A B C D E F G H I L M N O P R S U V W

A

addDynElement(DynElement) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Adds a new DynElement to the listOfDynElements.

addSpatialComponent(SpatialComponent) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Adds a new SpatialComponent to the ListOfSpatialComponents.

alpha - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to elemental rotation of an object about the X coordinate axis

applyToAll - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

B

beta - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to elemental rotation of an object about the Y coordinate axis

bundle - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

C

cartesianX - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to the X coordinate component of an object's position within a Cartesian coordinate system

cartesianY - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to the Y coordinate component of an object's position within a Cartesian coordinate system

cartesianZ - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to the Z coordinate component of an object's position within a Cartesian coordinate system

CBO - Class in org.sbml.jsbml.ext.dyn

Methods for interacting with Cell Behavior Ontology (CBO) terms.

CBO() - Constructor for class org.sbml.jsbml.ext.dyn.CBO

cboTerm - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

checkTerm(String) - Static method in class org.sbml.jsbml.ext.dyn.CBO

Checks the format of the given CBO string.

clone() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

clone() - Method in class org.sbml.jsbml.ext.dyn.DynElement

clone() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

clone() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

clone() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

createDynElement() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Creates a new DynElement element and adds it to the listOfDynElements list

createDynElement(String) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Creates a new DynElement element and adds it to the DynEventPlugin.getListOfDynElements().

createListOfChild(ListOf<?>, String) - Method in class org.sbml.jsbml.xml.parsers.DynParser

createPluginFor(ASTNode) - Method in class org.sbml.jsbml.xml.parsers.DynParser

createPluginFor(SBase) - Method in class org.sbml.jsbml.xml.parsers.DynParser

createSpatialComponent() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Creates a new SpatialComponent element and adds it to the listOfSpatialComponents list

createSpatialComponent(String) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Creates a new SpatialComponent element and adds it to the DynCompartmentPlugin.getListOfSpatialComponents()

D

DynCompartmentPlugin - Class in org.sbml.jsbml.ext.dyn

DynCompartmentPlugin() - Constructor for class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Empty constructor

DynCompartmentPlugin(Compartment) - Constructor for class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Constructor

DynCompartmentPlugin(DynCompartmentPlugin) - Constructor for class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Constructor

DynConstants - Class in org.sbml.jsbml.ext.dyn

Contains some constants related to the Dynamic Structures package.

DynConstants() - Constructor for class org.sbml.jsbml.ext.dyn.DynConstants

dynElement - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

DynElement - Class in org.sbml.jsbml.ext.dyn

DynElement() - Constructor for class org.sbml.jsbml.ext.dyn.DynElement

Empty constructor

DynElement(int, int) - Constructor for class org.sbml.jsbml.ext.dyn.DynElement

Constructor

DynElement(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.dyn.DynElement

Constructor

DynElement(DynElement) - Constructor for class org.sbml.jsbml.ext.dyn.DynElement

Constructor

DynEventPlugin - Class in org.sbml.jsbml.ext.dyn

DynEventPlugin() - Constructor for class org.sbml.jsbml.ext.dyn.DynEventPlugin

Empty constructor

DynEventPlugin(Event) - Constructor for class org.sbml.jsbml.ext.dyn.DynEventPlugin

Constructor

DynEventPlugin(DynEventPlugin) - Constructor for class org.sbml.jsbml.ext.dyn.DynEventPlugin

Constructor

DynParser - Class in org.sbml.jsbml.xml.parsers

This class is used to parse the dynamic structures extension package elements and attributes.

DynParser() - Constructor for class org.sbml.jsbml.xml.parsers.DynParser

DynSBasePlugin - Class in org.sbml.jsbml.ext.dyn

DynSBasePlugin() - Constructor for class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Empty constructor

DynSBasePlugin(DynSBasePlugin) - Constructor for class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Constructor

DynSBasePlugin(SBase) - Constructor for class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Constructor

E

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynElement

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

equals(Object) - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

F

F_x - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to the X component of the force vector that drives movement

F_y - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to the Y component of the force vector that drives movement

F_z - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to the Z component of the force vector that drives movement

G

gamma - org.sbml.jsbml.ext.dyn.SpatialKind

Refers to elemental rotation of an object about the Z coordinate axis

getAllowsChildren() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

getAllowsChildren() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getApplyToAll() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Returns the value of applyToAll

getCBOTerm() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Returns the value of CBO

getChildAt(int) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

getChildAt(int) - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getChildCount() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

getChildCount() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Returns the value of idRef

getListOfDynElements() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Returns the value of listOfDynElements

getListOfSBMLElementsToWrite(Object) - Method in class org.sbml.jsbml.xml.parsers.DynParser

getListOfSpatialComponents() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Returns the value of listOfSpatialComponents

getMetaIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Returns the value of metaIdRef

getNamespaceFor(int, int, int) - Method in class org.sbml.jsbml.xml.parsers.DynParser

getNamespaces() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getNamespaceURI() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getNamespaceURI(int, int) - Static method in class org.sbml.jsbml.ext.dyn.DynConstants

getOntology() - Static method in class org.sbml.jsbml.ext.dyn.CBO

Grants access to the underlying Ontology form BioJava.

getPackageName() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getPackageName() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getPackageNamespaces() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getParent() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getParentSBMLObject() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getPrefix() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getShortLabel() - Method in class org.sbml.jsbml.xml.parsers.DynParser

getSpatialIndex() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Returns the value of spatialIndex

getTerm(String) - Static method in class org.sbml.jsbml.ext.dyn.CBO

Gets the CBO term with the id 'cboTerm'.

getTerms() - Static method in class org.sbml.jsbml.ext.dyn.CBO

Return the set of terms of the CBO.

getTriples(Term, Term, Term) - Static method in class org.sbml.jsbml.ext.dyn.CBO

Returns a set of Triple which match the supplied subject, predicate and object.

getURI() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

getVariable() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Returns the value of variable

H

hashCode() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

hashCode() - Method in class org.sbml.jsbml.ext.dyn.DynElement

hashCode() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

hashCode() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

hashCode() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

I

idRef - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

initDefaults() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Initializes custom Class attributes

initDefaults() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

initDefaults() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Initializes custom Class attributes

isApplyToAll() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

isIdMandatory() - Method in class org.sbml.jsbml.ext.dyn.DynElement

isIdMandatory() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

isRequired() - Method in class org.sbml.jsbml.xml.parsers.DynParser

isSetApplyToAll() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Returns whether applyToAll is set

isSetCBOTerm() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Returns whether CBO is set

isSetIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Returns whether idRef is set

isSetListOfDynElements() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Returns whether listOfDynElements is set

isSetListOfSpatialComponents() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Returns whether listOfSpatialComponents is set

isSetMetaIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Returns whether metaIdRef is set

isSetSpatialIndex() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Returns whether spatialIndex is set

isSetVariable() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Returns whether variable is set

L

listOfDynElements - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

listOfDynElements - Variable in class org.sbml.jsbml.ext.dyn.DynEventPlugin

List of model components affected by the dynEvent

listOfSpatialComponents - Variable in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

List of spatial components which describe compartment in space

listOfSpatialComponents - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

M

main(String[]) - Static method in class org.sbml.jsbml.ext.dyn.CBO

Test main class

metaIdRef - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

MIN_SBML_LEVEL - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

MIN_SBML_VERSION - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

N

namespaces - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

namespaceURI - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

The latest namespace URI of this parser, this value can change between releases.

namespaceURI_L3V1V1 - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

The namespace URI of this parser for SBML level 3, version 1 and package version 1.

O

org.sbml.jsbml.ext.dyn - package org.sbml.jsbml.ext.dyn

Provides classes for the Dynamic Structures package.

org.sbml.jsbml.xml.parsers - package org.sbml.jsbml.xml.parsers

P

PACKAGE_VERSION - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

packageName - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

processAttribute(String, String, String, String, String, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DynParser

processStartElement(String, String, String, boolean, boolean, Object) - Method in class org.sbml.jsbml.xml.parsers.DynParser

R

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.dyn.DynElement

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

readAttribute(String, String, String) - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

removeDynElement(int) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Removes the ith element from the listOfDynElements

removeDynElement(DynElement) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Removes an element from the listOfDynElements

removeSpatialComponent(int) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Removes the ith element from the ListOfSpatialComponents

removeSpatialComponent(SpatialComponent) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Removes an element from the ListOfSpatialComponents

S

setApplyToAll(boolean) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Sets the value of applyToAll

setCBOTerm(Term) - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Sets the value of CBO

setIdRef(String) - Method in class org.sbml.jsbml.ext.dyn.DynElement

Sets the value of idRef

setListOfDynElements(ListOf<DynElement>) - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Sets the value of listOfDynElements

setListOfSpatialComponents(ListOf<SpatialComponent>) - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Sets the value of listOfSpatialComponents

setMetaIdRef(String) - Method in class org.sbml.jsbml.ext.dyn.DynElement

Sets the value of metaIdRef

setSpatialIndex(SpatialKind) - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Sets the value of spatialIndex

setVariable(String) - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Sets the value of SpatialComponent.variable

shortLabel - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

spatialComponent - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

SpatialComponent - Class in org.sbml.jsbml.ext.dyn

SpatialComponent() - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent

Empty constructor

SpatialComponent(int, int) - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent

Constructor

SpatialComponent(String, String, int, int) - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent

Constructor

SpatialComponent(SpatialComponent) - Constructor for class org.sbml.jsbml.ext.dyn.SpatialComponent

Constructor

spatialIndex - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

SpatialKind - Enum in org.sbml.jsbml.ext.dyn

This is a collection of possible values for the spatialIndex attribute within a SpatialComponent.

U

unsetApplyToAll() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Unsets the applyToAll field

unsetCBOTerm() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

Unsets the cboTerm field

unsetField() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Unsets the variable field

unsetIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Unsets the variable idRef

unsetListOfDynElements() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

Unsets the variable listOfDynElements

unsetListOfSpatialComponents() - Method in class org.sbml.jsbml.ext.dyn.DynCompartmentPlugin

Unsets the variable listOfSpatialComponents

unsetMetaIdRef() - Method in class org.sbml.jsbml.ext.dyn.DynElement

Unsets the variable metaIdRef

unsetSpatialIndex() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

Unsets the variable spatialIndex

V

valueOf(String) - Static method in enum org.sbml.jsbml.ext.dyn.SpatialKind

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.sbml.jsbml.ext.dyn.SpatialKind

Returns an array containing the constants of this enum type, in the order they are declared.

variable - Static variable in class org.sbml.jsbml.ext.dyn.DynConstants

W

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.dyn.DynElement

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.dyn.DynEventPlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.dyn.DynSBasePlugin

writeXMLAttributes() - Method in class org.sbml.jsbml.ext.dyn.SpatialComponent

A B C D E F G H I L M N O P R S U V W