object
    
    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 ListOfFluxObjectives.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 ListOfFluxObjectives.delete() themselves.
    
    Overrides:
    
    delete in class ListOf
  - cloneObject
```
public ListOfFluxObjectives cloneObject()
```
    Creates and returns a deep copy of this ListOfFluxObjectives object.
    
    Overrides:
    
    cloneObject in class ListOf
    
    Returns:
    
    a (deep) copy of this ListOfFluxObjectives object.
  - get
```
public FluxObjective get(long n)
```
    Get a FluxObjective from the ListOfFluxObjectives.
    
    Overrides:
    
    get in class ListOf
    
    Parameters:
    
    n - the index number of the FluxObjective to get.
    
    Returns:
    
    the nth FluxObjective in this ListOfFluxObjectives.
    
    See Also:
    
    ListOf.size()
  - get
```
public FluxObjective get(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:
    
    FluxObjective in this ListOfFluxObjectives with the given id or null if no such FluxObjective exists.
    
    See Also:
    
    *, ListOf.size()
  - addFluxObjective
```
public int addFluxObjective(FluxObjective fo)
```
    Adds a copy the given 'FluxObjective' to this ListOfFluxObjectives.
    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 ListOfFluxObjectives.
    
    Returns:
    
    the number of FluxObjective objects in this ListOfFluxObjectives
  - createFluxObjective
```
public FluxObjective createFluxObjective()
```
    Creates a new FluxObjective object, adds it to the ListOfFluxObjectives and returns the FluxObjective object created.
    
    Returns:
    
    a new FluxObjective object instance
    
    See Also:
    
    ListOfFluxObjectives.addFluxObjective(FluxObjective fo)
  - remove
```
public FluxObjective remove(long n)
```
    Removes the nth FluxObjective from this ListOfFluxObjectives and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Overrides:
    
    remove in class ListOf
    
    Parameters:
    
    n - the index of the FluxObjective to remove.
    
    See Also:
    
    ListOf.size()
  - remove
```
public FluxObjective remove(java.lang.String sid)
```
    Removes the FluxObjective from this ListOfFluxObjectives with the given identifier and returns a pointer to it.
    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 ListOfFluxObjectives, the XML element name is always 'listOfFluxObjectives'.
    
    Overrides:
    
    getElementName in class ListOf
    
    Returns:
    
    the name of this element, i.e. 'listOfFluxObjectives'.
  - 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 ListOf
    
    Returns:
    
    the SBML type code for this object: SBML_LIST_OF (default).
    
    See Also:
    
    ListOfFluxObjectives.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().
  - getItemTypeCode
```
public int getItemTypeCode()
```
    Returns the libSBML type code for the objects contained in this ListOf.
    
    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:
    
    getItemTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for the objects contained in this ListOf instance: SBML_FBC_FLUXOBJECTIVE (default).
    
    See Also:
    
    ListOfFluxObjectives.getElementName(), SBase.getPackageName()

Class ListOfFluxObjectives

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.ListOf

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

ListOfFluxObjectives

ListOfFluxObjectives

ListOfFluxObjectives

ListOfFluxObjectives

ListOfFluxObjectives

Method Detail

delete

cloneObject

get

get

addFluxObjective

getNumFluxObjectives

createFluxObjective

remove

remove

getElementName

getTypeCode

getItemTypeCode