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 &ldquofbc&rdquo package) an upper and lower flux bound, with the 'upperFluxBound' and 'lowerFluxBound' attributes, as well as a way to reference any GeneProduct associated with this Reaction, through the GeneProductAssociation child.

"Note:"

In Version 1 of &ldquofbc&rdquo, the FluxBound element is used instead of the 'upperFluxBound' and 'lowerFluxBound' attributes. There is no equivalent of the GeneProductAssociation, which was added in Version 2.

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` object using the given parameters.

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`	`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 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.
  - 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.
  - 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 SIdRef in 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.
    
    "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.
  - 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.
    
    "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.
  - 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
    "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.
  - createGeneProductAssociation
```
public GeneProductAssociation createGeneProductAssociation()
```
    Creates a new GeneProductAssociation object and adds it to the FbcReactionPlugin object.
    
    Returns:
    
    the newly created GeneProductAssociation object.
    
    "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.
  - 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.
    
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - 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.
    
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - 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.
    
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - 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.
    
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - setLowerFluxBound
```
public int setLowerFluxBound(java.lang.String lowerFluxBound)
```
    Sets the value of the 'lowerFluxBound' attribute of this FbcReactionPlugin.
    Parameters:
    
    lowerFluxBound - the 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
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - setUpperFluxBound
```
public int setUpperFluxBound(java.lang.String upperFluxBound)
```
    Sets the value of the 'upperFluxBound' attribute of this FbcReactionPlugin.
    Parameters:
    
    upperFluxBound - the 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
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - 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
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - 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
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.
  - 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
    "Note:"
    
    The 'upperFluxBound' and 'lowerFluxBound' attributes of the FbcReactionPlugin are only defined for version 2 of the 'Flux Balance Constraints' specification. In version 1, this information was encoded in the FluxBound children of the FbcModelPlugin.

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

renameSIdRefs

getGeneProductAssociation

isSetGeneProductAssociation

setGeneProductAssociation

createGeneProductAssociation

getLowerFluxBound

getUpperFluxBound

isSetLowerFluxBound

isSetUpperFluxBound

setLowerFluxBound

setUpperFluxBound

unsetLowerFluxBound

unsetUpperFluxBound

unsetGeneProductAssociation