GeneProductRef (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.FbcAssociation
  - - org.sbml.libsbml.GeneProductRef

```
public class GeneProductRef
extends FbcAssociation
```
fbc Reference to a gene product of a reaction
GeneProductRef encodes a references to a GeneProduct object declared in a ListOfGeneProducts attached to the enclosing Model object. GeneProductRef is derived from the FbcAssociation class.
GeneProductRef objects are used to construct the content of GeneProductAssociation objects. As described more fully in the documentation of the latter, a GeneProductAssociation is a container that may contain either (i) a single GeneProductRef or (ii) a logical expression built up with FbcAnd and FbcOr and ultimately containing two or more GeneProductRef objects.

"Note:"

This class of objects was introduced in Version 2 of the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) specification. In Version 1 of &ldquofbc&rdquo, the information encoded by this class can be stored instead using the Association and GeneAssociation annotation classes. Please see the Version 1 and Version 2 &ldquofbc&rdquo specifications for more details.

Constructor Summary

Constructors
Constructor and Description
`GeneProductRef()` Creates a new `GeneProductRef` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`GeneProductRef(FbcPkgNamespaces fbcns)` Creates a new `GeneProductRef` with the given `FbcPkgNamespaces` object.
`GeneProductRef(GeneProductRef orig)` Copy constructor for `GeneProductRef`.
`GeneProductRef(long level)` Creates a new `GeneProductRef` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`GeneProductRef(long level, long version)` Creates a new `GeneProductRef` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
`GeneProductRef(long level, long version, long pkgVersion)` Creates a new `GeneProductRef` with the given SBML Level, Version, and &ldquofbc&rdquopackage version.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`GeneProductRef`	`cloneObject()` Creates and returns a deep copy of this `GeneProductRef` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`java.lang.String`	`getGeneProduct()` Returns the value of the 'geneProduct' attribute of this `GeneProductRef`.
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `GeneProductRef`.
`java.lang.String`	`getName()` Returns the value of the 'name' attribute of this `GeneProductRef`.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`boolean`	`hasRequiredAttributes()` Predicate returning `true` if all the required attributes for this `GeneProductRef` object have been set.
`boolean`	`isSetGeneProduct()` Predicate returning `true` if this `GeneProductRef`'s 'geneProduct' attribute is set.
`boolean`	`isSetId()` Predicate returning `true` if this `GeneProductRef`'s 'id' attribute is set.
`boolean`	`isSetName()` Predicate returning `true` if this `GeneProductRef`'s 'name' 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`	`setGeneProduct(java.lang.String geneProduct)` Sets the value of the 'geneProduct' attribute of this `GeneProductRef`.
`int`	`setId(java.lang.String id)` Sets the value of the 'id' attribute of this `GeneProductRef`.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `GeneProductRef`.
`java.lang.String`	`toInfix()` Converts this `FbcAssociation` object into an infix string representation.
`int`	`unsetGeneProduct()` Unsets the value of the 'geneProduct' attribute of this `GeneProductRef`.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `GeneProductRef`.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `GeneProductRef`.

Methods inherited from class org.sbml.libsbml.FbcAssociation
isFbcAnd, isFbcOr, isGeneProductRef, parseFbcInfixAssociation, setElementName

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

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

- Constructor Detail
  - GeneProductRef
```
public GeneProductRef(long level,
                      long version,
                      long pkgVersion)
               throws SBMLConstructorException
```
    Creates a new GeneProductRef with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProductRef
    
    version - a long integer, the SBML Version to assign to this GeneProductRef
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProductRef
    
    Throws:
    
    SBMLConstructorException
  - GeneProductRef
```
public GeneProductRef(long level,
                      long version)
               throws SBMLConstructorException
```
    Creates a new GeneProductRef with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProductRef
    
    version - a long integer, the SBML Version to assign to this GeneProductRef
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProductRef
    
    Throws:
    
    SBMLConstructorException
  - GeneProductRef
```
public GeneProductRef(long level)
               throws SBMLConstructorException
```
    Creates a new GeneProductRef with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProductRef
    
    version - a long integer, the SBML Version to assign to this GeneProductRef
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProductRef
    
    Throws:
    
    SBMLConstructorException
  - GeneProductRef
```
public GeneProductRef()
               throws SBMLConstructorException
```
    Creates a new GeneProductRef with the given SBML Level, Version, and &ldquofbc&rdquopackage version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProductRef
    
    version - a long integer, the SBML Version to assign to this GeneProductRef
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProductRef
    
    Throws:
    
    SBMLConstructorException
  - GeneProductRef
```
public GeneProductRef(FbcPkgNamespaces fbcns)
               throws SBMLConstructorException
```
    Creates a new GeneProductRef with the given FbcPkgNamespaces object.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object
    
    Throws:
    
    SBMLConstructorException
  - GeneProductRef
```
public GeneProductRef(GeneProductRef orig)
               throws SBMLConstructorException
```
    Copy constructor for GeneProductRef.
    
    Parameters:
    
    orig - the GeneProductRef instance to copy.
    
    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 GeneProductRef.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 GeneProductRef.delete() themselves.
    
    Overrides:
    
    delete in class FbcAssociation
  - cloneObject
```
public GeneProductRef cloneObject()
```
    Creates and returns a deep copy of this GeneProductRef object.
    
    Overrides:
    
    cloneObject in class FbcAssociation
    
    Returns:
    
    a (deep) copy of this GeneProductRef object.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this GeneProductRef.
    
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the value of the 'id' attribute of this GeneProductRef as a string.
  - getGeneProduct
```
public java.lang.String getGeneProduct()
```
    Returns the value of the 'geneProduct' attribute of this GeneProductRef.
    
    Returns:
    
    the value of the 'geneProduct' attribute of this GeneProductRef as a string.
  - toInfix
```
public java.lang.String toInfix()
```
    Converts this FbcAssociation object into an infix string representation.
    
    Overrides:
    
    toInfix in class FbcAssociation
    
    Returns:
    
    the association as infix string.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this GeneProductRef.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the value of the 'name' attribute of this GeneProductRef as a string.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true if this GeneProductRef's 'id' attribute is set.
    
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if this GeneProductRef's 'id' attribute has been set, otherwise false is returned.
  - isSetGeneProduct
```
public boolean isSetGeneProduct()
```
    Predicate returning true if this GeneProductRef's 'geneProduct' attribute is set.
    
    Returns:
    
    true if this GeneProductRef's 'geneProduct' attribute has been set, otherwise false is returned.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true if this GeneProductRef's 'name' attribute is set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if this GeneProductRef's 'name' attribute has been set, otherwise false is returned.
  - setId
```
public int setId(java.lang.String id)
```
    Sets the value of the 'id' attribute of this GeneProductRef.
    Overrides:
    
    setId in class SBase
    
    Parameters:
    
    id - String value of the 'id' 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
  - setGeneProduct
```
public int setGeneProduct(java.lang.String geneProduct)
```
    Sets the value of the 'geneProduct' attribute of this GeneProductRef.
    Parameters:
    
    geneProduct - String value of the 'geneProduct' 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
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this GeneProductRef.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - String value of the 'name' 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
  - unsetId
```
public int unsetId()
```
    Unsets the value of the 'id' attribute of this GeneProductRef.
    Overrides:
    
    unsetId in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetGeneProduct
```
public int unsetGeneProduct()
```
    Unsets the value of the 'geneProduct' attribute of this GeneProductRef.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this GeneProductRef.
    Overrides:
    
    unsetName in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - 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 SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    For GeneProductRef, the XML element name is always 'geneProductRef'.
    
    Overrides:
    
    getElementName in class FbcAssociation
    
    Returns:
    
    the name of this element, i.e. 'geneProductRef'.
  - 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 FbcAssociation
    
    Returns:
    
    the SBML type code for this object: SBML_FBC_GENEPRODUCTREF (default).
    
    See Also:
    
    GeneProductRef.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().
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required attributes for this GeneProductRef object have been set.
    Overrides:
    
    hasRequiredAttributes in class FbcAssociation
    
    Returns:
    
    a boolean value indicating whether all the required attributes for this object have been defined.
    
    "Note:"
    The required attributes for a GeneProductRef object are:
    
    'geneProduct'

Class GeneProductRef

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.FbcAssociation

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

GeneProductRef

GeneProductRef

GeneProductRef

GeneProductRef

GeneProductRef

GeneProductRef

Method Detail

delete

cloneObject

getId

getGeneProduct

toInfix

getName

isSetId

isSetGeneProduct

isSetName

setId

setGeneProduct

setName

unsetId

unsetGeneProduct

unsetName

renameSIdRefs

getElementName

getTypeCode

hasRequiredAttributes