org.sbml.libsbml

Class ListOfReplacedElements

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.ListOf

org.sbml.libsbml.ListOfReplacedElements

public class ListOfReplacedElements
extends ListOf

comp A list of ReplacedElement objects.

The ListOfReplacedElements is a container for any SBase object. It contains ReplacedElement objects, which point to elements the parent SBase object is to replace.

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):

SBML Level 3 Version 1 has essentially the same structure as Level 2 Version 4, depicted above, but SBML Level 3 Version 2 allows containers to contain zero or more of the relevant object, instead of requiring at least one. As such, libsbml will write out an otherwise-empty ListOf___ element that has any optional attribute set (such as 'id' or 'metaid'), that has an optional child (such as a 'notes' or 'annotation'), or that has attributes or children set from any SBML Level 3 package, whether or not the ListOf___ has any other children.

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,

, ReplacedElement, ListOfDeletions, ListOfExternalModelDefinitions, ListOfModelDefinitions, ListOfPorts, ListOfSubmodels

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
ListOfReplacedElements	cloneObject() Creates and returns a deep copy of this ListOfReplacedElements object.
void	delete() Explicitly deletes the underlying native object.
SBase	get(long n) Get a ReplacedElement from the ListOfReplacedElements.
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., ReplacedElements objects, if the list is non-empty).
SBase	remove(long n) Removes the nth item from this ListOfReplacedElements items and returns a pointer to it.

Methods inherited from class org.sbml.libsbml.ListOf

append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, 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, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, 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, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ListOfReplacedElements

public ListOfReplacedElements(long level,
                              long version,
                              long pkgVersion)
                       throws SBMLConstructorException

Creates a new ListOfReplacedElements 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

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.

ListOfReplacedElements

public ListOfReplacedElements(long level,
                              long version)
                       throws SBMLConstructorException

Creates a new ListOfReplacedElements 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

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.

ListOfReplacedElements

public ListOfReplacedElements(long level)
                       throws SBMLConstructorException

Creates a new ListOfReplacedElements 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

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.

ListOfReplacedElements

public ListOfReplacedElements()
                       throws SBMLConstructorException

Creates a new ListOfReplacedElements 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

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.

ListOfReplacedElements

public ListOfReplacedElements(CompPkgNamespaces compns)
                       throws SBMLConstructorException

Creates a new ListOfReplacedElements with the given CompPkgNamespaces 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:

compns - the CompPkgNamespaces 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.

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 ListOfReplacedElements.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 ListOfReplacedElements.delete() themselves.

Overrides:

delete in class ListOf

cloneObject

public ListOfReplacedElements cloneObject()

Creates and returns a deep copy of this ListOfReplacedElements object.

Overrides:

cloneObject in class ListOf

Returns:

a (deep) copy of this ListOfReplacedElements.

get

public SBase get(long n)

Get a ReplacedElement from the ListOfReplacedElements.

Overrides:

get in class ListOf

Parameters:

n - the index number of the ReplacedElement to get.

Returns:

the nth ReplacedElement in this ListOfReplacedElements. If the index n is invalid, null is returned.

See Also:

ListOf.size()

remove

public SBase remove(long n)

Removes the nth item from this ListOfReplacedElements 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., ReplacedElements 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 SBase.getPackageName() method on the object.

The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.

Overrides:

getItemTypeCode in class ListOf

Returns:

the SBML type code for objects contained in this list: SBML_COMP_REPLACEDELEMENT (default).

See Also:

ListOfReplacedElements.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.