org.sbml.libsbml

Class ListOfOutwardBindingSites

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.ListOf

org.sbml.libsbml.ListOfOutwardBindingSites

public class ListOfOutwardBindingSites
extends ListOf

multi A list of OutwardBindingSite objects.

The ListOfOutwardBindingSites is a container for OutwardBindingSite objects.

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,

, OutwardBindingSite

Constructor Summary

Constructors

Constructor and Description
ListOfOutwardBindingSites() Creates a new ListOfOutwardBindingSites with the given level, version, and package version.
ListOfOutwardBindingSites(long level) Creates a new ListOfOutwardBindingSites with the given level, version, and package version.
ListOfOutwardBindingSites(long level, long version) Creates a new ListOfOutwardBindingSites with the given level, version, and package version.
ListOfOutwardBindingSites(long level, long version, long pkgVersion) Creates a new ListOfOutwardBindingSites with the given level, version, and package version.
ListOfOutwardBindingSites(MultiPkgNamespaces multins) Creates a new ListOfOutwardBindingSites with the given MultiPkgNamespaces object.

Method Summary

Modifier and Type	Method and Description
ListOfOutwardBindingSites	cloneObject() Creates and returns a deep copy of this ListOfOutwardBindingSites object.
void	delete() Explicitly deletes the underlying native object.
OutwardBindingSite	get(long n) Get a OutwardBindingSite from the ListOfOutwardBindingSites.
OutwardBindingSite	get(java.lang.String sid) Get a OutwardBindingSite from the ListOfOutwardBindingSites based on its identifier.
java.lang.String	getElementName() Returns the XML element name of this object, which for ListOfOutwardBindingSites, is always 'listOfOutwardBindingSites'.
int	getItemTypeCode() Returns the libSBML type code for the SBML objects contained in this ListOf object
int	getTypeCode() Returns the libSBML type code for this SBML object.
OutwardBindingSite	remove(long n) Removes the nth OutwardBindingSite from this ListOfOutwardBindingSites and returns a pointer to it.
OutwardBindingSite	remove(java.lang.String sid) Removes the OutwardBindingSite from this ListOfOutwardBindingSites with the given identifier and returns a pointer to it.

Methods inherited from class org.sbml.libsbml.ListOf

append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, 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

ListOfOutwardBindingSites

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

Creates a new ListOfOutwardBindingSites with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites

version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites

pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSites

Throws:

SBMLConstructorException

ListOfOutwardBindingSites

public ListOfOutwardBindingSites(long level,
                                 long version)
                          throws SBMLConstructorException

Creates a new ListOfOutwardBindingSites with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites

version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites

pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSites

Throws:

SBMLConstructorException

ListOfOutwardBindingSites

public ListOfOutwardBindingSites(long level)
                          throws SBMLConstructorException

Creates a new ListOfOutwardBindingSites with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites

version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites

pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSites

Throws:

SBMLConstructorException

ListOfOutwardBindingSites

public ListOfOutwardBindingSites()
                          throws SBMLConstructorException

Creates a new ListOfOutwardBindingSites with the given level, version, and package version.

Parameters:

level - a long integer, the SBML Level to assign to this ListOfOutwardBindingSites

version - a long integer, the SBML Version to assign to this ListOfOutwardBindingSites

pkgVersion - a long integer, the SBML Multi Version to assign to this ListOfOutwardBindingSites

Throws:

SBMLConstructorException

ListOfOutwardBindingSites

public ListOfOutwardBindingSites(MultiPkgNamespaces multins)
                          throws SBMLConstructorException

Creates a new ListOfOutwardBindingSites with the given MultiPkgNamespaces 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:

multins - the MultiPkgNamespaces 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 ListOfOutwardBindingSites.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 ListOfOutwardBindingSites.delete() themselves.

Overrides:

delete in class ListOf

cloneObject

public ListOfOutwardBindingSites cloneObject()

Creates and returns a deep copy of this ListOfOutwardBindingSites object.

Overrides:

cloneObject in class ListOf

Returns:

a (deep) copy of this ListOfOutwardBindingSites object.

get

public OutwardBindingSite get(long n)

Get a OutwardBindingSite from the ListOfOutwardBindingSites.

Overrides:

get in class ListOf

Parameters:

n - the index number of the OutwardBindingSite to get.

Returns:

the nth OutwardBindingSite in this ListOfOutwardBindingSites. If the index n is invalid, null is returned.

See Also:

ListOf.size()

get

public OutwardBindingSite get(java.lang.String sid)

Get a OutwardBindingSite from the ListOfOutwardBindingSites based on its identifier.

Parameters:

sid - a string representing the identifier of the OutwardBindingSite to get.

Returns:

OutwardBindingSite in this ListOfOutwardBindingSites with the given id or null if no such OutwardBindingSite exists.

See Also:

*, ListOf.size()

remove

public OutwardBindingSite remove(long n)

Removes the nth OutwardBindingSite from this ListOfOutwardBindingSites 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 OutwardBindingSite to remove.

See Also:

ListOf.size()

remove

public OutwardBindingSite remove(java.lang.String sid)

Removes the OutwardBindingSite from this ListOfOutwardBindingSites with the given identifier and returns a pointer to it.

The caller owns the returned item and is responsible for deleting it. If none of the items in this list have the identifier sid, then null is returned.

Parameters:

sid - the identifier of the OutwardBindingSite to remove.

Returns:

the OutwardBindingSite removed. As mentioned above, the caller owns the returned item.

getElementName

public java.lang.String getElementName()

Returns the XML element name of this object, which for ListOfOutwardBindingSites, is always 'listOfOutwardBindingSites'.

Overrides:

getElementName in class ListOf

Returns:

the name of this element, i.e. 'listOfOutwardBindingSites'.

getTypeCode

public int getTypeCode()

Returns the libSBML type code for this SBML object.

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In other languages, the set of type codes is stored in an enumeration; in the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. The names of the type codes all begin with the characters SBML_.

Overrides:

getTypeCode in class ListOf

Returns:

the SBML type code for this object, or SBML_UNKNOWN (default).

See Also:

ListOfOutwardBindingSites.getElementName()

getItemTypeCode

public int getItemTypeCode()

Returns the libSBML type code for the SBML objects contained in this ListOf object

LibSBML attaches an identifying code to every kind of SBML object. These are known as SBML type codes. In other languages, the set of type codes is stored in an enumeration; in the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. The names of the type codes all begin with the characters SBML_.

Overrides:

getItemTypeCode in class ListOf

Returns:

the SBML type code for the objects in this ListOf instance, or SBML_UNKNOWN (default).

See Also:

ListOfOutwardBindingSites.getElementName()