SimpleSpeciesReference (LibSBML Java API)

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

Direct Known Subclasses:

ModifierSpeciesReference, SpeciesReference
```
public class SimpleSpeciesReference
extends SBase
```
Abstract class for references to species in reactions.
As mentioned in the description of Reaction, every species that enters into a given reaction must appear in that reaction's lists of reactants, products and/or modifiers. In an SBML model, all species that may participate in any reaction are listed in the 'listOfSpecies' element of the top-level Model object. Lists of products, reactants and modifiers in Reaction objects do not introduce new species, but rather, they refer back to those listed in the model's top-level 'listOfSpecies'. For reactants and products, the connection is made using SpeciesReference objects; for modifiers, it is made using ModifierSpeciesReference objects. SimpleSpeciesReference is an abstract type that serves as the parent class of both SpeciesReference and ModifierSpeciesReference. It is used simply to hold the attributes and elements that are common to the latter two structures.
The SimpleSpeciesReference structure has a mandatory attribute, 'species', which must be a text string conforming to the identifer syntax permitted in SBML. This attribute is inherited by the SpeciesReference and ModifierSpeciesReference subclasses derived from SimpleSpeciesReference. The value of the 'species' attribute must be the identifier of a species defined in the enclosing Model. The species is thereby declared as participating in the reaction being defined. The precise role of that species as a reactant, product, or modifier in the reaction is determined by the subclass of SimpleSpeciesReference (i.e., either SpeciesReference or ModifierSpeciesReference) in which the identifier appears.
SimpleSpeciesReference also contains an optional attribute, 'id', allowing instances to be referenced from other structures. No SBML structures currently do this; however, such structures are anticipated in future SBML Levels.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `SimpleSpeciesReference`.
`java.lang.String`	`getName()` Returns the value of the 'name' attribute of this `SimpleSpeciesReference` object.
`java.lang.String`	`getSpecies()` Get the value of the 'species' attribute.
`boolean`	`isModifier()` Predicate returning `true` if this is a `ModifierSpeciesReference`.
`boolean`	`isSetId()` Predicate returning `true` if this `SimpleSpeciesReference`'s 'id' attribute is set.
`boolean`	`isSetName()` Predicate returning `true` if this `SimpleSpeciesReference`'s 'name' attribute is set.
`boolean`	`isSetSpecies()` Predicate returning `true` if this `SimpleSpeciesReference`'s 'species' 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`	`setId(java.lang.String sid)` Sets the value of the 'id' attribute of this `SimpleSpeciesReference`.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `SimpleSpeciesReference`.
`int`	`setSpecies(java.lang.String sid)` Sets the 'species' attribute of this `SimpleSpeciesReference`.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `SimpleSpeciesReference`.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `SimpleSpeciesReference`.
`int`	`unsetSpecies()` Unsets the value of the 'species' attribute of this `SimpleSpeciesReference`.

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, cloneObject, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getElementName, 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, getTypeCode, 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

- 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 SimpleSpeciesReference.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 SimpleSpeciesReference.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this SimpleSpeciesReference.
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the id of this SimpleSpeciesReference.
    
    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 SimpleSpeciesReference 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(), SimpleSpeciesReference.isSetName(), SimpleSpeciesReference.setName(String sid), SimpleSpeciesReference.unsetName()
  - getSpecies
```
public java.lang.String getSpecies()
```
    Get the value of the 'species' attribute.
    
    Returns:
    
    the value of the attribute 'species' for this SimpleSpeciesReference.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true if this SimpleSpeciesReference'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 SimpleSpeciesReference'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:
    
    SimpleSpeciesReference.getName(), SimpleSpeciesReference.setName(String sid), SimpleSpeciesReference.unsetName()
  - isSetSpecies
```
public boolean isSetSpecies()
```
    Predicate returning true if this SimpleSpeciesReference's 'species' attribute is set.
    
    Returns:
    
    true if the 'species' attribute of this SimpleSpeciesReference is set, false otherwise.
  - setSpecies
```
public int setSpecies(java.lang.String sid)
```
    Sets the 'species' attribute of this SimpleSpeciesReference.
    The identifier string passed in sid is copied.
    Parameters:
    
    sid - the identifier of a species defined in the enclosing Model's ListOfSpecies.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setId
```
public int setId(java.lang.String sid)
```
    Sets the value of the 'id' attribute of this SimpleSpeciesReference.
    
    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 SimpleSpeciesReference.
    
    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
  - unsetId
```
public int unsetId()
```
    Unsets the value of the 'id' attribute of this SimpleSpeciesReference.
    
    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 SimpleSpeciesReference.
    
    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:
    
    SimpleSpeciesReference.getName(), SimpleSpeciesReference.setName(String sid), SimpleSpeciesReference.isSetName()
  - unsetSpecies
```
public int unsetSpecies()
```
    Unsets the value of the 'species' attribute of this SimpleSpeciesReference.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - isModifier
```
public boolean isModifier()
```
    Predicate returning true if this is a ModifierSpeciesReference.
    
    Returns:
    
    true if this SimpleSpeciesReference's subclass is ModiferSpeciesReference, false if it is a plain SpeciesReference.
  - 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.

Class SimpleSpeciesReference

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Method Detail

delete

getId

getName

getSpecies

isSetId

isSetName

isSetSpecies

setSpecies

setId

setName

unsetId

unsetName

unsetSpecies

isModifier

renameSIdRefs