GeneAssociation (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.GeneAssociation

```
public class GeneAssociation
extends SBase
```
fbc Annotation helper class for &ldquofbc&rdquo Version 1.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

GeneAssociation is a helper class for creating annotations to store gene association information. It is part of a proposed approach to annotating models in Version 1 of the SBML Level 3 Flux Balance Constraints (&ldquofbc&rdquo) package. It is not part of the official &ldquofbc&rdquo specification, and not defined in Version 2 of the &ldquofbc&rdquo package specification. In &ldquofbc&rdquo Version 2, the equivalent capability is handled by the GeneProductAssociation class and this class (GeneAssociation) is not used.

See Also:

ListOfGeneAssociations, GeneProductAssociation, ListOfGeneProducts

Constructor Summary

Constructors
Constructor and Description
`GeneAssociation()` Creates a new `GeneAssociation` with the given `level`, `version`, and `pkgVersion`.
`GeneAssociation(FbcPkgNamespaces fbcns)` Creates a new `GeneAssociation` with the given `FbcPkgNamespaces` object.
`GeneAssociation(GeneAssociation source)` Copy constructor.
`GeneAssociation(long level)` Creates a new `GeneAssociation` with the given `level`, `version`, and `pkgVersion`.
`GeneAssociation(long level, long version)` Creates a new `GeneAssociation` with the given `level`, `version`, and `pkgVersion`.
`GeneAssociation(long level, long version, long pkgVersion)` Creates a new `GeneAssociation` with the given `level`, `version`, and `pkgVersion`.
`GeneAssociation(XMLNode node, FbcPkgNamespaces fbcns)` Creates a new `GeneAssociation` with the given `node` and `FbcPkgNamespaces` `fbcns`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`GeneAssociation`	`cloneObject()` Creates and returns a deep copy of this `GeneAssociation`.
`Association`	`createAssociation()` Creates a new association, sets it to this element and returns it.
`void`	`delete()` Explicitly deletes the underlying native object.
`Association`	`getAssociation()` Returns `Association` object of this `GeneAssociation`.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `GeneAssociation`.
`java.lang.String`	`getReaction()` Returns the string of the 'reaction' attribute of this `GeneAssociation`.
`int`	`getTypeCode()` Returns the libSBML type code of this object instance.
`boolean`	`isSetAssociation()` Predicate returning `true` if this `GeneAssociation`'s 'association' element is set.
`boolean`	`isSetId()` Predicate returning `true` if this `GeneAssociation`'s 'id' attribute is set.
`boolean`	`isSetReaction()` Predicate returning `true` if this `GeneAssociation`'s 'reaction' attribute is set.
`int`	`setAssociation(Association association)` Sets the `Association` object of this `GeneAssociation`.
`int`	`setId(java.lang.String sid)` Sets the value of the 'id' attribute of this `GeneAssociation`.
`int`	`setReaction(java.lang.String reaction)` Sets the SIdRef string of the 'reaction' attribute of this `GeneAssociation`.
`XMLNode`	`toXML()` Creates an `XMLNode` object from this.
`int`	`unsetAssociation()` Unsets the `Association` object of this `GeneAssociation`.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `GeneAssociation`.
`int`	`unsetReaction()` Unsets the value of the 'id' attribute of this `GeneAssociation`.

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, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - GeneAssociation
```
public GeneAssociation(long level,
                       long version,
                       long pkgVersion)
                throws SBMLConstructorException
```
    Creates a new GeneAssociation with the given level, version, and pkgVersion.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - GeneAssociation
```
public GeneAssociation(long level,
                       long version)
                throws SBMLConstructorException
```
    Creates a new GeneAssociation with the given level, version, and pkgVersion.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - GeneAssociation
```
public GeneAssociation(long level)
                throws SBMLConstructorException
```
    Creates a new GeneAssociation with the given level, version, and pkgVersion.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - GeneAssociation
```
public GeneAssociation()
                throws SBMLConstructorException
```
    Creates a new GeneAssociation with the given level, version, and pkgVersion.
    
    Parameters:
    
    level - the SBML Level.
    
    version - the Version within the SBML Level.
    
    pkgVersion - the version of the package.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - GeneAssociation
```
public GeneAssociation(XMLNode node,
                       FbcPkgNamespaces fbcns)
                throws SBMLConstructorException
```
    Creates a new GeneAssociation with the given node and FbcPkgNamespaces fbcns.
    
    The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
    
    Parameters:
    
    node - the XMLNode to copy.
    
    fbcns - the FbcPkgNamespaces object.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - GeneAssociation
```
public GeneAssociation(FbcPkgNamespaces fbcns)
                throws SBMLConstructorException
```
    Creates a new GeneAssociation with the given FbcPkgNamespaces object.
    
    The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
    
    Parameters:
    
    fbcns - the FbcPkgNamespaces object.
    
    Throws:
    
    SBMLConstructorException
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - GeneAssociation
```
public GeneAssociation(GeneAssociation source)
                throws SBMLConstructorException
```
    Copy constructor.
    
    Parameters:
    
    source - the 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 GeneAssociation.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 GeneAssociation.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this GeneAssociation.
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the id of this GeneAssociation.
    
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.isSetIdAttribute(), SBase.unsetIdAttribute()
    
    "Note:"
    Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the getIdAttribute() function instead.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
    letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
    
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true if this GeneAssociation's 'id' attribute is set.
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if the 'id' attribute of this SBML object is set, false otherwise.
    
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.unsetIdAttribute(), SBase.isSetIdAttribute()
    
    "Note:"
    Because of the inconsistent behavior of this function with respect to assignments and rules, it is now recommended to use the isSetIdAttribute() function instead.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
    letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
    
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
  - setId
```
public int setId(java.lang.String sid)
```
    Sets the value of the 'id' attribute of this GeneAssociation.
    
    The string sid is copied.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
```
   letter .= 'a'..'z','A'..'Z'
   digit  .= '0'..'9'
   idChar .= letter | digit | '_'
   SId    .= ( letter | '_' ) idChar*
 
```
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
    Overrides:
    
    setId in class SBase
    
    Parameters:
    
    sid - the string to use as the identifier of this object.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    LIBSBML_UNEXPECTED_ATTRIBUTE
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.isSetIdAttribute(), SBase.unsetIdAttribute()
  - unsetId
```
public int unsetId()
```
    Unsets the value of the 'id' attribute of this GeneAssociation.
    
    The identifier given by an object's 'id' attribute value is used to identify the object within the SBML model definition. Other objects can refer to the component using this identifier. The data type of 'id' is always SId or a type derived from that, such as UnitSId, depending on the object in question. All data types are defined as follows:
```
   letter .= 'a'..'z','A'..'Z'
   digit  .= '0'..'9'
   idChar .= letter | digit | '_'
   SId    .= ( letter | '_' ) idChar*
 
```
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. This applies to all uses of SId, SIdRef, and derived types.
    In SBML Level 3 Version 2, the 'id' and 'name' attributes were moved to SBase directly, instead of being defined individually for many (but not all) objects. Libsbml has for a long time provided functions defined on SBase itself to get, set, check, and unset those attributes, which would fail or otherwise return empty strings if executed on any object for which those attributes were not defined. Now that all SBase objects define those attributes, those functions now succeed for any object with the appropriate level and version.
    The exception to this rule is that for InitialAssignment, EventAssignment, AssignmentRule, and RateRule objects, the getId() function and the isSetId() functions (though not the setId() or unsetId() functions) would instead reference the value of the 'variable' attribute (for the rules and event assignments) or the 'symbol' attribute (for initial assignments). The AlgebraicRule fell into this category as well, though because it contained neither a 'variable' nor a 'symbol' attribute, getId() would always return an empty string, and isSetId() would always return false. For this reason, four new functions are now provided (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that will always act on the actual 'id' attribute, regardless of the object's type. The new functions should be used instead of the old ones unless the old behavior is somehow necessary.
    Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
    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
    See Also:
    
    SBase.getIdAttribute(), SBase.setIdAttribute(String sid), SBase.isSetIdAttribute(), SBase.unsetIdAttribute()
  - getReaction
```
public java.lang.String getReaction()
```
    Returns the string of the 'reaction' attribute of this GeneAssociation.
    
    Returns:
    
    the string of the 'reaction' attribute of this GeneAssociation.
  - isSetReaction
```
public boolean isSetReaction()
```
    Predicate returning true if this GeneAssociation's 'reaction' attribute is set.
    
    Returns:
    
    true if this GeneAssociation's 'reaction' attribute has been set, otherwise false is returned.
  - setReaction
```
public int setReaction(java.lang.String reaction)
```
    Sets the SIdRef string of the 'reaction' attribute of this GeneAssociation.
    Parameters:
    
    reaction - a SIdRef string 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
  - unsetReaction
```
public int unsetReaction()
```
    Unsets the value of the 'id' attribute of this GeneAssociation.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - createAssociation
```
public Association createAssociation()
```
    Creates a new association, sets it to this element and returns it.
  - getAssociation
```
public Association getAssociation()
```
    Returns Association object of this GeneAssociation.
    
    Returns:
    
    Association object of this GeneAssociation.
  - isSetAssociation
```
public boolean isSetAssociation()
```
    Predicate returning true if this GeneAssociation's 'association' element is set.
    
    Returns:
    
    true if this GeneAssociation's 'association' element has been set, otherwise false is returned.
  - setAssociation
```
public int setAssociation(Association association)
```
    Sets the Association object of this GeneAssociation.
    Parameters:
    
    association - a Association object 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
  - unsetAssociation
```
public int unsetAssociation()
```
    Unsets the Association object of this GeneAssociation.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    For GeneAssociation, the XML element name is always 'geneAssociation'.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, i.e. 'geneAssociation'.
  - cloneObject
```
public GeneAssociation cloneObject()
```
    Creates and returns a deep copy of this GeneAssociation.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this GeneAssociation.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code of this object instance.
    
    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 SBase.getPackageName() method on the object.
    
    Overrides:
    
    getTypeCode in class SBase
    
    Returns:
    
    the SBML type code for this object: SBML_FBC_GENEASSOCIATION
    
    See Also:
    
    GeneAssociation.getElementName(), SBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - toXML
```
public XMLNode toXML()
```
    Creates an XMLNode object from this.

Class GeneAssociation

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

GeneAssociation

GeneAssociation

GeneAssociation

GeneAssociation

GeneAssociation

GeneAssociation

GeneAssociation

Method Detail

delete

getId

isSetId

setId

unsetId

getReaction

isSetReaction

setReaction

unsetReaction

createAssociation

getAssociation

isSetAssociation

setAssociation

unsetAssociation

getElementName

cloneObject

getTypeCode

toXML