CompSBMLDocumentPlugin (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBasePlugin
- - org.sbml.libsbml.SBMLDocumentPlugin
  - - org.sbml.libsbml.CompSBMLDocumentPlugin

```
public class CompSBMLDocumentPlugin
extends SBMLDocumentPlugin
```
comp Extension of SBMLDocument.
The CompSBMLDocumentPlugin class inherits from the SBMLDocumentPlugin class, and codifies the extensions to the SBMLDocument class defined in the SBML Level 3 Hierarchical Model Composition (&ldquocomp&rdquo) package. This extension allows multiple Model objects to be defined in a single SBMLDocument, stored in an optional child ListOfModelDefinitions object, as well as define references to Model objects in other files, stored in the optional child ListOfExternalModelDefinitions object. These model definitions, if present, allow Submodel objects to reference other Models to instantiate.
The presence of any ModelDefinition or ExternalModelDefinition in an SBMLDocument does not change the default Model in the file. If a SBMLDocument is submitted somewhere to be simulated, it is still the <model> child of the <sbml> element that should be simulated.
In addition, as all packages do, the CompSBMLDocumentPlugin defines a required flag named required, which indicates whether &ldquocomp&rdquo constructs can be used to change the core mathematics of the <model> child of the <sbml> element. Because they can, this attribute must be set true.

Constructor Summary

Constructors
Constructor and Description
`CompSBMLDocumentPlugin(CompSBMLDocumentPlugin orig)` Copy constructor.
`CompSBMLDocumentPlugin(java.lang.String uri, java.lang.String prefix, CompPkgNamespaces compns)` Creates a new `CompSBMLDocumentPlugin` object using the given parameters.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addExternalModelDefinition(ExternalModelDefinition externalModelDefinition)` Adds a copy of the given `ExternalModelDefinition` object to the `ListOfExternalModelDefinitions`.
`int`	`addModelDefinition(ModelDefinition modelDefinition)` Adds a copy of the given `ModelDefinition` object to the `ListOfModelDefinitions`.
`SBasePlugin`	`cloneObject()` Creates and returns a deep copy of this `CompSBMLDocumentPlugin` object.
`ExternalModelDefinition`	`createExternalModelDefinition()` Creates a `ExternalModelDefinition` object, adds it to the end of the `ExternalModelDefinition` objects list and returns a pointer to the newly created object.
`ModelDefinition`	`createModelDefinition()` Creates a `ModelDefinition` object, adds it to the end of the `ModelDefinition` objects list and returns a pointer to the newly created object.
`void`	`delete()` Explicitly deletes the underlying native object.
`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.
`ExternalModelDefinition`	`getExternalModelDefinition(long n)` Returns the `ExternalModelDefinition` with the given index.
`ExternalModelDefinition`	`getExternalModelDefinition(java.lang.String sid)` Returns the model definition object based on its identifier.
`ListOfExternalModelDefinitions`	`getListOfExternalModelDefinitions()` Returns the `ListOf` object that holds each `ExternalModelDefinition`.
`ListOfModelDefinitions`	`getListOfModelDefinitions()` Returns the `ListOf` object that holds each `ModelDefinition`.
`SBase`	`getModel(java.lang.String sid)` Searches the model namespace of the document and returns the `Model`, `ModelDefinition`, or ExternalModelDefintion object with the given identifier.
`ModelDefinition`	`getModelDefinition(long n)` Returns the `ModelDefinition` with the given index.
`ModelDefinition`	`getModelDefinition(java.lang.String sid)` Returns the model definition object based on its identifier.
`long`	`getNumExternalModelDefinitions()` Returns the number of `ExternalModelDefinition` objects for this `SBMLDocumentPlugin`.
`long`	`getNumModelDefinitions()` Returns the number of `ModelDefinition` objects for this `SBMLDocumentPlugin`.
`ExternalModelDefinition`	`removeExternalModelDefinition(long index)` Removes the `ExternalModelDefinition` with the given index.
`ExternalModelDefinition`	`removeExternalModelDefinition(java.lang.String id)` Removes the `ExternalModelDefinition` with the given `id`.
`ModelDefinition`	`removeModelDefinition(long index)` Removes the `ModelDefinition` with the given index from the `CompSBMLDocumentPlugin`.
`ModelDefinition`	`removeModelDefinition(java.lang.String id)` Removes the `ModelDefinition` with the given `id` from the `CompSBMLDocumentPlugin`.
`int`	`setRequired(boolean value)` Sets the boolean value of 'required' attribute of corresponding package in `SBMLDocument` element.

Methods inherited from class org.sbml.libsbml.SBMLDocumentPlugin
getRequired, isSetRequired, unsetRequired

Methods inherited from class org.sbml.libsbml.SBasePlugin
getElementNamespace, getLevel, getListOfAllElements, getListOfAllElements, getPackageName, getPackageVersion, getParentSBMLObject, getPrefix, getSBMLDocument, getURI, getVersion, isValidTypeForList, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, setElementNamespace

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

- Constructor Detail
  - CompSBMLDocumentPlugin
```
public CompSBMLDocumentPlugin(java.lang.String uri,
                              java.lang.String prefix,
                              CompPkgNamespaces compns)
```
    Creates a new CompSBMLDocumentPlugin object using the given parameters.
    
    In the XML representation of an SBML document, XML namespaces are used to identify the origin of each XML construct used. XML namespaces are identified by their unique resource identifiers (URIs). The core SBML specifications stipulate the namespaces that must be used for core SBML constructs for example, all XML elements that belong to SBML Level 3 Version 1 Core must be placed in the XML namespace identified by the URI 'http://www.sbml.org/sbml/level3/version1/core'. Individual SBML Level 3 packages define their own XML namespaces for example, all elements belonging to the SBML Level 3 Layout Version 1 package must be placed in the XML namespace 'http://www.sbml.org/sbml/level3/version1/layout/version1/'.
    
    The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
    
    Parameters:
    
    uri - the URI of the SBML Level 3 package implemented by this libSBML package extension.
    
    prefix - the XML namespace prefix being used for the package.
    
    compns - the namespaces object for the package.
  - CompSBMLDocumentPlugin
```
public CompSBMLDocumentPlugin(CompSBMLDocumentPlugin orig)
```
    Copy constructor. Creates a copy of this CompSBMLDocumentPlugin object.
    
    Parameters:
    
    orig - the instance to copy.
- 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 CompSBMLDocumentPlugin.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 CompSBMLDocumentPlugin.delete() themselves.
    
    Overrides:
    
    delete in class SBMLDocumentPlugin
  - cloneObject
```
public SBasePlugin cloneObject()
```
    Creates and returns a deep copy of this CompSBMLDocumentPlugin object.
    
    Overrides:
    
    cloneObject in class SBMLDocumentPlugin
    
    Returns:
    
    a (deep) copy of this CompSBMLDocumentPlugin 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 SBasePlugin
    
    Parameters:
    
    id - string representing the identifier of the object to find.
    
    Returns:
    
    a pointer to the SBase element with the given id.
    
    "Note:"
    
    The comp SBML document plugin has multiple model-wide SId namespaces, so a valid document may well contain multiple elements with the same SId that reside in separate models. It is not recommended to ever call this function&mdashinstead, call the function on the child ModelDefinition objects.
  - 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 SBasePlugin
    
    Parameters:
    
    metaid - string representing the meta identifier of the object to find.
    
    Returns:
    
    a pointer to the SBase element with the given metaid.
  - getListOfModelDefinitions
```
public ListOfModelDefinitions getListOfModelDefinitions()
```
    Returns the ListOf object that holds each ModelDefinition.
    
    Returns:
    
    the ListOf object that holds each ModelDefinition.
  - getModelDefinition
```
public ModelDefinition getModelDefinition(long n)
```
    Returns the ModelDefinition with the given index.
    
    Parameters:
    
    n - the index number of the ModelDefinition to get.
    
    Returns:
    
    the nth ModelDefinition in the ListOfModelDefinitions. If the index is invalid, null is returned.
  - getModelDefinition
```
public ModelDefinition getModelDefinition(java.lang.String sid)
```
    Returns the model definition object based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the model definition to get.
    
    Returns:
    
    ModelDefinition in the ListOfModelDefinitions with the given sid or null if no such ModelDefinition exists.
    
    See Also:
    
    CompSBMLDocumentPlugin.getModelDefinition(long n), CompSBMLDocumentPlugin.getListOfModelDefinitions()
  - addModelDefinition
```
public int addModelDefinition(ModelDefinition modelDefinition)
```
    Adds a copy of the given ModelDefinition object to the ListOfModelDefinitions.
    Parameters:
    
    modelDefinition - the ModelDefinition object to be added to the ListOfModelDefinitions. Fails if the added ModelDefinition is null, does not match the level/version/package of the parent object, or cannot be added to the list of replaced elements.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
  - getNumModelDefinitions
```
public long getNumModelDefinitions()
```
    Returns the number of ModelDefinition objects for this SBMLDocumentPlugin.
    
    Returns:
    
    the number of ModelDefinition objects.
  - createModelDefinition
```
public ModelDefinition createModelDefinition()
```
    Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns a pointer to the newly created object.
    
    Returns:
    
    a newly created ModelDefinition object.
  - removeModelDefinition
```
public ModelDefinition removeModelDefinition(long index)
```
    Removes the ModelDefinition with the given index from the CompSBMLDocumentPlugin.
    A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, null is returned.
    
    Parameters:
    
    index - the index of the ModelDefinition object to remove.
    
    Returns:
    
    the ModelDefinition object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
  - removeModelDefinition
```
public ModelDefinition removeModelDefinition(java.lang.String id)
```
    Removes the ModelDefinition with the given id from the CompSBMLDocumentPlugin.
    A pointer to the ModelDefinition that was removed is returned. If no ModelDefinition has been removed, null is returned.
    
    Parameters:
    
    id - the id of the ModelDefinition object to remove.
    
    Returns:
    
    the ModelDefinition object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
  - getListOfExternalModelDefinitions
```
public ListOfExternalModelDefinitions getListOfExternalModelDefinitions()
```
    Returns the ListOf object that holds each ExternalModelDefinition.
    
    Returns:
    
    the ListOf object that each all ExternalModelDefinition.
  - getExternalModelDefinition
```
public ExternalModelDefinition getExternalModelDefinition(long n)
```
    Returns the ExternalModelDefinition with the given index.
    
    Parameters:
    
    n - the index number of the ExternalModelDefinition to get.
    
    Returns:
    
    the nth ExternalModelDefinition in the ListOfExternalModelDefinitions. If the index is invalid, null is returned.
  - getExternalModelDefinition
```
public ExternalModelDefinition getExternalModelDefinition(java.lang.String sid)
```
    Returns the model definition object based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the model definition to get.
    
    Returns:
    
    ExternalModelDefinition in the ListOfExternalModelDefinitions with the given sid or null if no such ExternalModelDefinition exists.
    
    See Also:
    
    CompSBMLDocumentPlugin.getExternalModelDefinition(long n), CompSBMLDocumentPlugin.getListOfExternalModelDefinitions()
  - getModel
```
public SBase getModel(java.lang.String sid)
```
    Searches the model namespace of the document and returns the Model, ModelDefinition, or ExternalModelDefintion object with the given identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the model definition to get.
    
    Returns:
    
    The SBase corresponding to the given sid or null if no such model exists. If no such model exists, this will return null.
  - setRequired
```
public int setRequired(boolean value)
```
    Sets the boolean value of 'required' attribute of corresponding package in SBMLDocument element. The only legal value is 'true' for the Hierarchical Model Composition package.
    Overrides:
    
    setRequired in class SBMLDocumentPlugin
    
    Parameters:
    
    value - the boolean value of 'required' attribute of corresponding package in SBMLDocument element.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_UNEXPECTED_ATTRIBUTE
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    
    SBMLDocumentPlugin.getRequired(), SBMLDocumentPlugin.isSetRequired(), SBMLDocumentPlugin.unsetRequired()
  - addExternalModelDefinition
```
public int addExternalModelDefinition(ExternalModelDefinition externalModelDefinition)
```
    Adds a copy of the given ExternalModelDefinition object to the ListOfExternalModelDefinitions.
    Parameters:
    
    externalModelDefinition - the ExternalModelDefinition object to be added to the ListOFExternalModelDefinitions. Fails if the added ExternalModelDefinition is null, does not match the level/version/package of the parent object, or cannot be added to the list of external model definitions.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
  - getNumExternalModelDefinitions
```
public long getNumExternalModelDefinitions()
```
    Returns the number of ExternalModelDefinition objects for this SBMLDocumentPlugin.
    
    Returns:
    
    the number of ExternalModelDefinition objects for this SBMLDocumentPlugin.
  - createExternalModelDefinition
```
public ExternalModelDefinition createExternalModelDefinition()
```
    Creates a ExternalModelDefinition object, adds it to the end of the ExternalModelDefinition objects list and returns a pointer to the newly created object.
    
    Returns:
    
    a newly created ExternalModelDefinition object.
  - removeExternalModelDefinition
```
public ExternalModelDefinition removeExternalModelDefinition(long index)
```
    Removes the ExternalModelDefinition with the given index.
    A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, null is returned.
    
    Parameters:
    
    index - the index of the ExternalModelDefinition object to remove.
    
    Returns:
    
    the ExternalModelDefinition object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
  - removeExternalModelDefinition
```
public ExternalModelDefinition removeExternalModelDefinition(java.lang.String id)
```
    Removes the ExternalModelDefinition with the given id.
    A pointer to the ExternalModelDefinition that was removed is returned. If no ExternalModelDefinition has been removed, null is returned.
    
    Parameters:
    
    id - the id of the ExternalModelDefinition object to remove.
    
    Returns:
    
    the ExternalModelDefinition object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.

Class CompSBMLDocumentPlugin

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBMLDocumentPlugin

Methods inherited from class org.sbml.libsbml.SBasePlugin

Methods inherited from class java.lang.Object

Constructor Detail

CompSBMLDocumentPlugin

CompSBMLDocumentPlugin

Method Detail

delete

cloneObject

getElementBySId

getElementByMetaId

getListOfModelDefinitions

getModelDefinition

getModelDefinition

addModelDefinition

getNumModelDefinitions

createModelDefinition

removeModelDefinition

removeModelDefinition

getListOfExternalModelDefinitions

getExternalModelDefinition

getExternalModelDefinition

getModel

setRequired

addExternalModelDefinition

getNumExternalModelDefinitions

createExternalModelDefinition

removeExternalModelDefinition

removeExternalModelDefinition