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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.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

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

JSBML_WRONG_SBO_TERM

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(java.lang.String id) Creates a Submodel instance with an id.
Submodel(java.lang.String id, int level, int version) Creates a Submodel instance with an id, level, and version.
Submodel(java.lang.String id, java.lang.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(java.lang.String id) Creates a new Deletion element and adds it to the ListOfDeletions list
boolean	equals(java.lang.Object obj) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
int	getDeletionCount() Returns the number of Deletion objects in this Submodel.
java.lang.String	getExtentConversionFactor() Returns the value of extentConversionFactor
ListOf<Deletion>	getListOfDeletions() Returns the listOfDeletions.
java.lang.String	getModelRef() Returns the value of modelRef
java.lang.String	getTimeConversionFactor() Returns the value of timeConversionFactor
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory() Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.
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(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
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(java.lang.String id) Removes an element from the listOfDeletions with the given id.
void	setExtentConversionFactor(java.lang.String extentConversionFactor) Sets the value of the optional 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) Sets the given ListOf<Deletion>.
void	setModelRef(java.lang.String modelRef) Sets the value of the required 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(java.lang.String timeConversionFactor) Sets the value of the optional 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
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

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, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, 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, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, 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, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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(java.lang.String id)

Creates a Submodel instance with an id.

Parameters:

id - the id

Submodel

public Submodel(int level,
                int version)

Creates a Submodel instance with a level and version.

Parameters:

level - the SBML level

version - the SBML version

Submodel

public Submodel(java.lang.String id,
                int level,
                int version)

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

Parameters:

id - the id

level - the SBML level

version - the SBML version

Submodel

public Submodel(java.lang.String id,
                java.lang.String name,
                int level,
                int version)

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

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

Submodel

public Submodel(Submodel obj)

Clone constructor

Parameters:

obj - the instance to clone

Method Detail

clone

public Submodel clone()

clones this class

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

equals

public boolean equals(java.lang.Object obj)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

Parameters:

obj - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: SBase

Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

Returns:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

getModelRef

public java.lang.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(java.lang.String modelRef)

Sets the value of the required 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).

Parameters:

modelRef - the value of modelRef

unsetModelRef

public boolean unsetModelRef()

Unsets the variable modelRef

Returns:

true, if modelRef was set before, otherwise false

getTimeConversionFactor

public java.lang.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(java.lang.String timeConversionFactor)

Sets the value of the optional 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.

Parameters:

timeConversionFactor - the value of timeConversionFactor

unsetTimeConversionFactor

public boolean unsetTimeConversionFactor()

Unsets the variable timeConversionFactor

Returns:

true, if timeConversionFactor was set before, otherwise false

getExtentConversionFactor

public java.lang.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(java.lang.String extentConversionFactor)

Sets the value of the optional 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.

Parameters:

extentConversionFactor - the value of the optional 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)

Sets the given ListOf<Deletion>.

If listOfDeletions was defined before and contains some elements, they are all unset.

This list specifies objects to be removed from the submodel when composing the overall model. (The "removal" is mathematical and conceptual, not physical.)

Parameters:

listOfDeletions - the list of Deletions

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(E))

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:

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

removeDeletion

public void removeDeletion(java.lang.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:

a new Deletion element

createDeletion

public Deletion createDeletion(java.lang.String id)

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

Parameters:

id - the id

Returns:

a new Deletion element

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:

a Map containing the XML attributes of this object.

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.