org.sbml.jsbml.ext.comp

Class ExternalModelDefinition

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.comp.ExternalModelDefinition

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, TreeNodeWithChangeSupport

public class ExternalModelDefinition
extends AbstractNamedSBase
implements UniqueNamedSBase

The ExternalModelDefinition objects are model definitions - in and of themselves, they are definitions of the models but not uses of those models. The class provides a way to declare and identify them so that Model objects in the present SBMLDocument can use them in SubModel objects.

Since:

1.0

Version:

$Rev: 1725 $

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	md5
private java.lang.String	modelRef
private static long	serialVersionUID Generated serial version identifier.
private java.lang.String	source

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
ExternalModelDefinition	clone() clones this class
java.lang.String	getMd5() Returns the value of md5 or an empty String if it is not set.
java.lang.String	getModelRef() Returns the value of modelRef or an empty String if it is not set.
java.lang.String	getSource() Returns the value of source or an empty String if it is not set.
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetMd5() Returns whether md5 is set
boolean	isSetModelRef() Returns whether modelRef is set
boolean	isSetSource() Returns whether source is set
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setMd5(java.lang.String md5) Sets the value of the optional md5 attribute.
void	setModelRef(java.lang.String modelRef) Sets the value of the optional modelRef attribute.
void	setSource(java.lang.String source) Sets the value of the required source attribute.
boolean	unsetMd5() Unsets the variable md5
boolean	unsetModelRef() Unsets the variable modelRef
boolean	unsetSource() Unsets the variable source
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

equals, getId, getName, hashCode, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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

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, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

source

private java.lang.String source

modelRef

private java.lang.String modelRef

md5

private java.lang.String md5

Constructor Detail

ExternalModelDefinition

public ExternalModelDefinition()

Creates an ExternalModelDefinition instance

ExternalModelDefinition

public ExternalModelDefinition(java.lang.String id)

Creates a ExternalModelDefinition instance with an id.

Parameters:

id -

ExternalModelDefinition

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

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

Parameters:

id -

level -

version -

ExternalModelDefinition

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

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

Parameters:

id -

name -

level -

version -

ExternalModelDefinition

public ExternalModelDefinition(ExternalModelDefinition obj)

Clone constructor

Method Detail

clone

public ExternalModelDefinition 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.

getSource

public java.lang.String getSource()

Returns the value of source or an empty String if it is not set.

Returns:

the value of source or an empty String if it is not set.

isSetSource

public boolean isSetSource()

Returns whether source is set

Returns:

whether source is set

setSource

public void setSource(java.lang.String source)

Sets the value of the required source attribute. The source attribute is used to locate the SBML document containing an ExternalModelDefinition. The value of the attribute must be a URI, which includes URLs, URNs, or relative/absolute file locations. The source attribute must refer specifically to an SBML Level 3 Version 1 document. The entire file at the given location is referenced. The source attribute must have a value for every ExternalModelDefinition.

unsetSource

public boolean unsetSource()

Unsets the variable source

Returns:

true , if source was set before, otherwise false

getModelRef

public java.lang.String getModelRef()

Returns the value of modelRef or an empty String if it is not set.

Returns:

the value of modelRef or an empty String if it is not set.

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 optional modelRef attribute. modelRef is used to identify a Model or ExternalModelDefinition object within the SBML document located at source. The object referenced may be the main model in the document, or it may be a model definition contained in the SBML document's listOfModelDefinitions or listOfExternalModelDefinitions. Loops are not allowed: it must be possible to follow a chain of ExternalModelDefinition objects to its end in a Model object. In core SBML, the id on Model is an optional attribute, and therefore, it is possible that the Model object in a given SBML document does not have an identifier. In that case, there is no value to give to the modelRef attribute in ExternalModelDefinition. If modelRef does not have a value, then the main model (i.e., the model element within the sbml element) in the referenced file is interpreted as being the model referenced by this ExternalModelDefinition instance.

unsetModelRef

public boolean unsetModelRef()

Unsets the variable modelRef

Returns:

true, if modelRef was set before, otherwise false

getMd5

public java.lang.String getMd5()

Returns the value of md5 or an empty String if it is not set.

Returns:

the value of md5 or an empty String if it is not set.

isSetMd5

public boolean isSetMd5()

Returns whether md5 is set

Returns:

whether md5 is set

setMd5

public void setMd5(java.lang.String md5)

Sets the value of the optional md5 attribute. The md5 attribute takes a string value. If set, it must be an MD5 checksum value computed over the document referenced by source. This checksum can serve as a data integrity check over the contents of the source. Applications may use this to verify that the contents have not changed since the time that the ExternalModelDefinition reference was constructed.

unsetMd5

public boolean unsetMd5()

Unsets the variable md5

Returns:

true, if md5 was set before, otherwise false

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 AbstractNamedSBase

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 AbstractNamedSBase

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.

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

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.