FbcModelPlugin (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBasePlugin
- - org.sbml.libsbml.FbcModelPlugin

```
public class FbcModelPlugin
extends SBasePlugin
```
fbc Extension of Model.
The FbcModelPlugin object is used to extend the standard SBML Model object with features used in the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package. In Version 1 of the &ldquofbc&rdquo specification, the extended Model class has two optional subobjects: ListOfObjectives and ListOfFluxBounds. In Version 2 of the specification, the extended Model object is defined differently: it is extended with a new required attribute named 'strict', and the two optional subobjects ListOfObjectives and ListOfGeneProducts. (ListOfFluxBounds is not used in Version 2.)

The 'strict' attribute on the (extended) Model class

The mandatory attribute 'strict', of type boolean, in Version 2 of this package, is used to apply an additional set of restrictions to the model. The 'strict' attribute helps ensure that the Flux Balance Constraints package can be used to encode legacy flux-balance analysis models expressible as Linear Programs (LP's) for software that is unable to analyze arbitrary mathematical expressions that may appear in an SBML model. In addition, a 'strict' model is fully described and mathematically consistent, for example, by ensuring that all fluxes have a valid upper or lower bound.
The following restrictions are in effect if an &ldquofbc&rdquo model object has a value of 'true' for the attribute 'strict' on Model:
- Each Reaction in a Model must define values for the attributes 'lowerFluxBound' and 'upperFluxBound', with each attribute pointing to a valid Parameter object defined in the current Model.
- Each Parameter object referred to by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound' must have its 'constant' attribute set to the value 'true' and its 'value' attribute set to a value of type double. This value may not be 'NaN'.
- SpeciesReference objects in Reaction objects must have their 'stoichiometry' attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'. In addition, the value of their 'constant' attribute must be set to 'true'.
- InitialAssignment objects may not target the Parameter objects referenced by the Reaction attributes 'lowerFluxBound' and 'upperFluxBound', nor any SpeciesReference objects.
- All defined FluxObjective objects must have their coefficient attribute set to a double value that is not 'NaN', nor '-INF', nor 'INF'.
- A Reaction 'lowerFluxBound' attribute may not point to a Parameter object that has a value of 'INF'.
- A Reaction 'upperFluxBound' attribute may not point to a Parameter object that has a value of '-INF'.
- For all Reaction objects, the value of a 'lowerFluxBound' attribute must be less than or equal to the value of the 'upperFluxBound' attribute.
While it is not compulsory for a 'strict' Flux Balance Constraints model to define an Objective, doing so does does allow the model to be formulated as a Linear Program and optimized. However, this decision is left to the modeler. Note that all other properties of the objects referred to in the list above are to be set as specified in the relevant SBML Level 3 Version 1 Core and Flux Balance Constraints (&ldquofbc&rdquo) specifications.
Alternatively, if the value of the strict attribute is 'false', then none of these restrictions apply and the model creator can choose to define &ldquofbc&rdquo models that are not necessarily encodable as an LP. For example, if strict is 'false', the InitialAssignment construct may be used to set any valid numerical entity, including Parameter values and stoichiometric coefficients, with any value of type double. In addition, Parameter elements are no longer required to be flagged as constant, thus allowing for a Flux Balance Constraints model's use in alternative, hybrid modeling strategies.

Lists of subobjects on the (extended) Model class

The ListOfObjectives is used to define the objectives of a given &ldquofbc&rdquo model. Objectives generally consist of linear combinations of model variables (fluxes) and a direction for the optimality constraint (either maximization or minimization). Each Objective has a ListOfFluxObjectives subobjects.
In Version 2 of &ldquofbc&rdquo, the ListOfGeneProducts is used to define the gene products represented by the &ldquofbc&rdquo model.
In Version 1 of &ldquofbc&rdquo, there is no ListOfGeneProducts, and instead, Model can have an optional ListOfFluxBounds.
See Also:

Objective, FluxObjective, FluxBound

Constructor Summary

Constructors
Constructor and Description
`FbcModelPlugin(FbcModelPlugin orig)` Copy constructor for `FbcModelPlugin`.
`FbcModelPlugin(java.lang.String uri, java.lang.String prefix, FbcPkgNamespaces fbcns)` Creates a new `FbcModelPlugin` object using the given parameters.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addFluxBound(FluxBound bound)` Adds a copy of the given `FluxBound` object to the list of FluxBounds.
`int`	`addGeneAssociation(GeneAssociation association)` Adds a copy of the given `GeneAssociation` annotation object to the list of GeneAssociations.
`int`	`addGeneProduct(GeneProduct gp)` Adds a copy the given `GeneProduct` to this `FbcModelPlugin`.
`int`	`addObjective(Objective o)` Adds a copy the given `Objective` to this `FbcModelPlugin`.
`SBasePlugin`	`cloneObject()` Creates and returns a deep copy of this `FbcModelPlugin` object.
`FluxBound`	`createFluxBound()` Creates a new `FluxBound` object and adds it to the list of `FluxBound` objects and returns it.
`GeneAssociation`	`createGeneAssociation()` Creates a new `GeneAssociation` annotation object and adds it to the list of `GeneAssociation` objects and returns it.
`GeneProduct`	`createGeneProduct()` Creates a new `GeneProduct` object, adds it to this `FbcModelPlugin`'s `ListOfGeneProducts` and returns the `GeneProduct` object created.
`Objective`	`createObjective()` Creates a new `Objective` object, adds it to this `FbcModelPlugin`'s `ListOfObjectives` and returns the `Objective` object created.
`void`	`delete()` Explicitly deletes the underlying native object.
`Objective`	`getActiveObjective()` Returns the current active objective.
`java.lang.String`	`getActiveObjectiveId()` Returns the id of the current active objective.
`FluxBound`	`getFluxBound(long n)` Returns the `FluxBound` object that belongs to the given index.
`FluxBound`	`getFluxBound(java.lang.String sid)` Returns the `FluxBound` object based on its identifier.
`ListOfFluxBounds`	`getFluxBoundsForReaction(java.lang.String reaction)` Creates a new `ListOfFluxBounds` object that contains only the `FluxBound` objects associated with the given `Reaction`.
`GeneAssociation`	`getGeneAssociation(long n)` Returns the `GeneAssociation` annotation object that belongs to the given index.
`GeneAssociation`	`getGeneAssociation(java.lang.String sid)` Returns the `GeneAssociation` annotation object based on its identifier.
`GeneProduct`	`getGeneProduct(long n)` Get a `GeneProduct` from the `ListOfGeneProducts`.
`GeneProduct`	`getGeneProduct(java.lang.String sid)` Get a `GeneProduct` from the `ListOfGeneProducts` based on its identifier.
`GeneProduct`	`getGeneProductByLabel(java.lang.String label)` Get a `GeneProduct` from the `ListOfGeneProducts` based on its label.
`ListOfFluxBounds`	`getListOfFluxBounds()` Returns the `ListOfFluxBounds` in this plugin object.
`ListOfGeneAssociations`	`getListOfGeneAssociations()` Returns the `ListOfGeneAssociations` annotation object for level 1 in this plugin object.
`ListOfGeneProducts`	`getListOfGeneProducts()` Returns the `ListOfGeneProducts` in this `FbcModelPlugin` object.
`ListOfObjectives`	`getListOfObjectives()` Returns the `ListOfObjectives` in this `FbcModelPlugin` object.
`long`	`getNumFluxBounds()` Returns the number of `FluxBound` object in this plugin object.
`int`	`getNumGeneAssociations()` Returns the number of `GeneAssociation` annotation object in this plugin object.
`long`	`getNumGeneProducts()` Get the number of `GeneProduct` objects in this `FbcModelPlugin`.
`long`	`getNumObjectives()` Get the number of `Objective` objects in this `FbcModelPlugin`.
`Objective`	`getObjective(long n)` Get an `Objective` from the `ListOfObjectives`.
`Objective`	`getObjective(java.lang.String sid)` Get an `Objective` from the `ListOfObjectives` based on its identifier.
`boolean`	`getStrict()` Returns the value of the 'strict' attribute of this `FbcModelPlugin`.
`boolean`	`isSetStrict()` Predicate returning `true` if this `FbcModelPlugin`'s 'strict' attribute is set.
`FluxBound`	`removeFluxBound(long n)` Removes the nth `FluxBound` object from this plugin object and returns a pointer to it.
`FluxBound`	`removeFluxBound(java.lang.String sid)` Removes the `FluxBound` object with the given `sid` attribute from this plugin object and returns a pointer to it.
`GeneAssociation`	`removeGeneAssociation(long n)` Removes the nth `GeneAssociation` annotation object from this plugin object and returns a pointer to it.
`GeneAssociation`	`removeGeneAssociation(java.lang.String sid)` Removes the `GeneAssociation` annotation object with the given `sid` attribute from this plugin object and returns a pointer to it.
`GeneProduct`	`removeGeneProduct(long n)` Removes the nth `GeneProduct` from the `ListOfGeneProducts` within this `FbcModelPlugin`.
`GeneProduct`	`removeGeneProduct(java.lang.String sid)` Removes the `GeneProduct` with the given identifier from the `ListOfGeneProducts` within this `FbcModelPlugin` and returns a pointer to it.
`Objective`	`removeObjective(long n)` Removes the nth `Objective` from the `ListOfObjectives` within this `FbcModelPlugin`.
`Objective`	`removeObjective(java.lang.String sid)` Removes the `Objective` with the given identifier from the `ListOfObjectives` within this `FbcModelPlugin` and returns a pointer to it.
`int`	`setActiveObjectiveId(java.lang.String objectiveId)` Sets the id of the active objective.
`int`	`setStrict(boolean strict)` Sets the value of the 'strict' attribute of this `FbcModelPlugin`.
`int`	`unsetActiveObjectiveId()` Unsets the 'activeObjective' attribute of the `ListOfObjectives`.
`int`	`unsetStrict()` Unsets the value of the 'strict' attribute of this `FbcModelPlugin`.

Methods inherited from class org.sbml.libsbml.SBasePlugin
getElementByMetaId, getElementBySId, getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, setElementNamespace

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

- Constructor Detail
  - FbcModelPlugin
```
public FbcModelPlugin(java.lang.String uri,
                      java.lang.String prefix,
                      FbcPkgNamespaces fbcns)
```
    Creates a new FbcModelPlugin object using the given parameters.
    
    In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.
    
    The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
    
    Parameters:
    
    uri - the URI of the SBML Level 3 package implemented by this libSBML package extension.
    
    prefix - the XML namespace prefix being used for the package.
    
    fbcns - the namespaces object for the package.
  - FbcModelPlugin
```
public FbcModelPlugin(FbcModelPlugin orig)
```
    Copy constructor for FbcModelPlugin.
    
    Parameters:
    
    orig - the FbcModelPlugin instance to copy.
- 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 FbcModelPlugin.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 FbcModelPlugin.delete() themselves.
    
    Overrides:
    
    delete in class SBasePlugin
  - cloneObject
```
public SBasePlugin cloneObject()
```
    Creates and returns a deep copy of this FbcModelPlugin object.
    
    Overrides:
    
    cloneObject in class SBasePlugin
    
    Returns:
    
    a (deep) copy of this FbcModelPlugin object.
  - getStrict
```
public boolean getStrict()
```
    Returns the value of the 'strict' attribute of this FbcModelPlugin.
    
    Returns:
    
    the value of the 'strict' attribute of this FbcModelPlugin as a boolean.
    
    "Note:"
    
    The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.
  - isSetStrict
```
public boolean isSetStrict()
```
    Predicate returning true if this FbcModelPlugin's 'strict' attribute is set.
    
    Returns:
    
    true if this FbcModelPlugin's 'strict' attribute has been set, otherwise false is returned.
    
    "Note:"
    
    The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.
  - setStrict
```
public int setStrict(boolean strict)
```
    Sets the value of the 'strict' attribute of this FbcModelPlugin.
    Parameters:
    
    strict - boolean value of the 'strict' attribute to be set.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    "Note:"
    
    The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.
  - unsetStrict
```
public int unsetStrict()
```
    Unsets the value of the 'strict' attribute of this FbcModelPlugin.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    "Note:"
    
    The 'strict' attribute of the FbcModelPlugin is only defined for version 2 of the 'Flux Balance Constraints' specification, and has no equivalent in version 1 of the specification.
  - getListOfFluxBounds
```
public ListOfFluxBounds getListOfFluxBounds()
```
    Returns the ListOfFluxBounds in this plugin object.
    
    Returns:
    
    ListOfFluxBounds object in this plugin object.
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - getFluxBound
```
public FluxBound getFluxBound(long n)
```
    Returns the FluxBound object that belongs to the given index. If the index is invalid, null is returned.
    
    Parameters:
    
    n - the index number of the FluxBound to get.
    
    Returns:
    
    the nth FluxBound in the ListOfFluxBounds.
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - getFluxBound
```
public FluxBound getFluxBound(java.lang.String sid)
```
    Returns the FluxBound object based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the FluxBound to get.
    
    Returns:
    
    FluxBound in the ListOfFluxBounds with the given sid or null if no such FluxBound exists.
    
    See Also:
    
    FbcModelPlugin.getFluxBound(long n), FbcModelPlugin.getListOfFluxBounds()
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - getFluxBoundsForReaction
```
public ListOfFluxBounds getFluxBoundsForReaction(java.lang.String reaction)
```
    Creates a new ListOfFluxBounds object that contains only the FluxBound objects associated with the given Reaction. If no such Reaction can be found, or if there are no FluxBound objects associated with it, returns null.
    
    Parameters:
    
    reaction - the id of an reaction to find FluxBound objects for.
    
    Returns:
    
    a ListOfFluxBounds for the given reaction id.
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - addFluxBound
```
public int addFluxBound(FluxBound bound)
```
    Adds a copy of the given FluxBound object to the list of FluxBounds.
    Parameters:
    
    bound - the FluxBound object to be added to the list of FluxBounds.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - createFluxBound
```
public FluxBound createFluxBound()
```
    Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.
    
    Returns:
    
    a newly created FluxBound object.
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - removeFluxBound
```
public FluxBound removeFluxBound(long n)
```
    Removes the nth FluxBound object from this plugin object and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the FluxBound object to remove.
    
    Returns:
    
    the FluxBound object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - removeFluxBound
```
public FluxBound removeFluxBound(java.lang.String sid)
```
    Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    sid - the id attribute of the FluxBound object to remove.
    
    Returns:
    
    the FluxBound object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - getNumFluxBounds
```
public long getNumFluxBounds()
```
    Returns the number of FluxBound object in this plugin object.
    
    Returns:
    
    the number of FluxBound object in this plugin object.
    
    "Note:"
    
    FluxBound objects are only defined for version 1 of the 'Flux Balance Constraints' specification, and are replaced in version 2 by the 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin.
  - getListOfObjectives
```
public ListOfObjectives getListOfObjectives()
```
    Returns the ListOfObjectives in this FbcModelPlugin object.
    
    Returns:
    
    the ListOfObjectives child of this FbcModelPlugin.
  - getObjective
```
public Objective getObjective(long n)
```
    Get an Objective from the ListOfObjectives.
    
    Parameters:
    
    n - the index number of the Objective to get.
    
    Returns:
    
    the nth Objective in the ListOfObjectives within this FbcModelPlugin.
    
    See Also:
    
    FbcModelPlugin.getNumObjectives()
  - getObjective
```
public Objective getObjective(java.lang.String sid)
```
    Get an Objective from the ListOfObjectives based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the Objective to get.
    
    Returns:
    
    the Objective in the ListOfObjectives with the given id or null if no such Objective exists.
    
    See Also:
    
    , FbcModelPlugin.getObjective(long n)
  - addObjective
```
public int addObjective(Objective o)
```
    Adds a copy the given Objective to this FbcModelPlugin.
    Parameters:
    
    o - the Objective object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
  - getNumObjectives
```
public long getNumObjectives()
```
    Get the number of Objective objects in this FbcModelPlugin.
    
    Returns:
    
    the number of Objective objects in this FbcModelPlugin.
  - createObjective
```
public Objective createObjective()
```
    Creates a new Objective object, adds it to this FbcModelPlugin's ListOfObjectives and returns the Objective object created.
    
    Returns:
    
    a new Objective object instance.
    
    See Also:
    
    FbcModelPlugin.addObjective(Objective o)
  - removeObjective
```
public Objective removeObjective(long n)
```
    Removes the nth Objective from the ListOfObjectives within this FbcModelPlugin. and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the Objective to remove.
    
    See Also:
    
    FbcModelPlugin.getNumObjectives()
  - removeObjective
```
public Objective removeObjective(java.lang.String sid)
```
    Removes the Objective with the given identifier from the ListOfObjectives within this FbcModelPlugin 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 Objective to remove.
    
    Returns:
    
    the Objective removed. As mentioned above, the caller owns the returned item.
  - getActiveObjective
```
public Objective getActiveObjective()
```
    Returns the current active objective.
    
    Returns:
    
    the Objective pointed to by the 'activeObjective' attribute, or null if no such Objective can be found.
  - setActiveObjectiveId
```
public int setActiveObjectiveId(java.lang.String objectiveId)
```
    Sets the id of the active objective.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - getActiveObjectiveId
```
public java.lang.String getActiveObjectiveId()
```
    Returns the id of the current active objective.
    
    Returns:
    
    the value of the 'activeObjective' attribute of the ListOfObjectives.
  - unsetActiveObjectiveId
```
public int unsetActiveObjectiveId()
```
    Unsets the 'activeObjective' attribute of the ListOfObjectives.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
  - getListOfGeneProducts
```
public ListOfGeneProducts getListOfGeneProducts()
```
    Returns the ListOfGeneProducts in this FbcModelPlugin object.
    
    Returns:
    
    the ListOfGeneProducts child of this FbcModelPlugin.
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - getGeneProduct
```
public GeneProduct getGeneProduct(long n)
```
    Get a GeneProduct from the ListOfGeneProducts.
    
    Parameters:
    
    n - the index number of the GeneProduct to get.
    
    Returns:
    
    the nth GeneProduct in the ListOfGeneProducts within this FbcModelPlugin.
    
    See Also:
    
    FbcModelPlugin.getNumGeneProducts()
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - getGeneProduct
```
public GeneProduct getGeneProduct(java.lang.String sid)
```
    Get a GeneProduct from the ListOfGeneProducts based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the GeneProduct to get.
    
    Returns:
    
    the GeneProduct in the ListOfGeneProducts with the given id or null if no such GeneProduct exists.
    
    See Also:
    
    , FbcModelPlugin.getGeneProduct(long n)
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - getGeneProductByLabel
```
public GeneProduct getGeneProductByLabel(java.lang.String label)
```
    Get a GeneProduct from the ListOfGeneProducts based on its label.
    
    Parameters:
    
    label - a string representing the label of the GeneProduct to get.
    
    Returns:
    
    the GeneProduct in the ListOfGeneProducts with the given label or null if no such GeneProduct exists.
    
    See Also:
    
    , FbcModelPlugin.getGeneProduct(long n)
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - addGeneProduct
```
public int addGeneProduct(GeneProduct gp)
```
    Adds a copy the given GeneProduct to this FbcModelPlugin.
    Parameters:
    
    gp - the GeneProduct object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - getNumGeneProducts
```
public long getNumGeneProducts()
```
    Get the number of GeneProduct objects in this FbcModelPlugin.
    
    Returns:
    
    the number of GeneProduct objects in this FbcModelPlugin.
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - createGeneProduct
```
public GeneProduct createGeneProduct()
```
    Creates a new GeneProduct object, adds it to this FbcModelPlugin's ListOfGeneProducts and returns the GeneProduct object created.
    
    Returns:
    
    a new GeneProduct object instance.
    
    See Also:
    
    FbcModelPlugin.addGeneProduct(GeneProduct gp)
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - removeGeneProduct
```
public GeneProduct removeGeneProduct(long n)
```
    Removes the nth GeneProduct from the ListOfGeneProducts within this FbcModelPlugin. and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the GeneProduct to remove.
    
    See Also:
    
    FbcModelPlugin.getNumGeneProducts()
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - removeGeneProduct
```
public GeneProduct removeGeneProduct(java.lang.String sid)
```
    Removes the GeneProduct with the given identifier from the ListOfGeneProducts within this FbcModelPlugin 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 GeneProduct to remove.
    
    Returns:
    
    the GeneProduct removed. As mentioned above, the caller owns the returned item.
    
    "Note:"
    
    GeneProduct objects are only defined for version 2 of the 'Flux Balance Constraints' specification, and have no equivalent in version 1 of the specification.
  - getListOfGeneAssociations
```
public ListOfGeneAssociations getListOfGeneAssociations()
```
    Returns the ListOfGeneAssociations annotation object for level 1 in this plugin object.
    
    Returns:
    
    ListOfGeneAssociations annotation object for level 1 in this plugin object.
    
    "Note:"
    
    GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.
  - getGeneAssociation
```
public GeneAssociation getGeneAssociation(long n)
```
    Returns the GeneAssociation annotation object that belongs to the given index. If the index is invalid, null is returned.
    
    Parameters:
    
    n - the index number of the GeneAssociation annotation to get.
    
    Returns:
    
    the nth GeneAssociation annotation in the ListOfGeneAssociations.
    
    "Note:"
    
    GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.
  - getGeneAssociation
```
public GeneAssociation getGeneAssociation(java.lang.String sid)
```
    Returns the GeneAssociation annotation object based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the GeneAssociation annotation to get.
    
    Returns:
    
    GeneAssociation annotation in the ListOfGeneAssociations with the given sid or null if no such GeneAssociation annotation exists.
    
    See Also:
    
    FbcModelPlugin.getGeneAssociation(long n), FbcModelPlugin.getListOfGeneAssociations()
    
    "Note:"
    
    GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.
  - addGeneAssociation
```
public int addGeneAssociation(GeneAssociation association)
```
    Adds a copy of the given GeneAssociation annotation object to the list of GeneAssociations.
    Parameters:
    
    association - the GeneAssociation annotation object to be added to the list of GeneAssociations.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
    "Note:"
    
    GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.
  - createGeneAssociation
```
public GeneAssociation createGeneAssociation()
```
    Creates a new GeneAssociation annotation object and adds it to the list of GeneAssociation objects and returns it.
    
    Returns:
    
    a newly created GeneAssociation annotation object.
  - removeGeneAssociation
```
public GeneAssociation removeGeneAssociation(long n)
```
    Removes the nth GeneAssociation annotation object from this plugin object and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the GeneAssociation annotation object to remove.
    
    Returns:
    
    the GeneAssociation annotation object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
    
    "Note:"
    
    GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.
  - removeGeneAssociation
```
public GeneAssociation removeGeneAssociation(java.lang.String sid)
```
    Removes the GeneAssociation annotation object with the given sid attribute from this plugin object and returns a pointer to it.
    The caller owns the returned object and is responsible for deleting it.
    
    Parameters:
    
    sid - the id attribute of the GeneAssociation annotation object to remove.
    
    Returns:
    
    the GeneAssociation annotation object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
    
    "Note:"
    
    GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.
  - getNumGeneAssociations
```
public int getNumGeneAssociations()
```
    Returns the number of GeneAssociation annotation object in this plugin object.
    
    Returns:
    
    the number of GeneAssociation annotation object in this plugin object.
    
    "Note:"
    
    GeneAssociation objects are not defined in any version of the 'Flux Balance Constraints' specification, and can only be used for annotation purposes. Version 2 instead defines the GeneProduct and GeneProductAssociation classes to cover the information otherwise encoded here.

Class FbcModelPlugin

The 'strict' attribute on the (extended) Model class

Lists of subobjects on the (extended) Model class

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBasePlugin

Methods inherited from class java.lang.Object

Constructor Detail

FbcModelPlugin

FbcModelPlugin

Method Detail

delete

cloneObject

getStrict

isSetStrict

setStrict

unsetStrict

getListOfFluxBounds

getFluxBound

getFluxBound

getFluxBoundsForReaction

addFluxBound

createFluxBound

removeFluxBound

removeFluxBound

getNumFluxBounds

getListOfObjectives

getObjective

getObjective

addObjective

getNumObjectives

createObjective

removeObjective

removeObjective

getActiveObjective

setActiveObjectiveId

getActiveObjectiveId

unsetActiveObjectiveId

getListOfGeneProducts

getGeneProduct

getGeneProduct

getGeneProductByLabel

addGeneProduct

getNumGeneProducts

createGeneProduct

removeGeneProduct

removeGeneProduct

getListOfGeneAssociations

getGeneAssociation

getGeneAssociation

addGeneAssociation

createGeneAssociation

removeGeneAssociation

removeGeneAssociation

getNumGeneAssociations

The 'strict' attribute on the (extended) `Model` class

Lists of subobjects on the (extended) `Model` class