ListOfPorts (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.ListOf
  - - org.sbml.libsbml.ListOfPorts

```
public class ListOfPorts
extends ListOf
```
comp A list of Port objects.
The ListOfPorts is a container for the extended Model for Port objects for that Model.

The various ListOf___ classes in SBML are merely containers used for organizing the main components of an SBML model. In libSBML's implementation, ListOf___ classes are derived from the intermediate utility class ListOf, which is not defined by the SBML specifications but serves as a useful programmatic construct. ListOf is itself is in turn derived from SBase, which provides all of the various ListOf___ classes with common features defined by the SBML specification, such as 'metaid' attributes and annotations.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):

Readers may wonder about the motivations for using the ListOf___ containers in SBML. A simpler approach in XML might be to place the components all directly at the top level of the model definition. The choice made in SBML is to group them within XML elements named after ListOfClassname, in part because it helps organize the components. More importantly, the fact that the container classes are derived from SBase means that software tools can add information about the lists themselves into each list container's 'annotation'.

See Also:

ListOfFunctionDefinitions, ListOfUnitDefinitions, ListOfCompartmentTypes, ListOfSpeciesTypes, ListOfCompartments, ListOfSpecies, ListOfParameters, ListOfInitialAssignments, ListOfRules, ListOfConstraints, ListOfReactions,
, Port, ListOfDeletions, ListOfExternalModelDefinitions, ListOfModelDefinitions, ListOfReplacedElements, ListOfSubmodels

Constructor Summary

Constructors
Constructor and Description
`ListOfPorts()` Creates a new `ListOfPorts` with the given level, version, and package version.
`ListOfPorts(CompPkgNamespaces compns)` Creates a new `ListOfPorts` with the given `CompPkgNamespaces` object.
`ListOfPorts(long level)` Creates a new `ListOfPorts` with the given level, version, and package version.
`ListOfPorts(long level, long version)` Creates a new `ListOfPorts` with the given level, version, and package version.
`ListOfPorts(long level, long version, long pkgVersion)` Creates a new `ListOfPorts` with the given level, version, and package version.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ListOfPorts`	`cloneObject()` Creates and returns a deep copy of this `ListOfPorts` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`SBase`	`get(long n)` Get a `Port` from the `ListOfPorts`.
`Port`	`get(java.lang.String sid)` Get a `Port` from the `ListOfPorts` based on its identifier.
`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 element name of this SBML object.
`int`	`getItemTypeCode()` Returns the libSBML type code for the objects contained in this `ListOf` (i.e., `Port` objects, if the list is non-empty).
`SBase`	`remove(long n)` Removes the nth item from this `ListOfPorts` items and returns a pointer to it.
`Port`	`remove(java.lang.String sid)` Removes an item from this `ListOfPorts` items based on the identifier and returns a pointer to it.

Methods inherited from class org.sbml.libsbml.ListOf
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, size

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - ListOfPorts
```
public ListOfPorts(long level,
                   long version,
                   long pkgVersion)
            throws SBMLConstructorException
```
    Creates a new ListOfPorts with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ListOfPorts
```
public ListOfPorts(long level,
                   long version)
            throws SBMLConstructorException
```
    Creates a new ListOfPorts with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ListOfPorts
```
public ListOfPorts(long level)
            throws SBMLConstructorException
```
    Creates a new ListOfPorts with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ListOfPorts
```
public ListOfPorts()
            throws SBMLConstructorException
```
    Creates a new ListOfPorts with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ListOfPorts
```
public ListOfPorts(CompPkgNamespaces compns)
            throws SBMLConstructorException
```
    Creates a new ListOfPorts with the given CompPkgNamespaces object.
    
    Parameters:
    
    compns - the namespace to use
    
    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 ListOfPorts.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 ListOfPorts.delete() themselves.
    
    Overrides:
    
    delete in class ListOf
  - cloneObject
```
public ListOfPorts cloneObject()
```
    Creates and returns a deep copy of this ListOfPorts object.
    
    Overrides:
    
    cloneObject in class ListOf
    
    Returns:
    
    a (deep) copy of this ListOfPorts.
  - get
```
public SBase get(long n)
```
    Get a Port from the ListOfPorts.
    
    Overrides:
    
    get in class ListOf
    
    Parameters:
    
    n - the index number of the Port to get.
    
    Returns:
    
    the nth Port in this ListOfPorts.
    
    See Also:
    
    ListOf.size()
  - get
```
public Port get(java.lang.String sid)
```
    Get a Port from the ListOfPorts based on its identifier.
    
    Parameters:
    
    sid - a string representing the identifier of the Port to get.
    
    Returns:
    
    Port in this ListOfPorts with the given sid or null if no such Member exists.
    
    See Also:
    
    ListOfPorts.get(long n), ListOf.size()
  - remove
```
public Port remove(java.lang.String sid)
```
    Removes an item from this ListOfPorts items based on the identifier and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Parameters:
    
    sid - string representing the id of the Port to remove
    
    See Also:
    
    ListOf.size()
  - remove
```
public SBase remove(long n)
```
    Removes the nth item from this ListOfPorts items and returns a pointer to it.
    The caller owns the returned item and is responsible for deleting it.
    
    Overrides:
    
    remove in class ListOf
    
    Parameters:
    
    n - the index of the item to remove
    
    See Also:
    
    ListOf.size()
  - getItemTypeCode
```
public int getItemTypeCode()
```
    Returns the libSBML type code for the objects contained in this ListOf (i.e., Port objects, if the list is non-empty).
    
    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 getPackageName() method on the object.
    
    Overrides:
    
    getItemTypeCode in class ListOf
    
    Returns:
    
    the SBML type code for objects contained in this list: SBML_COMP_PORT (default).
    
    See Also:
    
    ListOfPorts.getElementName(), SBase.getPackageName()
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this SBML object.
    
    Overrides:
    
    getElementName in class ListOf
    
    Returns:
    
    the name of this element, as a text string.
  - 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. Since the id of Port objects are in the PortSId namespace, no Port object is returned by this function.
    
    Overrides:
    
    getElementBySId in class ListOf
    
    Parameters:
    
    id - string representing the id of objects to find
    
    Returns:
    
    a pointer to the SBase element with the given id.

Class ListOfPorts

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.ListOf

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

ListOfPorts

ListOfPorts

ListOfPorts

ListOfPorts

ListOfPorts

Method Detail

delete

cloneObject

get

get

remove

remove

getItemTypeCode

getElementName

getElementBySId