FbcReactionPlugin (LibSBML Java API)

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

```
public class FbcReactionPlugin
extends SBasePlugin
```
fbc Extension of Reaction by the &ldquofbc&rdquo package.
The FbcReactionPlugin class inherits from the SBasePlugin class, and codifies the extentions to the Reaction class defined in the 'Flux Balance Constraints' package (&ldquofbc&rdquo). This extention allows the modeler to define (in version 2 of the package) an upper and lower flux bound, as well as a way to reference any GeneProduct associated with this Reaction.
Note that in version 1, the FluxBound element is used instead.

Constructor Summary

Constructors
Constructor and Description
`FbcReactionPlugin(FbcReactionPlugin orig)` Copy constructor for `FbcReactionPlugin`.
`FbcReactionPlugin(java.lang.String uri, java.lang.String prefix, FbcPkgNamespaces fbcns)` Creates a new `FbcReactionPlugin`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`SBasePlugin`	`cloneObject()` Creates and returns a deep copy of this `FbcReactionPlugin` object.
`GeneProductAssociation`	`createGeneProductAssociation()` Creates a new `GeneProductAssociation` object and adds it to the `FbcReactionPlugin` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`GeneProductAssociation`	`getGeneProductAssociation()` Returns the `GeneProductAssociation` from this `FbcReactionPlugin` object.
`java.lang.String`	`getLowerFluxBound()` Returns the value of the 'lowerFluxBound' attribute of this `FbcReactionPlugin`.
`java.lang.String`	`getUpperFluxBound()` Returns the value of the 'upperFluxBound' attribute of this `FbcReactionPlugin`.
`boolean`	`hasRequiredElements()` Checks if this plugin object has all the required elements.
`boolean`	`isSetGeneProductAssociation()` Predicate returning `true` if this `FbcReactionPlugin`'s 'GeneProductAssociation' element has been set.
`boolean`	`isSetLowerFluxBound()` Predicate returning `true` if this `FbcReactionPlugin`'s 'lowerFluxBound' attribute is set.
`boolean`	`isSetUpperFluxBound()` Predicate returning `true` if this `FbcReactionPlugin`'s 'upperFluxBound' attribute is set.
`void`	`renameSIdRefs(java.lang.String oldid, java.lang.String newid)` Replaces all uses of a given `SIdRef` type attribute value with another value.
`int`	`setGeneProductAssociation(GeneProductAssociation geneProductAssociation)` Sets the `GeneProductAssociation` element in this `FbcReactionPlugin` object.
`int`	`setLowerFluxBound(java.lang.String lowerFluxBound)` Sets the value of the 'lowerFluxBound' attribute of this `FbcReactionPlugin`.
`int`	`setUpperFluxBound(java.lang.String upperFluxBound)` Sets the value of the 'upperFluxBound' attribute of this `FbcReactionPlugin`.
`int`	`unsetGeneProductAssociation()` Unsets the the 'geneProduct' element of this `FbcReactionPlugin`.
`int`	`unsetLowerFluxBound()` Unsets the value of the 'lowerFluxBound' attribute of this `FbcReactionPlugin`.
`int`	`unsetUpperFluxBound()` Unsets the value of the 'upperFluxBound' attribute of this `FbcReactionPlugin`.

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

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

- Constructor Detail
  - FbcReactionPlugin
```
public FbcReactionPlugin(java.lang.String uri,
                         java.lang.String prefix,
                         FbcPkgNamespaces fbcns)
```
    Creates a new FbcReactionPlugin
  - FbcReactionPlugin
```
public FbcReactionPlugin(FbcReactionPlugin orig)
```
    Copy constructor for FbcReactionPlugin.
    
    Parameters:
    
    orig - the FbcReactionPlugin 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 FbcReactionPlugin.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 FbcReactionPlugin.delete() themselves.
    
    Overrides:
    
    delete in class SBasePlugin
  - cloneObject
```
public SBasePlugin cloneObject()
```
    Creates and returns a deep copy of this FbcReactionPlugin object.
    
    Overrides:
    
    cloneObject in class SBasePlugin
    
    Returns:
    
    a (deep) copy of this FbcReactionPlugin 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.
  - renameSIdRefs
```
public void renameSIdRefs(java.lang.String oldid,
                          java.lang.String newid)
```
    Replaces all uses of a given SIdRef type attribute value with another value.
    
    In SBML, object identifiers are of a data type called SId. In SBML Level 3, an explicit data type called SIdRef was introduced for attribute values that refer to SId values in previous Levels of SBML, this data type did not exist and attributes were simply described to as 'referring to an identifier', but the effective data type was the same as SIdRefin Level 3. These and other methods of libSBML refer to the type SIdRef for all Levels of SBML, even if the corresponding SBML specification did not explicitly name the data type.
    This method works by looking at all attributes and (if appropriate) mathematical formulas in MathML content, comparing the referenced identifiers to the value of oldid. If any matches are found, the matching values are replaced with newid. The method does not descend into child elements.
    
    Overrides:
    
    renameSIdRefs in class SBasePlugin
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - getGeneProductAssociation
```
public GeneProductAssociation getGeneProductAssociation()
```
    Returns the GeneProductAssociation from this FbcReactionPlugin object.
    
    Returns:
    
    the GeneProductAssociation from object in this FbcReactionPlugin object.
  - isSetGeneProductAssociation
```
public boolean isSetGeneProductAssociation()
```
    Predicate returning true if this FbcReactionPlugin's 'GeneProductAssociation' element has been set.
    
    Returns:
    
    true if the 'GeneProductAssociation' element has been set, otherwise false is returned.
  - setGeneProductAssociation
```
public int setGeneProductAssociation(GeneProductAssociation geneProductAssociation)
```
    Sets the GeneProductAssociation element in this FbcReactionPlugin object.
    Parameters:
    
    geneProductAssociation - the geneProductAssociation to be set.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
  - createGeneProductAssociation
```
public GeneProductAssociation createGeneProductAssociation()
```
    Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object.
    
    Returns:
    
    the newly created GeneProductAssociation object.
  - getLowerFluxBound
```
public java.lang.String getLowerFluxBound()
```
    Returns the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.
    
    Returns:
    
    the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin as a string.
  - getUpperFluxBound
```
public java.lang.String getUpperFluxBound()
```
    Returns the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.
    
    Returns:
    
    the value of the 'upperFluxBound' attribute of this FbcReactionPlugin as a string.
  - isSetLowerFluxBound
```
public boolean isSetLowerFluxBound()
```
    Predicate returning true if this FbcReactionPlugin's 'lowerFluxBound' attribute is set.
    
    Returns:
    
    true if this FbcReactionPlugin's 'lowerFluxBound' attribute has been set, otherwise false is returned.
  - isSetUpperFluxBound
```
public boolean isSetUpperFluxBound()
```
    Predicate returning true if this FbcReactionPlugin's 'upperFluxBound' attribute is set.
    
    Returns:
    
    true if this FbcReactionPlugin's 'upperFluxBound' attribute has been set, otherwise false is returned.
  - setLowerFluxBound
```
public int setLowerFluxBound(java.lang.String lowerFluxBound)
```
    Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.
    Parameters:
    
    lowerFluxBound - String value of the 'lowerFluxBound' 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
  - setUpperFluxBound
```
public int setUpperFluxBound(java.lang.String upperFluxBound)
```
    Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.
    Parameters:
    
    upperFluxBound - String value of the 'upperFluxBound' 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
  - unsetLowerFluxBound
```
public int unsetLowerFluxBound()
```
    Unsets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetUpperFluxBound
```
public int unsetUpperFluxBound()
```
    Unsets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetGeneProductAssociation
```
public int unsetGeneProductAssociation()
```
    Unsets the the 'geneProduct' element of this FbcReactionPlugin.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED

Class FbcReactionPlugin

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBasePlugin

Methods inherited from class java.lang.Object

Constructor Detail

FbcReactionPlugin

FbcReactionPlugin

Method Detail

delete

cloneObject

hasRequiredElements

renameSIdRefs

getGeneProductAssociation

isSetGeneProductAssociation

setGeneProductAssociation

createGeneProductAssociation

getLowerFluxBound

getUpperFluxBound

isSetLowerFluxBound

isSetUpperFluxBound

setLowerFluxBound

setUpperFluxBound

unsetLowerFluxBound

unsetUpperFluxBound

unsetGeneProductAssociation