Package 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, UniqueSId, 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

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	Description
ExternalModelDefinition()	Creates an ExternalModelDefinition instance
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.
ExternalModelDefinition(ExternalModelDefinition obj)	Clone constructor

Method Summary

Modifier and Type	Method	Description
ExternalModelDefinition	clone()	clones this class
boolean	equals(java.lang.Object obj)
java.net.URI	getAbsoluteSourceURI()	Finds the absolute URI of the source-file specified: If the source is specified through a relative path, will try to use the containing SBMLDocument's SBMLDocument.getLocationURI() to turn it into an absolute URI in the current context.
java.net.URI	getAbsoluteSourceURI(java.net.URI absoluteContainingURI)	Finds the absolute URI of the source-file specified: If the source is specified through a relative path, will try to use the given absoluteContainingURI to turn it into an absolute URI in the current context.
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.
Model	getReferencedModel()	Resolves the external Model referenced by this and returns that model, under the assumption that the containing SBMLDocument a) exists and b) has a valid locationURI set (cf SBMLDocument.isSetLocationURI()).
Model	getReferencedModel(java.net.URI absoluteContainingURI)	Resolves the external Model referenced by this and returns that model, for a given path to the directory containing the SBML-file wherein this ExternalModelDefinition was made/the root directory for references by relative paths.
java.lang.String	getSource()	Returns the value of source or an empty String if it is not set.
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isIdMandatory()
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)
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()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, 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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, 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, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

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

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, hasExtension, 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 javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

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

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 - the id

ExternalModelDefinition

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

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

Parameters:

id - the id

level - the SBML level

version - the SBML 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 - the id

name - the name

level - the SBML level

version - the SBML version

ExternalModelDefinition

public ExternalModelDefinition(ExternalModelDefinition obj)

Clone constructor

Parameters:

obj - the instance to clone

Method Detail

clone

public ExternalModelDefinition clone()

clones this class

Specified by:

clone in interface SBase

Specified by:

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(java.lang.Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

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.

Parameters:

source - the value of the source

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.

Parameters:

modelRef - the value of modelRef

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.

Parameters:

md5 - the value of md5

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()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

getReferencedModel

public Model getReferencedModel(java.net.URI absoluteContainingURI)
                         throws javax.xml.stream.XMLStreamException,
                                java.io.IOException,
                                java.net.URISyntaxException

Resolves the external Model referenced by this and returns that model, for a given path to the directory containing the SBML-file wherein this ExternalModelDefinition was made/the root directory for references by relative paths.
The referenced Model is not modified and may thus contain Submodels referencing further (external) ModelDefinitions.

Parameters:

absoluteContainingURI - absolute URI to the directory containing the file that defines this (needed to resolve local references): Undefined behaviour for opaque URIs (URNs or other), resolve URNs before calling this method

Returns:

The referenced Model

Throws:

java.io.IOException - if the source cannot be found/resolved

javax.xml.stream.XMLStreamException - if the file at source is not a valid SBMLDocument.

java.net.URISyntaxException

getReferencedModel

public Model getReferencedModel()
                         throws javax.xml.stream.XMLStreamException,
                                java.io.IOException,
                                java.net.URISyntaxException

Resolves the external Model referenced by this and returns that model, under the assumption that the containing SBMLDocument a) exists and b) has a valid locationURI set (cf SBMLDocument.isSetLocationURI()). This location of the containing file is needed to resolve references to external models by relative paths. URNs/opaque URIs cannot be resolved by this method, resolve them before calling it.
The referenced Model is not modified and may thus contain Submodels referencing further (external) ModelDefinitions.

Returns:

the Model referenced by this

Throws:

javax.xml.stream.XMLStreamException - if the file referenced by this is not a valid xml/sbml

java.io.IOException - if the file referenced by this cannot be found

java.net.URISyntaxException - if parent's locationURI is not a valid URI

java.lang.NullPointerException - if the parent SBMLDocument's locationURI is not set.

getAbsoluteSourceURI

public java.net.URI getAbsoluteSourceURI()
                                  throws java.net.URISyntaxException,
                                         java.net.MalformedURLException

Finds the absolute URI of the source-file specified: If the source is specified through a relative path, will try to use the containing SBMLDocument's SBMLDocument.getLocationURI() to turn it into an absolute URI in the current context.
The actual source is not changed in the process

Returns:

The absolute URI to the source (getSource()) of this ExternalModelDefinition

Throws:

java.net.URISyntaxException

java.net.MalformedURLException

getAbsoluteSourceURI

public java.net.URI getAbsoluteSourceURI(java.net.URI absoluteContainingURI)
                                  throws java.net.MalformedURLException,
                                         java.net.URISyntaxException

Finds the absolute URI of the source-file specified: If the source is specified through a relative path, will try to use the given absoluteContainingURI to turn it into an absolute URI in the current context.
The actual source is not changed in the process

Parameters:

absoluteContainingURI - absolute URI to the directory containing the file that defines this (needed to resolve local references)

Returns:

The absolute URI to the source (getSource()) of this ExternalModelDefinition

Throws:

java.net.MalformedURLException

java.net.URISyntaxException