org.sbml.libsbml

Class ListOfGradientStops

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.ListOf

org.sbml.libsbml.ListOfGradientStops

public class ListOfGradientStops
extends ListOf

render A list of one or more GradientStop objects.

The ListOfGradientStops is used in linear and radial gradient objects to store the GradientStop objects that define the gradient. A valid gradient should have two or more gradient stops.

The ListOfGradientStops is a container for the GradientStop elements of a GradientBase object.

Note that the ListOfGradientStops class is only defined in libsbml for convenience: GradientStop objects are actually direct children of GradientBase-derived objects (i.e., LinearGradient or RadialGradient 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,

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

, GradientStop, GradientBase, LinearGradient, RadialGradient

Constructor Summary

Constructors

Constructor and Description
ListOfGradientStops() Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.
ListOfGradientStops(ListOfGradientStops orig) Copy constructor for ListOfGradientStops.
ListOfGradientStops(long level) Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.
ListOfGradientStops(long level, long version) Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.
ListOfGradientStops(long level, long version, long pkgVersion) Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.
ListOfGradientStops(RenderPkgNamespaces renderns) Creates a new ListOfGradientStops using the given RenderPkgNamespaces object.
ListOfGradientStops(XMLNode node) Creates a new ListOfGradientStops object from the given XMLNode object.
ListOfGradientStops(XMLNode node, long l2version) Creates a new ListOfGradientStops object from the given XMLNode object.

Method Summary

Modifier and Type	Method and Description
int	addGradientStop(GradientStop gs) Adds a copy of the given GradientStop to this ListOfGradientStops.
ListOfGradientStops	cloneObject() Creates and returns a deep copy of this ListOfGradientStops object.
GradientStop	createGradientStop() Creates a new GradientStop object, adds it to this ListOfGradientStops object and returns the GradientStop object created.
void	delete() Explicitly deletes the underlying native object.
SBase	get(long n) Get a GradientStop from the ListOfGradientStops.
GradientStop	get(java.lang.String sid) Get a GradientStop from the ListOfGradientStops based on its identifier.
java.lang.String	getElementName() Returns the XML element name of this ListOfGradientStops object.
int	getItemTypeCode() Returns the libSBML type code for the SBML objects contained in this ListOfGradientStops object.
long	getNumGradientStops() Get the number of GradientStop objects in this ListOfGradientStops.
int	getTypeCode() Returns the libSBML type code for this ListOfGradientStops object.
SBase	remove(long n) Removes the nth GradientStop from this ListOfGradientStops and returns a pointer to it.
GradientStop	remove(java.lang.String sid) Removes the GradientStop from this ListOfGradientStops based on its identifier and returns a pointer to it.
XMLNode	toXML() Creates an XMLNode object from this ListOfGradientStops object.

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

ListOfGradientStops

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

Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.

Parameters:

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

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

pkgVersion - a long integer, the SBML Render Version to assign to this ListOfGradientStops.

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.

ListOfGradientStops

public ListOfGradientStops(long level,
                           long version)
                    throws SBMLConstructorException

Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.

Parameters:

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

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

pkgVersion - a long integer, the SBML Render Version to assign to this ListOfGradientStops.

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.

ListOfGradientStops

public ListOfGradientStops(long level)
                    throws SBMLConstructorException

Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.

Parameters:

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

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

pkgVersion - a long integer, the SBML Render Version to assign to this ListOfGradientStops.

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.

ListOfGradientStops

public ListOfGradientStops()
                    throws SBMLConstructorException

Creates a new ListOfGradientStops using the given SBML Level, Version and “render” package version.

Parameters:

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

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

pkgVersion - a long integer, the SBML Render Version to assign to this ListOfGradientStops.

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.

ListOfGradientStops

public ListOfGradientStops(RenderPkgNamespaces renderns)
                    throws SBMLConstructorException

Creates a new ListOfGradientStops using the given RenderPkgNamespaces 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:

renderns - the RenderPkgNamespaces 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.

ListOfGradientStops

public ListOfGradientStops(XMLNode node,
                           long l2version)
                    throws SBMLConstructorException

Creates a new ListOfGradientStops object from the given XMLNode object. The XMLNode object has to contain a valid XML representation of a ListOfGradientStops object as defined in the render extension specification. This method is normally called when render information is read from a file and should normally not have to be called explicitly.

Parameters:

node - the XMLNode object reference that describes the ListOfGradientStops object to be instantiated.

l2version - an integer indicating the version of SBML Level 2

Throws:

SBMLConstructorException

ListOfGradientStops

public ListOfGradientStops(XMLNode node)
                    throws SBMLConstructorException

Creates a new ListOfGradientStops object from the given XMLNode object. The XMLNode object has to contain a valid XML representation of a ListOfGradientStops object as defined in the render extension specification. This method is normally called when render information is read from a file and should normally not have to be called explicitly.

Parameters:

node - the XMLNode object reference that describes the ListOfGradientStops object to be instantiated.

l2version - an integer indicating the version of SBML Level 2

Throws:

SBMLConstructorException

ListOfGradientStops

public ListOfGradientStops(ListOfGradientStops orig)
                    throws SBMLConstructorException

Copy constructor for ListOfGradientStops.

Parameters:

orig - the ListOfGradientStops instance to copy.

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 ListOfGradientStops.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 ListOfGradientStops.delete() themselves.

Overrides:

delete in class ListOf

cloneObject

public ListOfGradientStops cloneObject()

Creates and returns a deep copy of this ListOfGradientStops object.

Overrides:

cloneObject in class ListOf

Returns:

a (deep) copy of this ListOfGradientStops object.

get

public SBase get(long n)

Get a GradientStop from the ListOfGradientStops.

Overrides:

get in class ListOf

Parameters:

n - a long integer representing the index of the GradientStop to retrieve.

Returns:

the nth GradientStop in this ListOfGradientStops. If the index n is invalid, null is returned.

See Also:

ListOfGradientStops.addGradientStop(GradientStop object), ListOfGradientStops.createGradientStop(), ListOfGradientStops.get(String sid), ListOfGradientStops.getNumGradientStops(), ListOfGradientStops.remove(String sid), ListOfGradientStops.remove(long n)

Note:

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

get

public GradientStop get(java.lang.String sid)

Get a GradientStop from the ListOfGradientStops based on its identifier.

Parameters:

sid - a string representing the identifier of the GradientStop to retrieve.

Returns:

the GradientStop in this ListOfGradientStops with the given sid or null if no such GradientStop exists.

See Also:

ListOfGradientStops.addGradientStop(GradientStop object), ListOfGradientStops.createGradientStop(), ListOfGradientStops.get(long n), ListOfGradientStops.getNumGradientStops(), ListOfGradientStops.remove(String sid), ListOfGradientStops.remove(long n)

Note:

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

remove

public SBase remove(long n)

Removes the nth GradientStop from this ListOfGradientStops and returns a pointer to it.

Overrides:

remove in class ListOf

Parameters:

n - a long integer representing the index of the GradientStop to remove.

Returns:

a pointer to the nth GradientStop in this ListOfGradientStops.

See Also:

ListOfGradientStops.addGradientStop(GradientStop object), ListOfGradientStops.createGradientStop(), ListOfGradientStops.get(String sid), ListOfGradientStops.get(long n), ListOfGradientStops.getNumGradientStops(), ListOfGradientStops.remove(String sid)

Warning:

The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the 'disownedItem' in the * ListOf#appendAndOwn() or ListOf#insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

remove

public GradientStop remove(java.lang.String sid)

Removes the GradientStop from this ListOfGradientStops based on its identifier and returns a pointer to it.

Parameters:

sid - a string representing the identifier of the GradientStop to remove.

Returns:

the GradientStop in this ListOfGradientStops based on the identifier or null if no such GradientStop exists.

See Also:

ListOfGradientStops.addGradientStop(GradientStop object), ListOfGradientStops.createGradientStop(), ListOfGradientStops.get(String sid), ListOfGradientStops.get(long n), ListOfGradientStops.getNumGradientStops(), ListOfGradientStops.remove(long n)

Warning:

The pointer that is returned by this function is owned by the caller, who is responsible for deleting it. Any changes made to the element will not be reflected in any resulting SBML document unless the element is added to an SBML Document. Even in this case, the element's deletion is still the responsibility of the caller with two exceptions: if it is used as the 'disownedItem' in the * ListOf#appendAndOwn() or ListOf#insertAndOwn() functions. All other functions in libsbml add a copy of the element, and do not transfer ownership of the pointer.

addGradientStop

public int addGradientStop(GradientStop gs)

Adds a copy of the given GradientStop to this ListOfGradientStops.

Parameters:

gs - the GradientStop object to add.

Returns:

integer value indicating success/failure of the function. The possible values returned by this function are:

• LIBSBML_OPERATION_SUCCESS
• LIBSBML_OPERATION_FAILED
• LIBSBML_INVALID_OBJECT
• LIBSBML_LEVEL_MISMATCH
• LIBSBML_VERSION_MISMATCH
• LIBSBML_PKG_VERSION_MISMATCH
• LIBSBML_DUPLICATE_OBJECT_ID

See Also:

ListOfGradientStops.createGradientStop(), ListOfGradientStops.get(String sid), ListOfGradientStops.get(long n), ListOfGradientStops.getNumGradientStops(), ListOfGradientStops.remove(String sid), ListOfGradientStops.remove(long n)

Note:

This method should be used with some caution. The fact that this method copies the object passed to it means that the caller will be left holding a physically different object instance than the one contained inside this object. Changes made to the original object instance (such as resetting attribute values) will not affect the instance in this object. In addition, the caller should make sure to free the original object if it is no longer being used, or else a memory leak will result. Please see other methods on this class (particularly a corresponding method whose name begins with the word create) for alternatives that do not lead to these issues.

getNumGradientStops

public long getNumGradientStops()

Get the number of GradientStop objects in this ListOfGradientStops.

Returns:

the number of GradientStop objects in this ListOfGradientStops.

See Also:

ListOfGradientStops.addGradientStop(GradientStop object), ListOfGradientStops.createGradientStop(), ListOfGradientStops.get(String sid), ListOfGradientStops.get(long n), ListOfGradientStops.remove(String sid), ListOfGradientStops.remove(long n)

createGradientStop

public GradientStop createGradientStop()

Creates a new GradientStop object, adds it to this ListOfGradientStops object and returns the GradientStop object created.

Returns:

a new GradientStop object instance.

See Also:

ListOfGradientStops.addGradientStop(GradientStop object), ListOfGradientStops.get(String sid), ListOfGradientStops.get(long n), ListOfGradientStops.getNumGradientStops(), ListOfGradientStops.remove(String sid), ListOfGradientStops.remove(long n)

Note:

The pointer that is returned by this function is not owned by the caller, but may be queried and modified. Any changes made will be reflected in any resulting SBML document containing the pointer's parent.

getElementName

public java.lang.String getElementName()

Returns the XML element name of this ListOfGradientStops object.

For ListOfGradientStops, the XML element name is always 'listOfGradientStops'.

Overrides:

getElementName in class ListOf

Returns:

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

getTypeCode

public int getTypeCode()

Returns the libSBML type code for this ListOfGradientStops object.

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:

getTypeCode in class ListOf

Returns:

the SBML type code for this object: SBML_LIST_OF.

See Also:

ListOf.getItemTypeCode(), ListOf.getElementName(), SBase.getPackageName()

Warning:

The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf.getItemTypeCode()).

getItemTypeCode

public int getItemTypeCode()

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

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 typecode for the objects contained in this ListOfGradientStops: SBML_RENDER_GRADIENT_STOP.

See Also:

ListOfGradientStops.getElementName(), SBase.getPackageName()

Warning:

The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf.getItemTypeCode()).

toXML

public XMLNode toXML()

Creates an XMLNode object from this ListOfGradientStops object.

Returns:

the XMLNode with the XML representation for the ListOfGradientStops object.