CompModelPlugin (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBasePlugin
- - org.sbml.libsbml.CompSBasePlugin
  - - org.sbml.libsbml.CompModelPlugin

```
public class CompModelPlugin
extends CompSBasePlugin
```
comp Extension of Model.
The CompModelPlugin class inherits from the SBMLSBasePlugin class, and codifies the extentions to the Model class defined in the SBML Level 3 'Hierarchical Model Composition' package (&ldquocomp&rdquo). This extention allows a Model to define Submodels (other Models that are instantiated as new parts of the parent Model), and Ports, a defined interface for including the given Model as a Submodel of a different Model.
Submodels are stored in an optional child ListOfSubmodels object, which, if present, must contain one or more Submodel objects. All of the Submodels present in the ListOfSubmodels are defined to be instantiated in the 'complete' Model.
Ports are stored in an optional child ListOfPorts object, which, if present, must contain one or more Port objects. All of the Ports present in the ListOfPorts collectively define the 'port interface' of the Model.

Constructor Summary

Constructors
Constructor and Description
`CompModelPlugin(CompModelPlugin orig)` Copy constructor.
`CompModelPlugin(java.lang.String uri, java.lang.String prefix, CompPkgNamespaces compns)` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addPort(Port port)` Adds a copy of the given `Port` object to the list of ports.
`int`	`addSubmodel(Submodel submodel)` Adds a copy of the given `Submodel` object to the list of submodels.
`SBasePlugin`	`cloneObject()` Creates and returns a deep copy of this `CompModelPlugin` object.
`Port`	`createPort()` Creates a `Port` object, adds it to the end of the port objects list and returns a pointer to the newly created object.
`Submodel`	`createSubmodel()` Creates a `Submodel` object, adds it to the end of the submodel objects list and returns a pointer to the newly created object.
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getDivider()` Get the string used as the divider between names when renaming and flattening models.
`SBase`	`getElementByMetaId(java.lang.String metaid)` Returns the first child element it can find with the given meta identifier, 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.
`ListOfPorts`	`getListOfPorts()` Returns the `ListOf` object that holds all ports.
`ListOfSubmodels`	`getListOfSubmodels()` Returns the `ListOf` object that holds all submodels.
`long`	`getNumPorts()` Returns the number of ports for this `CompModelPlugin`.
`long`	`getNumSubmodels()` Returns the number of submodels for this `CompModelPlugin`.
`Port`	`getPort(long n)` Returns the port with the given index.
`Port`	`getPort(java.lang.String id)` Returns the port with the given identifier.
`Submodel`	`getSubmodel(long n)` Returns the submodel with the given index.
`Submodel`	`getSubmodel(java.lang.String id)` Returns the submodel with the given identifier.
`SWIGTYPE_p_PrefixTransformer`	`getTransformer()`
`boolean`	`isSetTransformer()`
`Port`	`removePort(long index)` Removes the port with the given index.
`Submodel`	`removeSubmodel(long index)` Removes the submodel with the given index.
`int`	`setDivider(java.lang.String divider)` Set the string used as the divider between names when renaming and flattening models.
`void`	`setTransformer(SWIGTYPE_p_PrefixTransformer transformer)` Sets the custom transformer that is to be used, instead of the standard prefixing with the given divider.
`void`	`unsetTransformer()` Unsets any custom prefix transformers.

Methods inherited from class org.sbml.libsbml.CompSBasePlugin
addReplacedElement, clearReplacedElements, createReplacedBy, createReplacedElement, getListOfReplacedElements, getNumReplacedElements, getReplacedBy, getReplacedElement, isSetReplacedBy, logInvalidId, removeReplacedElement, setReplacedBy, unsetReplacedBy

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
  - CompModelPlugin
```
public CompModelPlugin(java.lang.String uri,
                       java.lang.String prefix,
                       CompPkgNamespaces compns)
```
    Constructor.
  - CompModelPlugin
```
public CompModelPlugin(CompModelPlugin orig)
```
    Copy constructor. Creates a copy of this CompModelPlugin object.
- 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 CompModelPlugin.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 CompModelPlugin.delete() themselves.
    
    Overrides:
    
    delete in class CompSBasePlugin
  - cloneObject
```
public SBasePlugin cloneObject()
```
    Creates and returns a deep copy of this CompModelPlugin object.
    
    Overrides:
    
    cloneObject in class CompSBasePlugin
    
    Returns:
    
    a (deep) copy of this CompModelPlugin 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 CompSBasePlugin
    
    Parameters:
    
    id - a string representing the id of objects 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 meta identifier, or itself if it has the given metaid, or null if no such object is found.
    
    Overrides:
    
    getElementByMetaId in class CompSBasePlugin
    
    Parameters:
    
    metaid - a string representing the metaid of objects to find.
    
    Returns:
    
    a pointer to the SBase element with the given metaid.
  - getListOfSubmodels
```
public ListOfSubmodels getListOfSubmodels()
```
    Returns the ListOf object that holds all submodels.
    
    Returns:
    
    the ListOf object that holds all submodels.
  - getSubmodel
```
public Submodel getSubmodel(long n)
```
    Returns the submodel with the given index. If the index is invalid, null is returned.
    
    Parameters:
    
    n - the index number of the Submodel to get.
    
    Returns:
    
    the nth Submodel in the ListOfSubmodels.
  - getSubmodel
```
public Submodel getSubmodel(java.lang.String id)
```
    Returns the submodel with the given identifier.
    
    Parameters:
    
    id - the identifier of the Submodel to get.
    
    Returns:
    
    the Submodel in the ListOfSubmodels with the given identifier. If no such submodel with identifier id exists, null is returned.
  - addSubmodel
```
public int addSubmodel(Submodel submodel)
```
    Adds a copy of the given Submodel object to the list of submodels.
    Fails if the added submodel is null, does not match the level/version/package of the parent object, or cannot be added to the list of submodels.
    Parameters:
    
    submodel - the Submodel object to be added to the list of submodels.
    
    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
  - getNumSubmodels
```
public long getNumSubmodels()
```
    Returns the number of submodels for this CompModelPlugin.
    
    Returns:
    
    the number of submodels for this CompModelPlugin.
  - createSubmodel
```
public Submodel createSubmodel()
```
    Creates a Submodel object, adds it to the end of the submodel objects list and returns a pointer to the newly created object.
    
    Returns:
    
    a newly created Submodel object
  - removeSubmodel
```
public Submodel removeSubmodel(long index)
```
    Removes the submodel with the given index. A pointer to the submodel that was removed is returned.
    
    Parameters:
    
    index - the index of the Submodel object to remove
    
    Returns:
    
    the Submodel object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range and no submodel has been removed, null is returned.
  - getListOfPorts
```
public ListOfPorts getListOfPorts()
```
    Returns the ListOf object that holds all ports.
    
    Returns:
    
    the ListOf object that holds all ports.
  - getPort
```
public Port getPort(long n)
```
    Returns the port with the given index.
    
    Parameters:
    
    n - the index number of the Port to get.
    
    Returns:
    
    the nth Port in the ListOfPorts. If the index n is invalid, null is returned.
  - getPort
```
public Port getPort(java.lang.String id)
```
    Returns the port with the given identifier.
    
    Parameters:
    
    id - the id of the Port to get.
    
    Returns:
    
    the Port in the ListOfPorts with the given identifier. If the identifier is invalid, null is returned.
  - addPort
```
public int addPort(Port port)
```
    Adds a copy of the given Port object to the list of ports.
    Parameters:
    
    port - the Port object to be added to the list of ports. Fails if the added port is null, does not match the level/version/package of the parent object, or cannot be added to the list of ports.
    
    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
  - getNumPorts
```
public long getNumPorts()
```
    Returns the number of ports for this CompModelPlugin.
    
    Returns:
    
    the number of ports for this CompModelPlugin.
  - createPort
```
public Port createPort()
```
    Creates a Port object, adds it to the end of the port objects list and returns a pointer to the newly created object.
    
    Returns:
    
    a newly created Port object
  - removePort
```
public Port removePort(long index)
```
    Removes the port with the given index.
    
    Parameters:
    
    index - the index of the Port object to remove
    
    Returns:
    
    the Port object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
  - setDivider
```
public int setDivider(java.lang.String divider)
```
    Set the string used as the divider between names when renaming and flattening models.
    The divider string consists of two underscore characters ("__") by default. This method will fail if called with an empty divider, or a divider that cannot be used internally as part of a valid SBML SId.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getDivider
```
public java.lang.String getDivider()
```
    Get the string used as the divider between names when renaming and flattening models.
    The divider string consists of two underscore characters ("__") by default, and can be overridden with the setDivider() function.
    
    See Also:
    
    CompModelPlugin.setDivider(String divider)
  - setTransformer
```
public void setTransformer(SWIGTYPE_p_PrefixTransformer transformer)
```
    Sets the custom transformer that is to be used, instead of the standard prefixing with the given divider. This makes it possible to finely control how elements are altered.
    If not set, only ids and meta ids will be prefixed.
    NOTE: the model plugin only holds the pointer to the element it does not take ownership of it. Thus the calling program is responsible of freeing the transformer when no longer needed (i.e after the SBML document has been deleted)
  - getTransformer
```
public SWIGTYPE_p_PrefixTransformer getTransformer()
```
    Returns:
    
    any custom transformer set for prefix operations, will be null by default.
  - isSetTransformer
```
public boolean isSetTransformer()
```
    Returns:
    
    an indicator, whether a custom transformer has been set.
  - unsetTransformer
```
public void unsetTransformer()
```
    Unsets any custom prefix transformers.

Class CompModelPlugin

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.CompSBasePlugin

Methods inherited from class org.sbml.libsbml.SBasePlugin

Methods inherited from class java.lang.Object

Constructor Detail

CompModelPlugin

CompModelPlugin

Method Detail

delete

cloneObject

getElementBySId

getElementByMetaId

getListOfSubmodels

getSubmodel

getSubmodel

addSubmodel

getNumSubmodels

createSubmodel

removeSubmodel

getListOfPorts

getPort

getPort

addPort

getNumPorts

createPort

removePort

setDivider

getDivider

setTransformer

getTransformer

isSetTransformer

unsetTransformer