FbcModelPlugin (LibSBML Java API)

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

public class FbcModelPlugin
extends SBasePlugin

fbc Extension of Model.

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`

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 FbcModelPlugins `ListOfGeneProducts` and returns the `GeneProduct` object created.
`Objective`	`createObjective()` Creates a new `Objective` object, adds it to this FbcModelPlugins `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)`
`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 a `Objective` from the `ListOfObjectives`.
`Objective`	`getObjective(java.lang.String sid)` Get a `Objective` from the `ListOfObjectives` based on its identifier.
`boolean`	`getStrict()` Returns the value of the 'strict' attribute of this `FbcModelPlugin`.
`boolean`	`hasRequiredElements()` Checks if this plugin object has all the required elements.
`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`.
`void`	`unsetActiveObjectiveId()` Unsets the active objective.
`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
  - 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.
  - hasRequiredElements
```
public boolean hasRequiredElements()
```
    Checks if this plugin object has all the required elements.
    Subclasses must override this method if they have their specific elements.
    
    Returns:
    
    true if this plugin object has all the required elements otherwise false will be returned.
  - 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.
  - 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.
  - 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
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - 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
    LIBSBML_OPERATION_FAILED
  - getListOfFluxBounds
```
public ListOfFluxBounds getListOfFluxBounds()
```
    Returns the ListOfFluxBounds in this plugin object.
    
    Returns:
    
    ListOfFluxBounds object in this plugin object.
  - 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.
  - 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()
  - getFluxBoundsForReaction
```
public ListOfFluxBounds getFluxBoundsForReaction(java.lang.String reaction)
```
    Parameters:
    
    reaction - the id of an reaction to find fluxBounds for
    
    Returns:
    
    a listOfFluxBounds for the given reaction id
  - 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
  - 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
  - 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.
  - 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.
  - getNumFluxBounds
```
public long getNumFluxBounds()
```
    Returns the number of FluxBound object in this plugin object.
    
    Returns:
    
    the number of FluxBound object in this plugin object.
  - getListOfObjectives
```
public ListOfObjectives getListOfObjectives()
```
    Returns the 'ListOfObjectives' in this FbcModelPlugin object.
    
    Returns:
    
    the 'ListOfObjectives' attribute of this FbcModelPlugin.
  - getObjective
```
public Objective getObjective(long n)
```
    Get a 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 a 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_INVALID_ATTRIBUTE_VALUE
  - 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 FbcModelPlugins 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.
  - setActiveObjectiveId
```
public int setActiveObjectiveId(java.lang.String objectiveId)
```
    Sets the id of the active objective.
  - getActiveObjectiveId
```
public java.lang.String getActiveObjectiveId()
```
    returns the id of the current active objective.
  - unsetActiveObjectiveId
```
public void unsetActiveObjectiveId()
```
    Unsets the active objective.
  - getListOfGeneProducts
```
public ListOfGeneProducts getListOfGeneProducts()
```
    Returns the 'ListOfGeneProducts' in this FbcModelPlugin object.
    
    Returns:
    
    the 'ListOfGeneProducts' attribute of this FbcModelPlugin.
  - 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()
  - 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)
  - 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)
  - 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_INVALID_ATTRIBUTE_VALUE
  - getNumGeneProducts
```
public long getNumGeneProducts()
```
    Get the number of GeneProduct objects in this FbcModelPlugin.
    
    Returns:
    
    the number of GeneProduct objects in this FbcModelPlugin
  - createGeneProduct
```
public GeneProduct createGeneProduct()
```
    Creates a new GeneProduct object, adds it to this FbcModelPlugins ListOfGeneProducts and returns the GeneProduct object created.
    
    Returns:
    
    a new GeneProduct object instance
    
    See Also:
    
    FbcModelPlugin.addGeneProduct(GeneProduct gp)
  - 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()
  - 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.
  - 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.
  - 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.
  - 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()
  - 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
  - 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.
  - 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.
  - 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.

Class FbcModelPlugin

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

hasRequiredElements

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