CompSBasePlugin (LibSBML Java API)

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

Direct Known Subclasses:

CompModelPlugin
```
public class CompSBasePlugin
extends SBasePlugin
```
comp Extension of SBase.
The CompSBasePlugin class inherits from the SBasePlugin class, and codifies the extentions to the SBase class defined in the 'Hierarchical Model Composition' package (&ldquocomp&rdquo). This extention allows the modeler to define one or more submodel elements which the parent SBase object replaces, and/or a single submodel element which replaces the parent SBase object.
This is accomplished through the addition of an optional ListOfReplacedElements child, which may contain one or more ReplacedElement objects, each of which references a submodel object to be replaced by the containing SBase object, and through the addition of a single optional ReplacedBy child, which references a submodel object which is to replace the containing SBase object.
If a single SBase element both contains a ListOfReplacedElements and has a ReplacedBy child, it and all the referenced ReplacedElement objects are to be replaced by the object referenced by the ReplacedBy element.

See Also:

ReplacedElement, ReplacedBy

Constructor Summary

Constructors
Constructor and Description
`CompSBasePlugin(CompSBasePlugin orig)` Copy constructor.
`CompSBasePlugin(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`	`addReplacedElement(ReplacedElement replacedElement)` Adds a copy of the given `ReplacedElement` object to the list of ReplacedElements.
`void`	`clearReplacedElements()` Remove all ReplacedElements, if any exist.
`SBasePlugin`	`cloneObject()` Creates and returns a deep copy of this `CompSBasePlugin` object.
`ReplacedBy`	`createReplacedBy()` Creates a new, empty `ReplacedBy`, adds it to this `CompSBasePlugin` and returns the created `ReplacedBy`.
`ReplacedElement`	`createReplacedElement()` Creates a `ReplacedElement` object, adds it to the end of the `ReplacedElement` 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.
`ListOfReplacedElements`	`getListOfReplacedElements()` Returns the `ListOf` object that holds all replacedElements.
`long`	`getNumReplacedElements()` Returns the number of ReplacedElements for this `CompSBasePlugin`.
`ReplacedBy`	`getReplacedBy()` Get the child `ReplacedBy` of this `SBase`.
`ReplacedElement`	`getReplacedElement(long n)` Returns the `ReplacedElement` with the given index.
`boolean`	`isSetReplacedBy()` Predicate for testing whether the `ReplacedBy` for this `SBase` is set.
`void`	`logInvalidId(java.lang.String attribute, java.lang.String wrongattribute)` Helper to log a common type of error.
`ReplacedElement`	`removeReplacedElement(long index)` Removes the `ReplacedElement` with the given index.
`int`	`setReplacedBy(ReplacedBy replacedBy)` Sets the `ReplacedBy` definition of this `SBase` to a copy of the given `ReplacedBy` object instance.
`int`	`unsetReplacedBy()` Unsets the child `ReplacedBy` of this `SBase`.

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
  - CompSBasePlugin
```
public CompSBasePlugin(java.lang.String uri,
                       java.lang.String prefix,
                       CompPkgNamespaces compns)
```
    Constructor.
  - CompSBasePlugin
```
public CompSBasePlugin(CompSBasePlugin orig)
```
    Copy constructor. Creates a copy of this CompSBasePlugin 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 CompSBasePlugin.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 CompSBasePlugin.delete() themselves.
    
    Overrides:
    
    delete in class SBasePlugin
  - cloneObject
```
public SBasePlugin cloneObject()
```
    Creates and returns a deep copy of this CompSBasePlugin object.
    
    Overrides:
    
    cloneObject in class SBasePlugin
    
    Returns:
    
    a (deep) copy of this CompSBasePlugin 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 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 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 metaid of objects to find
    
    Returns:
    
    a pointer to the SBase element with the given metaid.
  - getListOfReplacedElements
```
public ListOfReplacedElements getListOfReplacedElements()
```
    Returns the ListOf object that holds all replacedElements.
    
    Returns:
    
    the ListOf object that holds all replacedElements.
  - getReplacedElement
```
public ReplacedElement getReplacedElement(long n)
```
    Returns the ReplacedElement with the given index.
    
    Parameters:
    
    n - the index number of the ReplacedElement to get.
    
    Returns:
    
    the nth ReplacedElement in the ListOfReplacedElements. If the index is invalid, null is returned.
  - addReplacedElement
```
public int addReplacedElement(ReplacedElement replacedElement)
```
    Adds a copy of the given ReplacedElement object to the list of ReplacedElements.
    Parameters:
    
    replacedElement - the ReplacedElement object to be added to the list of ReplacedElements. Fails if the added ReplacedElement 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
  - getNumReplacedElements
```
public long getNumReplacedElements()
```
    Returns the number of ReplacedElements for this CompSBasePlugin.
    
    Returns:
    
    the number of ReplacedElements for this CompSBasePlugin.
  - clearReplacedElements
```
public void clearReplacedElements()
```
    Remove all ReplacedElements, if any exist.
  - createReplacedElement
```
public ReplacedElement createReplacedElement()
```
    Creates a ReplacedElement object, adds it to the end of the ReplacedElement objects list and returns a pointer to the newly created object.
    
    Returns:
    
    a newly created ReplacedElement object
  - removeReplacedElement
```
public ReplacedElement removeReplacedElement(long index)
```
    Removes the ReplacedElement with the given index.
    A pointer to the ReplacedElement that was removed is returned. If no ReplacedElement has been removed, null is returned.
    
    Parameters:
    
    index - the index of the ReplacedElement object to remove
    
    Returns:
    
    the ReplacedElement object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
  - getReplacedBy
```
public ReplacedBy getReplacedBy()
```
    Get the child ReplacedBy of this SBase.
    
    Returns:
    
    the ReplacedBy child of this SBase
  - isSetReplacedBy
```
public boolean isSetReplacedBy()
```
    Predicate for testing whether the ReplacedBy for this SBase is set.
    
    Returns:
    
    true if the ReplacedBy of this SBase is set, false otherwise.
  - setReplacedBy
```
public int setReplacedBy(ReplacedBy replacedBy)
```
    Sets the ReplacedBy definition of this SBase to a copy of the given ReplacedBy object instance.
    This method fails if the added ReplacedBy does not match the level/version/package of the parent object or if the added ReplacedBy cannot be copied.
    Parameters:
    
    replacedBy - the ReplacedBy object instance to use.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
  - createReplacedBy
```
public ReplacedBy createReplacedBy()
```
    Creates a new, empty ReplacedBy, adds it to this CompSBasePlugin and returns the created ReplacedBy.
    
    Returns:
    
    the newly created ReplacedBy object instance
  - unsetReplacedBy
```
public int unsetReplacedBy()
```
    Unsets the child ReplacedBy of this SBase.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - logInvalidId
```
public void logInvalidId(java.lang.String attribute,
                         java.lang.String wrongattribute)
```
    Helper to log a common type of error.

Class CompSBasePlugin

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBasePlugin

Methods inherited from class java.lang.Object

Constructor Detail

CompSBasePlugin

CompSBasePlugin

Method Detail

delete

cloneObject

getElementBySId

getElementByMetaId

getListOfReplacedElements

getReplacedElement

addReplacedElement

getNumReplacedElements

clearReplacedElements

createReplacedElement

removeReplacedElement

getReplacedBy

isSetReplacedBy

setReplacedBy

createReplacedBy

unsetReplacedBy

logInvalidId