Transition (LibSBML Java API)

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

```
public class Transition
extends SBase
```
qual A transition of a QualitativeSpecies.
A Transition element contains at most one ListOfInputs and one ListOfOutputs and exactly one ListOfFunctionTerms.
A Transition defines the changes in level associated with the QualitativeSpecies that occur when a Transition is enabled.
In logical models, a Transition is used to specify the logical rule associated with a QualitativeSpecies (that appears as an Output of this Transition). For example, the rule 'if A > 1 : B = 2' would be encapsulated as a Transition with QualitativeSpecies 'A' as an Input and 'B' as an Output the 'if A > 1' rule being encode by the math element of a FunctionTerm with the resultLevel attribute having a value '2'.
In Petri net models, a Transition is interpreted, using the common Petri net semantics, as events that might occur within the system causing tokens to be moved.

Constructor Summary

Constructors
Constructor and Description
`Transition()` Creates a new `Transition` with the given level, version, and package version.
`Transition(long level)` Creates a new `Transition` with the given level, version, and package version.
`Transition(long level, long version)` Creates a new `Transition` with the given level, version, and package version.
`Transition(long level, long version, long pkgVersion)` Creates a new `Transition` with the given level, version, and package version.
`Transition(QualPkgNamespaces qualns)` Creates a new `Transition` with the given `QualPkgNamespaces` object.
`Transition(Transition orig)` Copy constructor for `Transition`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addExpectedAttributes(SWIGTYPE_p_ExpectedAttributes attributes)` Get the list of expected attributes for this element.
`int`	`addFunctionTerm(FunctionTerm ft)` Adds a copy the given `FunctionTerm` to this `Transition`.
`int`	`addInput(Input i)` Adds a copy the given `Input` to this `Transition`.
`int`	`addOutput(Output o)` Adds a copy the given `Output` to this `Transition`.
`Transition`	`cloneObject()` Creates and returns a deep copy of this `Transition` object.
`DefaultTerm`	`createDefaultTerm()` Creates a new `DefaultTerm` object, adds it to this `Transition`'s `ListOfFunctionTerms` and returns the `DefaultTerm` object created.
`FunctionTerm`	`createFunctionTerm()` Creates a new `FunctionTerm` object, adds it to this `Transition`'s `ListOfFunctionTerms` and returns the `FunctionTerm` object created.
`Input`	`createInput()` Creates a new `Input` object, adds it to this `Transition`'s `ListOfInputs` and returns the `Input` object created.
`SBase`	`createObject(XMLInputStream stream)` Create and return an SBML object of this class, if present.
`Output`	`createOutput()` Creates a new `Output` object, adds it to this `Transition`'s `ListOfOutputs` and returns the `Output` object created.
`void`	`delete()` Explicitly deletes the underlying native object.
`DefaultTerm`	`getDefaultTerm()` Get the `DefaultTerm` from the `ListOfFunctionTerms`.
`SBase`	`getElementByMetaId(java.lang.String metaid)` Returns the first child element it can find with the given `metaid`, or itself if it has the given `metaid`, or `null` if no such object is found.
`SBase`	`getElementBySId(java.lang.String id)` Returns the first child element found that has the given `id` in the model-wide SId namespace, or `null` if no such object is found.
`java.lang.String`	`getElementName()` Returns the XML name of this object.
`FunctionTerm`	`getFunctionTerm(long n)` Get a `FunctionTerm` from the `ListOfFunctionTerms`.
`FunctionTerm`	`getFunctionTerm(java.lang.String sid)` Get a `FunctionTerm` from the `ListOfFunctionTerms` based on its identifier.
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `Transition`.
`Input`	`getInput(long n)` Get a `Input` from the `ListOfInputs`.
`Input`	`getInput(java.lang.String sid)` Get a `Input` from the `ListOfInputs` based on its identifier.
`Input`	`getInputBySpecies(java.lang.String sid)` Get a `Input` from the `ListOfInputs` based on its qualitativeSpecies attribute.
`ListOfFunctionTerms`	`getListOfFunctionTerms()` Returns the `ListOfFunctionTerms` in this `Transition` object.
`ListOfInputs`	`getListOfInputs()` Returns the `ListOfInputs` in this `Transition` object.
`ListOfOutputs`	`getListOfOutputs()` Returns the `ListOfOutputs` in this `Transition` object.
`java.lang.String`	`getName()`
`long`	`getNumFunctionTerms()` Get the number of `FunctionTerm` objects in this `Transition`.
`long`	`getNumInputs()` Get the number of `Input` objects in this `Transition`.
`long`	`getNumOutputs()` Get the number of `Output` objects in this `Transition`.
`Output`	`getOutput(long n)` Get a `Output` from the `ListOfOutputs`.
`Output`	`getOutput(java.lang.String sid)` Get a `Output` from the `ListOfOutputs` based on its identifier.
`Output`	`getOutputBySpecies(java.lang.String sid)` Get a `Output` from the `ListOfOutputs` based on its qualitativeSpecies attribute.
`int`	`getTypeCode()` Returns the libSBML type code of this object instance.
`boolean`	`hasRequiredElements()` Predicate returning `true` if all the required attributes for this `Transition` object have been set.
`boolean`	`isSetDefaultTerm()` Predicate returning `true` if the defaultTerm for this `Transition` object has been set.
`boolean`	`isSetId()` Predicate returning `true` or `false` depending on whether this `Transition`'s 'id' attribute has been set.
`boolean`	`isSetName()` Predicate returning `true` or `false` depending on whether this `Transition`'s 'name' attribute has been set.
`FunctionTerm`	`removeFunctionTerm(long n)` Removes the nth `FunctionTerm` from the `ListOfFunctionTerms` within this `Transition`.
`FunctionTerm`	`removeFunctionTerm(java.lang.String sid)` Removes the `FunctionTerm` with the given identifier from the `ListOfFunctionTerms` within this `Transition` and returns a pointer to it.
`Input`	`removeInput(long n)` Removes the nth `Input` from the `ListOfInputs` within this `Transition`.
`Input`	`removeInput(java.lang.String sid)` Removes the `Input` with the given identifier from the `ListOfInputs` within this `Transition` and returns a pointer to it.
`Output`	`removeOutput(long n)` Removes the nth `Output` from the `ListOfOutputs` within this `Transition`.
`Output`	`removeOutput(java.lang.String sid)` Removes the `Output` with the given identifier from the `ListOfOutputs` within this `Transition` and returns a pointer to it.
`int`	`setDefaultTerm(DefaultTerm dt)` Sets the given `DefaultTerm` to this `Transition`.
`int`	`setId(java.lang.String sid)` Sets the value of the 'id' attribute of this `Transition`.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `Transition`.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `Transition`.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `Transition`.

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, 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, renameSIdRefs, 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
  - Transition
```
public Transition(long level,
                  long version,
                  long pkgVersion)
           throws SBMLConstructorException
```
    Creates a new Transition with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transition.
    
    version - a long integer, the SBML Version to assign to this Transition.
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this Transition.
    
    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.
  - Transition
```
public Transition(long level,
                  long version)
           throws SBMLConstructorException
```
    Creates a new Transition with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transition.
    
    version - a long integer, the SBML Version to assign to this Transition.
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this Transition.
    
    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.
  - Transition
```
public Transition(long level)
           throws SBMLConstructorException
```
    Creates a new Transition with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transition.
    
    version - a long integer, the SBML Version to assign to this Transition.
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this Transition.
    
    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.
  - Transition
```
public Transition()
           throws SBMLConstructorException
```
    Creates a new Transition with the given level, version, and package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transition.
    
    version - a long integer, the SBML Version to assign to this Transition.
    
    pkgVersion - a long integer, the SBML Qual Version to assign to this Transition.
    
    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.
  - Transition
```
public Transition(QualPkgNamespaces qualns)
           throws SBMLConstructorException
```
    Creates a new Transition with the given QualPkgNamespaces 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:
    
    qualns - the QualPkgNamespaces 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.
  - Transition
```
public Transition(Transition orig)
           throws SBMLConstructorException
```
    Copy constructor for Transition.
    
    Parameters:
    
    orig - the Transition 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 Transition.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 Transition.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public Transition cloneObject()
```
    Creates and returns a deep copy of this Transition object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this Transition object.
  - getElementBySId
```
public SBase getElementBySId(java.lang.String id)
```
    Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
    
    Overrides:
    
    getElementBySId in class SBase
    
    Parameters:
    
    id - string representing the id of the object to find.
    
    Returns:
    
    a pointer to the SBase element with the given id.
  - getElementByMetaId
```
public SBase getElementByMetaId(java.lang.String metaid)
```
    Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
    
    Overrides:
    
    getElementByMetaId in class SBase
    
    Parameters:
    
    metaid - string representing the metaid of the object to find.
    
    Returns:
    
    a pointer to the SBase element with the given metaid.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this Transition.
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the id of this Transition.
    
    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.
  - getName
```
public java.lang.String getName()
```
    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(), Transition.isSetName(), Transition.setName(String sid), Transition.unsetName()
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true or false depending on whether this Transition's 'id' attribute has been 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.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true or false depending on whether this Transition's 'name' attribute has been 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:
    
    Transition.getName(), Transition.setName(String sid), Transition.unsetName()
  - setId
```
public int setId(java.lang.String sid)
```
    Sets the value of the 'id' attribute of this Transition.
    
    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()
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this Transition.
    
    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 Transition.
    
    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()
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this Transition.
    
    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:
    
    Transition.getName(), Transition.setName(String sid), Transition.isSetName()
  - getListOfInputs
```
public ListOfInputs getListOfInputs()
```
    Returns the ListOfInputs in this Transition object.
    
    Returns:
    
    the ListOfInputs child of this Transition.
  - getInput
```
public Input getInput(long n)
```
    Get a Input from the ListOfInputs.
    
    Parameters:
    
    n - the index number of the Input to get.
    
    Returns:
    
    the nth Input in the ListOfInputs within this Transition.
    
    See Also:
    
    Transition.getNumInputs()
  - getInput
```
public Input getInput(java.lang.String sid)
```
    Get a Input from the ListOfInputs based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the Input to get.
    
    Returns:
    
    the Input in the ListOfInputs with the given id or null if no such Input exists.
    
    See Also:
    
    Transition.getInput(long n), Transition.getNumInputs()
  - getInputBySpecies
```
public Input getInputBySpecies(java.lang.String sid)
```
    Get a Input from the ListOfInputs based on its qualitativeSpecies attribute.
    
    Parameters:
    
    sid - a string representing the qualitativeSpecies of the Input to get.
    
    Returns:
    
    the first Input in the ListOfInputs with the given qualitativeSpecies or null if no such Input exists.
    
    See Also:
    
    , Transition.getInput(long n)
  - addInput
```
public int addInput(Input i)
```
    Adds a copy the given Input to this Transition.
    Parameters:
    
    i - the Input object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - getNumInputs
```
public long getNumInputs()
```
    Get the number of Input objects in this Transition.
    
    Returns:
    
    the number of Input objects in this Transition.
  - createInput
```
public Input createInput()
```
    Creates a new Input object, adds it to this Transition's ListOfInputs and returns the Input object created.
    
    Returns:
    
    a new Input object instance.
    
    See Also:
    
    Transition.addInput(Input i)
  - removeInput
```
public Input removeInput(long n)
```
    Removes the nth Input from the ListOfInputs within this Transition. and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the Input to remove.
    
    See Also:
    
    Transition.getNumInputs()
  - removeInput
```
public Input removeInput(java.lang.String sid)
```
    Removes the Input with the given identifier from the ListOfInputs within this Transition and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.
    
    Parameters:
    
    sid - the identifier of the Input to remove.
    
    Returns:
    
    the Input removed. As mentioned above, the caller owns the returned item.
  - getListOfOutputs
```
public ListOfOutputs getListOfOutputs()
```
    Returns the ListOfOutputs in this Transition object.
    
    Returns:
    
    the ListOfOutputs child of this Transition.
  - getOutput
```
public Output getOutput(long n)
```
    Get a Output from the ListOfOutputs.
    
    Parameters:
    
    n - the index number of the Output to get.
    
    Returns:
    
    the nth Output in the ListOfOutputs within this Transition.
    
    See Also:
    
    Transition.getNumOutputs()
  - getOutput
```
public Output getOutput(java.lang.String sid)
```
    Get a Output from the ListOfOutputs based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the Output to get.
    
    Returns:
    
    the Output in the ListOfOutputs with the given id or null if no such Output exists.
    
    See Also:
    
    , Transition.getOutput(long n)
  - getOutputBySpecies
```
public Output getOutputBySpecies(java.lang.String sid)
```
    Get a Output from the ListOfOutputs based on its qualitativeSpecies attribute.
    
    Parameters:
    
    sid - a string representing the qualitativeSpecies of the Output to get.
    
    Returns:
    
    the first Output in the ListOfOutputs with the given qualitativeSpecies or null if no such Output exists.
    
    See Also:
    
    , Transition.getOutput(long n)
  - addOutput
```
public int addOutput(Output o)
```
    Adds a copy the given Output to this Transition.
    Parameters:
    
    o - the Output object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - getNumOutputs
```
public long getNumOutputs()
```
    Get the number of Output objects in this Transition.
    
    Returns:
    
    the number of Output objects in this Transition.
  - createOutput
```
public Output createOutput()
```
    Creates a new Output object, adds it to this Transition's ListOfOutputs and returns the Output object created.
    
    Returns:
    
    a new Output object instance.
    
    See Also:
    
    Transition.addOutput(Output o)
  - removeOutput
```
public Output removeOutput(long n)
```
    Removes the nth Output from the ListOfOutputs within this Transition. and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the Output to remove.
    
    See Also:
    
    Transition.getNumOutputs()
  - removeOutput
```
public Output removeOutput(java.lang.String sid)
```
    Removes the Output with the given identifier from the ListOfOutputs within this Transition and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.
    
    Parameters:
    
    sid - the identifier of the Output to remove.
    
    Returns:
    
    the Output removed. As mentioned above, the caller owns the returned item.
  - getListOfFunctionTerms
```
public ListOfFunctionTerms getListOfFunctionTerms()
```
    Returns the ListOfFunctionTerms in this Transition object.
    
    Returns:
    
    the ListOfFunctionTerms child of this Transition.
  - getFunctionTerm
```
public FunctionTerm getFunctionTerm(long n)
```
    Get a FunctionTerm from the ListOfFunctionTerms.
    
    Parameters:
    
    n - the index number of the FunctionTerm to get.
    
    Returns:
    
    the nth FunctionTerm in the ListOfFunctionTerms within this Transition.
    
    See Also:
    
    Transition.getNumFunctionTerms()
  - getFunctionTerm
```
public FunctionTerm getFunctionTerm(java.lang.String sid)
```
    Get a FunctionTerm from the ListOfFunctionTerms based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the FunctionTerm to get.
    
    Returns:
    
    the FunctionTerm in the ListOfFunctionTerms with the given id or null if no such FunctionTerm exists.
    
    See Also:
    
    , Transition.getFunctionTerm(long n)
  - addFunctionTerm
```
public int addFunctionTerm(FunctionTerm ft)
```
    Adds a copy the given FunctionTerm to this Transition.
    Parameters:
    
    ft - the FunctionTerm object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - getNumFunctionTerms
```
public long getNumFunctionTerms()
```
    Get the number of FunctionTerm objects in this Transition.
    
    Returns:
    
    the number of FunctionTerm objects in this Transition.
  - createFunctionTerm
```
public FunctionTerm createFunctionTerm()
```
    Creates a new FunctionTerm object, adds it to this Transition's ListOfFunctionTerms and returns the FunctionTerm object created.
    
    Returns:
    
    a new FunctionTerm object instance.
    
    See Also:
    
    Transition.addFunctionTerm(FunctionTerm ft)
  - removeFunctionTerm
```
public FunctionTerm removeFunctionTerm(long n)
```
    Removes the nth FunctionTerm from the ListOfFunctionTerms within this Transition. and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    n - the index of the FunctionTerm to remove.
    
    See Also:
    
    Transition.getNumFunctionTerms()
  - removeFunctionTerm
```
public FunctionTerm removeFunctionTerm(java.lang.String sid)
```
    Removes the FunctionTerm with the given identifier from the ListOfFunctionTerms within this Transition and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.
    
    Parameters:
    
    sid - the identifier of the FunctionTerm to remove.
    
    Returns:
    
    the FunctionTerm removed. As mentioned above, the caller owns the returned item.
  - createDefaultTerm
```
public DefaultTerm createDefaultTerm()
```
    Creates a new DefaultTerm object, adds it to this Transition's ListOfFunctionTerms and returns the DefaultTerm object created.
    
    Returns:
    
    a new DefaultTerm object instance.
    
    See Also:
    
    Transition.setDefaultTerm(DefaultTerm ft)
  - setDefaultTerm
```
public int setDefaultTerm(DefaultTerm dt)
```
    Sets the given DefaultTerm to this Transition.
    Parameters:
    
    dt - the DefaultTerm object to add.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - isSetDefaultTerm
```
public boolean isSetDefaultTerm()
```
    Predicate returning true if the defaultTerm for this Transition object has been set.
    
    Returns:
    
    a boolean value indicating whether the defaultTerm child for this object has been defined.
  - getDefaultTerm
```
public DefaultTerm getDefaultTerm()
```
    Get the DefaultTerm from the ListOfFunctionTerms.
    
    Returns:
    
    the DefaultTerm in the ListOfFunctionTerms within this Transition, or null if no such value is set.
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML name of this object.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element.
  - 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_QUAL_TRANSITION.
    
    See Also:
    
    Transition.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().
  - hasRequiredElements
```
public boolean hasRequiredElements()
```
    Predicate returning true if all the required attributes for this Transition object have been set.
    Overrides:
    
    hasRequiredElements in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required elements for this object have been defined.
    
    "Note:"
    The required elements for a Transition object are:
    
    a 'defaultTerm' child of the child ListOfFunctionTerms.
  - createObject
```
public SBase createObject(XMLInputStream stream)
```
    Create and return an SBML object of this class, if present.
    
    Returns:
    
    the SBML object corresponding to next XMLToken in the XMLInputStream or null if the token was not recognized.
  - addExpectedAttributes
```
public void addExpectedAttributes(SWIGTYPE_p_ExpectedAttributes attributes)
```
    Get the list of expected attributes for this element.

Class Transition

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

Transition

Transition

Transition

Transition

Transition

Transition

Method Detail

delete

cloneObject

getElementBySId

getElementByMetaId

getId

getName

isSetId

isSetName

setId

setName

unsetId

unsetName

getListOfInputs

getInput

getInput

getInputBySpecies

addInput

getNumInputs

createInput

removeInput

removeInput

getListOfOutputs

getOutput

getOutput

getOutputBySpecies

addOutput

getNumOutputs

createOutput

removeOutput

removeOutput

getListOfFunctionTerms

getFunctionTerm

getFunctionTerm

addFunctionTerm

getNumFunctionTerms

createFunctionTerm

removeFunctionTerm

removeFunctionTerm

createDefaultTerm

setDefaultTerm

isSetDefaultTerm

getDefaultTerm

getElementName

getTypeCode

hasRequiredElements

createObject

addExpectedAttributes