org.sbml.jsbml.ext.comp

Class Submodel

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.comp.Submodel

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class Submodel
extends AbstractNamedSBase
implements UniqueNamedSBase

Submodels are instantiations of models contained within other models. Submodel instances represent submodels contained within CompModelPlugin.

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
Submodel() Creates an Submodel instance
Submodel(int level, int version) Creates a Submodel instance with a level and version.
Submodel(String id) Creates a Submodel instance with an id.
Submodel(String id, int level, int version) Creates a Submodel instance with an id, level, and version.
Submodel(String id, String name, int level, int version) Creates a Submodel instance with an id, name, level, and version.
Submodel(Submodel obj) Clone constructor

Method Summary

Modifier and Type	Method and Description
boolean	addDeletion(Deletion deletion) Adds a new Deletion to the listOfDeletions.
Submodel	clone() clones this class
Deletion	createDeletion() Creates a new Deletion element and adds it to the ListOfDeletions list
Deletion	createDeletion(String id) Creates a new Deletion element and adds it to the ListOfDeletions list
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
int	getDeletionCount() Returns the number of Deletion objects in this Submodel.
String	getExtentConversionFactor() Returns the value of extentConversionFactor
ListOf<Deletion>	getListOfDeletions() Returns the listOfDeletions.
String	getModelRef() Returns the value of modelRef
String	getTimeConversionFactor() Returns the value of timeConversionFactor
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetExtentConversionFactor() Returns whether extentConversionFactor is set
boolean	isSetListOfDeletions() Returns true, if listOfDeletions contains at least one element.
boolean	isSetModelRef() Returns whether modelRef is set
boolean	isSetTimeConversionFactor() Returns whether timeConversionFactor is set
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeDeletion(Deletion deletion) Removes an element from the listOfDeletions.
void	removeDeletion(int i) Removes an element from the listOfDeletions at the given index.
void	removeDeletion(String id) Removes an element from the listOfDeletions with the given id.
void	setExtentConversionFactor(String extentConversionFactor) The optional extentConversionFactor attribute is provided to allow references and assumptions about the scale of a model's reaction extent to be converted to the scale of the containing model.
void	setListOfDeletions(ListOf<Deletion> listOfDeletions) This list specifies objects to be removed from the submodel when composing the overall model.
void	setModelRef(String modelRef) The whole purpose of a Submodel object is to instantiate a model definition, which is to say, either a Model object defined in the same enclosing SBML document, or a model defined in an external SBML document.
void	setTimeConversionFactor(String timeConversionFactor) The optional timeConversionFactor attribute is provided to allow references and assumptions about the scale of time in the Submodel to be converted to the scale of time in the containing model.
boolean	unsetExtentConversionFactor() Unsets the variable extentConversionFactor
boolean	unsetListOfDeletions() Returns true, if listOfDeletions contain at least one element, otherwise false
boolean	unsetModelRef() Unsets the variable modelRef
boolean	unsetTimeConversionFactor() Unsets the variable timeConversionFactor
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, toString, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Constructor Detail

Submodel

public Submodel()

Creates an Submodel instance

Submodel

public Submodel(String id)

Creates a Submodel instance with an id.

Parameters:

id -

Submodel

public Submodel(int level,
                int version)

Creates a Submodel instance with a level and version.

Parameters:

level -

version -

Submodel

public Submodel(String id,
                int level,
                int version)

Creates a Submodel instance with an id, level, and version.

Parameters:

id -

level -

version -

Submodel

public Submodel(String id,
                String name,
                int level,
                int version)

Creates a Submodel instance with an id, name, level, and version.

Parameters:

id -

name -

level -

version -

Submodel

public Submodel(Submodel obj)

Clone constructor

Parameters:

obj -

Method Detail

clone

public Submodel clone()

clones this class

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

getModelRef

public String getModelRef()

Returns the value of modelRef

Returns:

the value of modelRef

isSetModelRef

public boolean isSetModelRef()

Returns whether modelRef is set

Returns:

whether modelRef is set

setModelRef

public void setModelRef(String modelRef)

The whole purpose of a Submodel object is to instantiate a model definition, which is to say, either a Model object defined in the same enclosing SBML document, or a model defined in an external SBML document. The modelRef attribute is the means by which that model is identified. This required attribute must refer to the identifier of a Model or ExternalModelDefinition object within the enclosing SBML document (i.e., in the model namespace of the document). Sets the value of the required modelRef

Parameters:

modelRef -

unsetModelRef

public boolean unsetModelRef()

Unsets the variable modelRef

Returns:

true, if modelRef was set before, otherwise false

getTimeConversionFactor

public String getTimeConversionFactor()

Returns the value of timeConversionFactor

Returns:

the value of timeConversionFactor

isSetTimeConversionFactor

public boolean isSetTimeConversionFactor()

Returns whether timeConversionFactor is set

Returns:

whether timeConversionFactor is set

setTimeConversionFactor

public void setTimeConversionFactor(String timeConversionFactor)

The optional timeConversionFactor attribute is provided to allow references and assumptions about the scale of time in the Submodel to be converted to the scale of time in the containing model. If set, it must be the identifier of a Parameter object in the parent Model object. The units of that Parameter object, if present, should reduce to being dimensionless, and the Parameter must be constant. Sets the value of the optional timeConversionFactor

Parameters:

timeConversionFactor -

unsetTimeConversionFactor

public boolean unsetTimeConversionFactor()

Unsets the variable timeConversionFactor

Returns:

true, if timeConversionFactor was set before, otherwise false

getExtentConversionFactor

public String getExtentConversionFactor()

Returns the value of extentConversionFactor

Returns:

the value of extentConversionFactor

isSetExtentConversionFactor

public boolean isSetExtentConversionFactor()

Returns whether extentConversionFactor is set

Returns:

whether extentConversionFactor is set

setExtentConversionFactor

public void setExtentConversionFactor(String extentConversionFactor)

The optional extentConversionFactor attribute is provided to allow references and assumptions about the scale of a model's reaction extent to be converted to the scale of the containing model. If set, it must be the identifier of a Parameter object in the parent Model object. The units of that Parameter object, if present, should reduce to being dimensionless, and the Parameter must be constant. Sets the value of the optional extentConversionFactor

Parameters:

extentConversionFactor -

unsetExtentConversionFactor

public boolean unsetExtentConversionFactor()

Unsets the variable extentConversionFactor

Returns:

true, if extentConversionFactor was set before, otherwise false

isSetListOfDeletions

public boolean isSetListOfDeletions()

Returns true, if listOfDeletions contains at least one element.

Returns:

true, if listOfDeletions contains at least one element, otherwise false

getDeletionCount

public int getDeletionCount()

Returns the number of Deletion objects in this Submodel.

Returns:

the number of Deletion objects in this Submodel.

getListOfDeletions

public ListOf<Deletion> getListOfDeletions()

Returns the listOfDeletions. Creates it if it is not already existing.

Returns:

the listOfDeletions

setListOfDeletions

public void setListOfDeletions(ListOf<Deletion> listOfDeletions)

This list specifies objects to be removed from the submodel when composing the overall model. (The "removal" is mathematical and conceptual, not physical.) Sets the given ListOf<Deletion>. If listOfDeletions was defined before and contains some elements, they are all unset.

Parameters:

listOfDeletions -

unsetListOfDeletions

public boolean unsetListOfDeletions()

Returns true, if listOfDeletions contain at least one element, otherwise false

Returns:

true, if listOfDeletions contain at least one element, otherwise false

addDeletion

public boolean addDeletion(Deletion deletion)

Adds a new Deletion to the listOfDeletions.

The listOfDeletions is initialized if necessary.

Parameters:

deletion - the element to add to the list

Returns:

true (as specified by Collection#add)

removeDeletion

public boolean removeDeletion(Deletion deletion)

Removes an element from the listOfDeletions.

Parameters:

deletion - the element to be removed from the list

Returns:

true if the list contained the specified element

See Also:

List#remove(Object)

removeDeletion

public void removeDeletion(int i)

Removes an element from the listOfDeletions at the given index.

Parameters:

i - the index where to remove the Deletion

Throws:

IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size)

removeDeletion

public void removeDeletion(String id)

Removes an element from the listOfDeletions with the given id.

Parameters:

id - the id of the Deletion element to remove.

createDeletion

public Deletion createDeletion()

Creates a new Deletion element and adds it to the ListOfDeletions list

Returns:

createDeletion

public Deletion createDeletion(String id)

Creates a new Deletion element and adds it to the ListOfDeletions list

Parameters:

id -

Returns:

a new Deletion element

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase