GeneProduct (LibSBML Java API)

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

```
public class GeneProduct
extends SBase
```
fbc Association of a gene product with a Reaction
In the SBML Level 3 Flux Balance Constraints (“fbc”) package representation format, a GeneProduct object represents a single gene or implied gene product. The gene or gene product is identified using the required attribute 'label', which is a text string. (This attribute is separate from the usual SBML 'id' attribute, which is used to cross-reference entities within an SBML model.) A GeneProduct object can also possess an optional 'associatedSpecies' attribute; if this a attribute is defined, it should have a value of type SIdRef and be the identifier of a Species object defined in the enclosing Model. An 'associatedSpecies', if it exists, is interpreted to be a species associated with the gene or gene product that is represented by the GeneProduct object.

Note:

This class of objects was introduced in Version 2 of the SBML Level 3 Flux Balance Constraints (“fbc”) specification. In Version 1 of “fbc”, 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 “fbc” specifications for more details.

Constructor Summary

Constructors
Constructor and Description
`GeneProduct()` Creates a new `GeneProduct` with the given SBML Level, Version, and “fbc”package version.
`GeneProduct(FbcPkgNamespaces fbcns)` Creates a new `GeneProduct` with the given `FbcPkgNamespaces` object.
`GeneProduct(GeneProduct orig)` Copy constructor for `GeneProduct`.
`GeneProduct(long level)` Creates a new `GeneProduct` with the given SBML Level, Version, and “fbc”package version.
`GeneProduct(long level, long version)` Creates a new `GeneProduct` with the given SBML Level, Version, and “fbc”package version.
`GeneProduct(long level, long version, long pkgVersion)` Creates a new `GeneProduct` with the given SBML Level, Version, and “fbc”package version.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`GeneProduct`	`cloneObject()` Creates and returns a deep copy of this `GeneProduct` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getAssociatedSpecies()` Returns the value of the 'associatedSpecies' attribute of this `GeneProduct`.
`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 `GeneProduct`.
`java.lang.String`	`getLabel()` Returns the value of the 'label' attribute of this `GeneProduct`.
`java.lang.String`	`getName()` Returns the value of the 'name' attribute of this `GeneProduct` object.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`boolean`	`hasRequiredAttributes()` Predicate returning `true` if all the required attributes for this `GeneProduct` object have been set.
`boolean`	`isSetAssociatedSpecies()` Predicate returning `true` if this `GeneProduct`'s 'associatedSpecies' attribute is set.
`boolean`	`isSetId()` Predicate returning `true` if this `GeneProduct`'s 'id' attribute is set.
`boolean`	`isSetLabel()` Predicate returning `true` if this `GeneProduct`'s 'label' attribute is set.
`boolean`	`isSetName()` Predicate returning `true` if this `GeneProduct`'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`	`setAssociatedSpecies(java.lang.String associatedSpecies)` Sets the value of the 'associatedSpecies' attribute of this `GeneProduct`.
`int`	`setId(java.lang.String sid)` Sets the value of the 'id' attribute of this `GeneProduct`.
`int`	`setLabel(java.lang.String label)` Sets the value of the 'label' attribute of this `GeneProduct`.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `GeneProduct`.
`int`	`unsetAssociatedSpecies()` Unsets the value of the 'associatedSpecies' attribute of this `GeneProduct`.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `GeneProduct`.
`int`	`unsetLabel()` Unsets the value of the 'label' attribute of this `GeneProduct`.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `GeneProduct`.

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, 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, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setIdAttribute, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - GeneProduct
```
public GeneProduct(long level,
                   long version,
                   long pkgVersion)
            throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProduct.
    
    version - a long integer, the SBML Version to assign to this GeneProduct.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProduct.
    
    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.
  - GeneProduct
```
public GeneProduct(long level,
                   long version)
            throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProduct.
    
    version - a long integer, the SBML Version to assign to this GeneProduct.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProduct.
    
    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.
  - GeneProduct
```
public GeneProduct(long level)
            throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProduct.
    
    version - a long integer, the SBML Version to assign to this GeneProduct.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProduct.
    
    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.
  - GeneProduct
```
public GeneProduct()
            throws SBMLConstructorException
```
    Creates a new GeneProduct with the given SBML Level, Version, and “fbc”package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this GeneProduct.
    
    version - a long integer, the SBML Version to assign to this GeneProduct.
    
    pkgVersion - a long integer, the SBML Fbc Version to assign to this GeneProduct.
    
    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.
  - GeneProduct
```
public GeneProduct(FbcPkgNamespaces fbcns)
            throws SBMLConstructorException
```
    Creates a new GeneProduct 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.
  - GeneProduct
```
public GeneProduct(GeneProduct orig)
            throws SBMLConstructorException
```
    Copy constructor for GeneProduct.
    
    Parameters:
    
    orig - the GeneProduct 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 GeneProduct.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 GeneProduct.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public GeneProduct cloneObject()
```
    Creates and returns a deep copy of this GeneProduct object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this GeneProduct object.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this GeneProduct.
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the id of this GeneProduct.
    
    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.
    Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
    With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this GeneProduct object.
    
    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, 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 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
    The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
    As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
    An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
    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 names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the name of this SBML object, or the empty string if not set or unsettable.
    
    See Also:
    
    SBase.getIdAttribute(), GeneProduct.isSetName(), GeneProduct.setName(String sid), GeneProduct.unsetName()
  - getLabel
```
public java.lang.String getLabel()
```
    Returns the value of the 'label' attribute of this GeneProduct.
    
    Returns:
    
    the value of the 'label' attribute of this GeneProduct as a string.
  - getAssociatedSpecies
```
public java.lang.String getAssociatedSpecies()
```
    Returns the value of the 'associatedSpecies' attribute of this GeneProduct.
    
    Returns:
    
    the value of the 'associatedSpecies' attribute of this GeneProduct as a string.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true if this GeneProduct's 'id' attribute is set.
    
    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.
    Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
    With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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:
    
    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 recommended that callers use isSetIdAttribute() instead.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true if this GeneProduct's 'name' attribute is set.
    
    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, 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 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
    The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
    As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
    An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
    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 names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if the 'name' attribute of this SBML object is set, false otherwise.
    
    See Also:
    
    GeneProduct.getName(), GeneProduct.setName(String sid), GeneProduct.unsetName()
  - isSetLabel
```
public boolean isSetLabel()
```
    Predicate returning true if this GeneProduct's 'label' attribute is set.
    
    Returns:
    
    true if this GeneProduct's 'label' attribute has been set, otherwise false is returned.
  - isSetAssociatedSpecies
```
public boolean isSetAssociatedSpecies()
```
    Predicate returning true if this GeneProduct's 'associatedSpecies' attribute is set.
    
    Returns:
    
    true if this GeneProduct's 'associatedSpecies' attribute has been set, otherwise false is returned.
  - setId
```
public int setId(java.lang.String sid)
```
    Sets the value of the 'id' attribute of this GeneProduct.
    
    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.
    Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
    With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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()
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this GeneProduct.
    
    The string in name is copied.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - the new name for the SBML 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
  - setLabel
```
public int setLabel(java.lang.String label)
```
    Sets the value of the 'label' attribute of this GeneProduct.
    Parameters:
    
    label - the value of the 'label' 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
  - setAssociatedSpecies
```
public int setAssociatedSpecies(java.lang.String associatedSpecies)
```
    Sets the value of the 'associatedSpecies' attribute of this GeneProduct.
    Parameters:
    
    associatedSpecies - the value of the 'associatedSpecies' 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 GeneProduct.
    
    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.
    Users need to be aware of some important API issues that are the result of the history of SBML and libSBML. Prior to SBML Level 3 Version 2, SBML defined 'id' and 'name' attributes on only a subset of SBML objects. To simplify the work of programmers, libSBML's API provided get, set, check, and unset on the SBase object class itself instead of on individual subobject classes. This made the get/set/etc. methods uniformly available on all objects in the libSBML API. LibSBML simply returned empty strings or otherwise did not act when the methods were applied to SBML objects that were not defined by the SBML specification to have 'id' or 'name' attributes. Additional complications arose with the rule and assignment objects: InitialAssignment, EventAssignment, AssignmentRule, and RateRule. In early versions of SBML, the rule object hierarchy was different, and in addition, then as now, they possess different attributes: 'variable' (for the rules and event assignments), 'symbol' (for initial assignments), or neither (for algebraic rules). Prior to SBML Level 3 Version 2, getId() would always return an empty string, and isSetId() would always return false for objects of these classes.
    With the addition of 'id' and 'name' attributes on SBase in Level 3 Version 2, it became necessary to introduce a new way to interact with the attributes more consistently in libSBML to avoid breaking backward compatibility in the behavior of the original 'id' methods. For this reason, libSBML provides four functions (getIdAttribute(), setIdAttribute(String), isSetIdAttribute(), and unsetIdAttribute()) that always act on the actual 'id' attribute inherited from SBase, regardless of the object's type. These new methods should be used instead of the older getId()/setId()/etc. methods 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()
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this GeneProduct.
    
    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, 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 'name' attribute is optional and is not intended to be used for cross-referencing purposes within a model. Its purpose instead is to provide a human-readable label for the component. The data type of 'name' is the type string defined in XML Schema. SBML imposes no restrictions as to the content of 'name' attributes beyond those restrictions defined by the string type in XML Schema.
    The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
    As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read; and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
    An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
    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 names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
    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
    See Also:
    
    GeneProduct.getName(), GeneProduct.setName(String sid), GeneProduct.isSetName()
  - unsetLabel
```
public int unsetLabel()
```
    Unsets the value of the 'label' attribute of this GeneProduct.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetAssociatedSpecies
```
public int unsetAssociatedSpecies()
```
    Unsets the value of the 'associatedSpecies' attribute of this GeneProduct.
    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 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 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 GeneProduct, the XML element name is always 'geneProduct'.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, i.e. 'geneProduct'.
  - 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 SBase.getPackageName() method on the object.
    The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
    
    Overrides:
    
    getTypeCode in class SBase
    
    Returns:
    
    the SBML type code for this object: SBML_FBC_GENEPRODUCT (default).
    
    See Also:
    
    GeneProduct.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 getPackageName() and getTypeCode() (or ListOf.getItemTypeCode()).
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required attributes for this GeneProduct object have been set.
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required attributes for this object have been defined.
    
    Note:
    The required attributes for a GeneProduct object are:
    
    'id'
    'label'

Class GeneProduct

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

GeneProduct

GeneProduct

GeneProduct

GeneProduct

GeneProduct

GeneProduct

Method Detail

delete

cloneObject

getId

getName

getLabel

getAssociatedSpecies

isSetId

isSetName

isSetLabel

isSetAssociatedSpecies

setId

setName

setLabel

setAssociatedSpecies

unsetId

unsetName

unsetLabel

unsetAssociatedSpecies

renameSIdRefs

getElementName

getTypeCode

hasRequiredAttributes