org.sbml.jsbml

Class SBMLDocument

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.SBMLDocument

All Implemented Interfaces:

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

public class SBMLDocument
extends AbstractSBase

Represents the 'sbml' root node of a SBML file.

Since:

0.8

Author:

Andreas Dräger, Marine Dumousseau

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.Map<java.lang.String,java.lang.Boolean>	checkConsistencyParameters Contains all the parameter to validate the SBML document
private java.util.Map<java.lang.String,java.lang.Boolean>	enabledPackageMap Stores a package namespace associated with it's status.
private SBMLErrorLog	listOfErrors Memorizes all SBMLError when parsing the file containing this document.
private static org.apache.log4j.Logger	logger logger used to print messages
private java.util.Map<java.lang.String,SBase>	mappingFromMetaId2SBase Stores all the meta identifiers within this SBMLDocument to avoid the creation of multiple identical meta identifiers.
private Model	model Represents the 'model' XML subnode of a SBML file.
private java.util.Map<java.lang.String,java.lang.String>	SBMLDocumentAttributes Contains all the XML attributes of the sbml XML node.
private static long	serialVersionUID Generated serial version identifier.
static java.lang.String	URI_NAMESPACE_L1 The namespace URI of SBML Level 1 Version 1 and 2.
static java.lang.String	URI_NAMESPACE_L2V1 The namespace URI of SBML Level 2 Version 1.
static java.lang.String	URI_NAMESPACE_L2V2 The namespace URI of SBML Level 2 Version 2.
static java.lang.String	URI_NAMESPACE_L2V3 The namespace URI of SBML Level 2 Version 3.
static java.lang.String	URI_NAMESPACE_L2V4 The namespace URI of SBML Level 2 Version 4.
static java.lang.String	URI_NAMESPACE_L2V5 The namespace URI of SBML Level 2 Version 5.
static java.lang.String	URI_NAMESPACE_L3V1Core The namespace URI of SBML Level 3 Version 1.
static java.lang.String	URI_NAMESPACE_L3V2Core The namespace URI of SBML Level 3 Version 2.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
SBMLDocument() Creates a SBMLDocument instance.
SBMLDocument(int level, int version) Creates a SBMLDocument instance from a level and version.
SBMLDocument(SBMLDocument sb) Creates a new SBMLDocument instance from a given SBMLDocument.

Method Summary

Modifier and Type	Method and Description
void	addNamespace(java.lang.String namespaceName, java.lang.String prefix, java.lang.String URI) Deprecated. use SBase.addDeclaredNamespace(String, String)
private void	addPackageDeclaration(java.lang.String packageName, java.lang.String packageURI, boolean required) Adds the package namespace declaration in this SBMLDocument, adds as well the required attribute for this package.
int	checkConsistency() Validates the SBMLDocument using the SBML.org online validator (http://sbml.org/validator/).
int	checkConsistencyOffline() Validates the SBMLDocument using the BETA version of the offline validator (do not use for production).
private void	checkMetaId(java.lang.String metaId) Checks if the given meta identifier can be added in this SBMLDocument 's mappingFromMetaId2SBase.
SBMLDocument	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
private void	collectMetaIds(java.util.Map<java.lang.String,SBase> metaIds, SBase sbase, boolean recursively, boolean delete) Collects all meta identifiers of this AbstractSBase and all of its sub-elements if recursively is true.
boolean	containsMetaId(java.lang.String metaId) A check to see whether elements have been registered to this SBMLDocument with the given meta identifier.
Model	createModel() Creates a new Model inside this SBMLDocument, and returns a pointer to it.
Model	createModel(java.lang.String id) Creates a new instance of Model from id and the level and version of this SBMLDocument.
void	disablePackage(java.lang.String packageURIOrName) Disables the given SBML Level 3 package on this SBMLDocument.
void	enablePackage(java.lang.String packageURIOrName) Enables the given SBML Level 3 package on this SBMLDocument.
void	enablePackage(java.lang.String packageURIOrName, boolean enabled) Enables or disables the given SBML Level 3 package on this SBMLDocument.
boolean	equals(java.lang.Object o) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
SBase	findSBase(java.lang.String metaId) Looks up the SBase registered in this SBMLDocument for the given metaId.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
int	getDefaultLevel() Returns the default SBML Level of new SBMLDocument objects.
int	getDefaultVersion() Returns the default Version of new SBMLDocument objects.
SBase	getElementByMetaId(java.lang.String metaid) Returns the SBase with the given metaid in this SBMLDocument or null if no such SBase is found.
java.lang.String	getElementName() Returns the XML element name of this object.
java.lang.String	getEnabledPackageNamespace(java.lang.String packageURIOrName) Return the package namespace enabled on this SBMLDocument or null if the package is not enabled.
SBMLError	getError(int i) Returns the ith error or warning encountered during consistency checking.
int	getErrorCount() Returns the number of errors or warnings encountered during consistency checking.
SBMLErrorLog	getErrorLog() Returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.
SBMLErrorLog	getListOfErrors() Returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.
Model	getModel() Returns the model of this SBMLDocument.
int	getNumErrors() Returns the number of errors or warnings encountered during consistency checking.
boolean	getPackageRequired(java.lang.String nameOrUri) Returns the required attribute of the given package extension.
boolean	getPkgRequired(java.lang.String pckage) Deprecated. use getPackageRequired(String)
java.util.Map<java.lang.String,java.lang.String>	getSBMLDocumentAttributes() Returns the map of attribute names and values of this SBMLDocument.
java.util.Map<java.lang.String,java.lang.String>	getSBMLDocumentNamespaces() Deprecated. use SBase.getDeclaredNamespaces()
int	hashCode() Returns a hash code value for this SBase instance.
private void	initDefaults()
boolean	isIgnoredPackage(java.lang.String nameOrURI) Returns true if the given package extension is one of an ignored packages, otherwise returns false.
boolean	isIgnoredPkg(java.lang.String pkgURI) Deprecated. use isIgnoredPackage(String)
boolean	isPackageEnabled(java.lang.String packageURIOrName) Returns true if the given SBML Level 3 package is enabled within the SBMLDocument.
java.lang.Boolean	isPackageEnabledOrDisabled(java.lang.String packageURIOrName) Returns true if the given SBML Level 3 package is enabled within the SBMLDocument, false if the package was disabled using the method disablePackage(String) or null if this package was neither enabled or disabled on this SBMLDocument.
private boolean	isSetListOfErrors() Returns true if the list of errors is defined and contain at least one error.
boolean	isSetModel() Returns true if the Model of this SBMLDocument is not null.
boolean	isSetPackageRequired(java.lang.String nameOrURI) Returns true.
boolean	isSetPkgRequired(java.lang.String pckage) Deprecated. use isSetPackageRequired(String)
java.util.Collection<java.lang.String>	metaIds() Provides access to all registered metaIds in this SBMLDocument.
java.lang.String	nextMetaId() Randomly creates a new String that can be used as a metaid, i.e., a String that is a valid metaid and that is not yet used by any other element within this SBMLDocument.
void	printErrors(java.io.PrintStream stream) Prints all the errors or warnings encountered trying to check this SBML document.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
(package private) boolean	registerMetaId(SBase sbase, boolean add) Saves or removes the given meta identifier in this SBMLDocument's mappingFromMetaId2SBase.
(package private) void	registerMetaIds(SBase sbase, boolean recursively, boolean delete) Collects all meta identifiers of this AbstractSBase and all of its sub-elements if recursively is true.
private void	removePackageDeclaration(java.lang.String packageName) Removes the package namespace declaration in this SBMLDocument, removes as well the required attribute for this package.
void	setConsistencyChecks(SBMLValidator.CHECK_CATEGORY category, boolean apply) Controls the consistency checks that are performed when checkConsistency() is called.
boolean	setLevelAndVersion(int level, int version) Sets the SBML Level and Version of this SBMLDocument instance, without attempting to convert the model.
boolean	setLevelAndVersion(int level, int version, boolean strict) Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.
void	setModel(Model model) Sets the Model for this SBMLDocument to the given Model.
boolean	setPackageRequired(java.lang.String nameOrUri, boolean flag) Sets the required attribute value of the given package extension (does nothing in fact!).
boolean	setPkgRequired(java.lang.String pckage, boolean flag) Deprecated. use setPackageRequired(String, boolean)
void	setSBMLDocumentAttributes(java.util.Map<java.lang.String,java.lang.String> attributes) Sets the SBMLDocumentAttributes.
java.lang.String	toString() Returns a String representing this SBase with all the attributes that are defined.
boolean	unsetModel() Sets the Model of this SBMLDocument to null and notifies all TreeNodeChangeListener about changes.
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.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementBySId, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, 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, setPackageNamespaceAndVersion, 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, userObjectKeySet

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.SBase

removeTreeNodeChangeListener

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

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

URI_NAMESPACE_L1

public static final transient java.lang.String URI_NAMESPACE_L1

The namespace URI of SBML Level 1 Version 1 and 2.

See Also:

Constant Field Values

URI_NAMESPACE_L2V1

public static final transient java.lang.String URI_NAMESPACE_L2V1

The namespace URI of SBML Level 2 Version 1.

See Also:

Constant Field Values

URI_NAMESPACE_L2V2

public static final java.lang.String URI_NAMESPACE_L2V2

The namespace URI of SBML Level 2 Version 2.

See Also:

Constant Field Values

URI_NAMESPACE_L2V3

public static final transient java.lang.String URI_NAMESPACE_L2V3

The namespace URI of SBML Level 2 Version 3.

See Also:

Constant Field Values

URI_NAMESPACE_L2V4

public static final transient java.lang.String URI_NAMESPACE_L2V4

The namespace URI of SBML Level 2 Version 4.

See Also:

Constant Field Values

URI_NAMESPACE_L2V5

public static final transient java.lang.String URI_NAMESPACE_L2V5

The namespace URI of SBML Level 2 Version 5.

See Also:

Constant Field Values

URI_NAMESPACE_L3V1Core

public static final transient java.lang.String URI_NAMESPACE_L3V1Core

The namespace URI of SBML Level 3 Version 1.

See Also:

Constant Field Values

URI_NAMESPACE_L3V2Core

public static final transient java.lang.String URI_NAMESPACE_L3V2Core

The namespace URI of SBML Level 3 Version 2.

See Also:

Constant Field Values

checkConsistencyParameters

private java.util.Map<java.lang.String,java.lang.Boolean> checkConsistencyParameters

Contains all the parameter to validate the SBML document

listOfErrors

private SBMLErrorLog listOfErrors

Memorizes all SBMLError when parsing the file containing this document.

logger

private static final transient org.apache.log4j.Logger logger

logger used to print messages

mappingFromMetaId2SBase

private java.util.Map<java.lang.String,SBase> mappingFromMetaId2SBase

Stores all the meta identifiers within this SBMLDocument to avoid the creation of multiple identical meta identifiers. These identifiers have to be unique within the document.

model

private Model model

Represents the 'model' XML subnode of a SBML file.

enabledPackageMap

private java.util.Map<java.lang.String,java.lang.Boolean> enabledPackageMap

Stores a package namespace associated with it's status. The status being: enabled if the Boolean is true, disable otherwise

SBMLDocumentAttributes

private java.util.Map<java.lang.String,java.lang.String> SBMLDocumentAttributes

Contains all the XML attributes of the sbml XML node.

Constructor Detail

SBMLDocument

public SBMLDocument()

Creates a SBMLDocument instance. By default, the parent SBML object of this object is itself. The model is null. The SBMLDocumentAttributes and the SBMLDocumentNamespaces are empty.

SBMLDocument

public SBMLDocument(int level,
                    int version)

Creates a SBMLDocument instance from a level and version. By default, the parent SBML object of this object is itself. The model is null. The SBMLDocumentAttributes and the SBMLDocumentNamespaces are empty.

Parameters:

level - the SBML level

version - the SBML version

SBMLDocument

public SBMLDocument(SBMLDocument sb)

Creates a new SBMLDocument instance from a given SBMLDocument.

Parameters:

sb -

Method Detail

addNamespace

@Deprecated
public void addNamespace(java.lang.String namespaceName,
                                     java.lang.String prefix,
                                     java.lang.String URI)

Deprecated. use SBase.addDeclaredNamespace(String, String)

Adds a name space to the SBMLNamespaces of this SBMLDocument.

Parameters:

namespaceName -

prefix -

URI -

addPackageDeclaration

private void addPackageDeclaration(java.lang.String packageName,
                                   java.lang.String packageURI,
                                   boolean required)

Adds the package namespace declaration in this SBMLDocument, adds as well the required attribute for this package.

Parameters:

packageName - the name or short label of the package, for example: layout, comp, qual, ...

packageURI - the package namespace uri

required - the value of the required attribute

removePackageDeclaration

private void removePackageDeclaration(java.lang.String packageName)

Removes the package namespace declaration in this SBMLDocument, removes as well the required attribute for this package.

Parameters:

packageName - the name or short label of the package, for example: layout, comp, qual, ...

checkConsistencyOffline

public int checkConsistencyOffline()

Validates the SBMLDocument using the BETA version of the offline validator (do not use for production).

WARNING: the offline validator is still under development and there is only a subset of rules which will be tested at the moment and you might have errors reported that should not be. As well, the error messages are not very informative, at the moment it is only a generic string not customized to provide any context to help to know which SBML element generated the error.

For testing only, do not use for production.

You can control the consistency checks that are performed when checkConsistencyOffline() is called with the #setConsistencyChecks(CHECK_CATEGORY, boolean) method. It will fill this SBMLDocument's listOfErrors with SBMLErrors for each problem within this whole data structure. You will then be able to obtain this list by calling getError(int) or getListOfErrors().

If this method returns a nonzero value (meaning, one or more consistency checks have failed for SBML document), the failures may be due to warnings or errors. Callers should inspect the severity flag in the individual SBMLError objects returned by getError(int) to determine the nature of the failures.

Returns:

the number of errors

checkConsistency

public int checkConsistency()

Validates the SBMLDocument using the SBML.org online validator (http://sbml.org/validator/).

you can control the consistency checks that are performed when checkConsistency() is called with the #setConsistencyChecks(CHECK_CATEGORY, boolean) method. It will fill this SBMLDocument's listOfErrors with SBMLErrors for each problem within this whole data structure. You will then be able to obtain this list by calling getError(int) or getListOfErrors().

If this method returns a nonzero value (meaning, one or more consistency checks have failed for SBML document), the failures may be due to warnings or errors. Callers should inspect the severity flag in the individual SBMLError objects returned by getError(int) to determine the nature of the failures.

Returns:

the number of errors found

See Also:

#setConsistencyChecks(CHECK_CATEGORY, boolean)

checkMetaId

private void checkMetaId(java.lang.String metaId)

Checks if the given meta identifier can be added in this SBMLDocument 's mappingFromMetaId2SBase.

Parameters:

metaId - the identifier whose value is to be checked.

Throws:

java.lang.IllegalArgumentException - if a metaid to add is already present in the list of registered metaids.

clone

public SBMLDocument clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

collectMetaIds

private void collectMetaIds(java.util.Map<java.lang.String,SBase> metaIds,
                            SBase sbase,
                            boolean recursively,
                            boolean delete)

Collects all meta identifiers of this AbstractSBase and all of its sub-elements if recursively is true.

Parameters:

metaIds - the Map that gathers the result.

sbase - The SBase whose meta identifier is to be collected and from which we maybe have to recursively go through all of its children.

recursively - if true, this method will also consider all sub-elements of this AbstractSBase.

delete - if true this method will not check if the meta identifier can be added to the SBMLDocument.

Throws:

java.lang.IllegalArgumentException - However, duplications are not legal and an IllegalArgumentException will be thrown in such cases.

containsMetaId

public boolean containsMetaId(java.lang.String metaId)

A check to see whether elements have been registered to this SBMLDocument with the given meta identifier.

Parameters:

metaId -

Returns:

createModel

public Model createModel()

Creates a new Model inside this SBMLDocument, and returns a pointer to it. In SBML Level 2, the use of an identifier on a Model object is optional. This method takes an optional argument, sid, for setting the identifier. If not supplied, the identifier attribute on the Model instance is not set.

Returns:

the new Model instance.

createModel

public Model createModel(java.lang.String id)

Creates a new instance of Model from id and the level and version of this SBMLDocument.

Parameters:

id -

Returns:

the new Model instance.

disablePackage

public void disablePackage(java.lang.String packageURIOrName)

Disables the given SBML Level 3 package on this SBMLDocument.

Specified by:

disablePackage in interface SBase

Overrides:

disablePackage in class AbstractSBase

Parameters:

packageURIOrName - a package namespace URI or package name

enablePackage

public void enablePackage(java.lang.String packageURIOrName)

Enables the given SBML Level 3 package on this SBMLDocument.

Specified by:

enablePackage in interface SBase

Overrides:

enablePackage in class AbstractSBase

Parameters:

packageURIOrName - a package namespace URI or package name

enablePackage

public void enablePackage(java.lang.String packageURIOrName,
                          boolean enabled)

Enables or disables the given SBML Level 3 package on this SBMLDocument.

Specified by:

enablePackage in interface SBase

Overrides:

enablePackage in class AbstractSBase

Parameters:

packageURIOrName - a package namespace URI or package name

enabled - a boolean to tell if the package need to be enabled or disabled. It true the package will be enabled, otherwise it will be disabled.

equals

public boolean equals(java.lang.Object o)

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:

o - 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.

findSBase

public SBase findSBase(java.lang.String metaId)

Looks up the SBase registered in this SBMLDocument for the given metaId.

Parameters:

metaId -

Returns:

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren 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

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

getDefaultLevel

public int getDefaultLevel()

Returns the default SBML Level of new SBMLDocument objects.

Returns:

the default SBML Level of new SBMLDocument objects.

getDefaultVersion

public int getDefaultVersion()

Returns the default Version of new SBMLDocument objects.

Returns:

the default Version of new SBMLDocument objects.

getElementName

public java.lang.String getElementName()

Description copied from interface: SBase

Returns the XML element name of this object.

Specified by:

getElementName in interface SBase

Overrides:

getElementName in class AbstractSBase

Returns:

the XML element name of this object.

getElementByMetaId

public SBase getElementByMetaId(java.lang.String metaid)

Returns the SBase with the given metaid in this SBMLDocument or null if no such SBase is found.

This method make use of HashMap so it is more efficient to search for metaid than anywhere else down in the SBML hierarchy.

Specified by:

getElementByMetaId in interface SBase

Overrides:

getElementByMetaId in class AbstractSBase

Parameters:

metaid - - the metaid of SBase to find

Returns:

the SBase with the given metaid or null

See Also:

findSBase(String)

getEnabledPackageNamespace

public java.lang.String getEnabledPackageNamespace(java.lang.String packageURIOrName)

Return the package namespace enabled on this SBMLDocument or null if the package is not enabled.

Parameters:

packageURIOrName - the name or URI of the package extension.

Returns:

the package namespace enabled on this SBMLDocument or null if the package is not enabled.

getError

public SBMLError getError(int i)

Returns the i^th error or warning encountered during consistency checking.

Parameters:

i - - the index of the SBMLError to get

Returns:

the i^th error or warning encountered during consistency checking.

Throws:

java.lang.IndexOutOfBoundsException - if the index is wrong

See Also:

getNumErrors()

getErrorCount

public int getErrorCount()

Returns the number of errors or warnings encountered during consistency checking.

Returns:

the number of errors or warnings encountered during consistency checking.

getErrorLog

public SBMLErrorLog getErrorLog()

Returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.

Returns:

a collection of all SBMLErrors encountered during consistency checking.

getListOfErrors

public SBMLErrorLog getListOfErrors()

Returns a collection of all SBMLErrors reflecting problems in the overall data structure of this SBMLDocument.

Returns:

a collection of all SBMLErrors encountered during consistency checking.

getModel

public Model getModel()

Returns the model of this SBMLDocument.

Specified by:

getModel in interface SBase

Overrides:

getModel in class AbstractSBase

Returns:

the model of this SBMLDocument. Can be null if it is not set.

getNumErrors

public int getNumErrors()

Returns the number of errors or warnings encountered during consistency checking.

Returns:

the number of errors or warnings encountered during consistency checking.

See Also:

getErrorCount()

getPackageRequired

public boolean getPackageRequired(java.lang.String nameOrUri)

Returns the required attribute of the given package extension.

Parameters:

nameOrUri - the name or URI of the package extension.

Returns:

a boolean indicating whether the package is flagged as being required. If the name or uri is not recognized by this version of JSBML, false is returned.

getPkgRequired

@Deprecated
public boolean getPkgRequired(java.lang.String pckage)

Deprecated. use getPackageRequired(String)

Returns the required attribute of the given package extension. The name of package must not be given if the package is not enabled.

Parameters:

pckage - the name or URI of the package extension.

Returns:

a boolean value indicating whether the package is flagged as being required in this SBMLDocument.

getSBMLDocumentAttributes

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

Returns the map of attribute names and values of this SBMLDocument.

Returns:

the map of attribute names and values of this SBMLDocument.

getSBMLDocumentNamespaces

@Deprecated
public java.util.Map<java.lang.String,java.lang.String> getSBMLDocumentNamespaces()

Deprecated. use SBase.getDeclaredNamespaces()

Returns the map of declared namespaces of this SBMLDocument.

Returns:

the map of declared namespaces of this SBMLDocument.

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()

initDefaults

private void initDefaults()

isIgnoredPackage

public boolean isIgnoredPackage(java.lang.String nameOrURI)

Returns true if the given package extension is one of an ignored packages, otherwise returns false.

An ignored package is one that is defined to be used in this SBMLDocument, but the package is not supported in this copy of JSBML.

Parameters:

nameOrURI - the name or URI of the package extension.

Returns:

a Boolean, true if the package is being ignored and false otherwise.

isIgnoredPkg

@Deprecated
public boolean isIgnoredPkg(java.lang.String pkgURI)

Deprecated. use isIgnoredPackage(String)

Returns true if the given package extension is one of ignored packages, otherwise returns false.

An ignored package is one that is defined to be used in this SBMLDocument, but the package is not supported in this copy of JSBML.

Parameters:

pkgURI - the URI of the package extension.

Returns:

a boolean

isPackageEnabled

public boolean isPackageEnabled(java.lang.String packageURIOrName)

Returns true if the given SBML Level 3 package is enabled within the SBMLDocument.

If the namespace was declared on the sbml element, or if any elements of this package were found while building the SBMLDocument structure, the package will be enabled.

For the parameter 'packageNameorUri', you should use the package shortLabel or name, for example 'distrib', as given by org.sbml.jsbml.ext.distrib.DistribConstants#shortLabel, this way, you don't mind about the specific package version. If you want to check for a specific package version, then you can use the namespace instead.

Specified by:

isPackageEnabled in interface SBase

Overrides:

isPackageEnabled in class AbstractSBase

Parameters:

packageURIOrName - the name or URI of the package extension.

Returns:

true if the given SBML Level 3 package is enabled within the SBMLDocument, false otherwise.

isPackageEnabledOrDisabled

public java.lang.Boolean isPackageEnabledOrDisabled(java.lang.String packageURIOrName)

Returns true if the given SBML Level 3 package is enabled within the SBMLDocument, false if the package was disabled using the method disablePackage(String) or null if this package was neither enabled or disabled on this SBMLDocument.

This method can be used, for example, by the SBMLWriter to know if a package was really disabled, in which case the package elements won't be written down, or if the user forgot to enable it, in which case it will be enabled and the package elements will be written.

Parameters:

packageURIOrName - the name or URI of the package extension.

Returns:

true if the given SBML Level 3 package is enabled within the SBMLDocument, false if the package was disabled using the method disablePackage(String) or null if this package was neither enabled or disabled on this SBMLDocument.

isSetListOfErrors

private boolean isSetListOfErrors()

Returns true if the list of errors is defined and contain at least one error.

Returns:

true if the list of errors is defined and contain at least one error.

isSetModel

public boolean isSetModel()

Returns true if the Model of this SBMLDocument is not null.

Returns:

true if the Model of this SBMLDocument is not null.

isSetPackageRequired

public boolean isSetPackageRequired(java.lang.String nameOrURI)

Returns true.

Parameters:

nameOrURI - the name or URI of the package extension.

Returns:

true

isSetPkgRequired

@Deprecated
public boolean isSetPkgRequired(java.lang.String pckage)

Deprecated. use isSetPackageRequired(String)

Returns true

Parameters:

pckage - the name or URI of the package extension.

Returns:

a boolean value.

nextMetaId

public java.lang.String nextMetaId()

Randomly creates a new String that can be used as a metaid, i.e., a String that is a valid metaid and that is not yet used by any other element within this SBMLDocument.

Returns:

a valid metaid that is not yet used by any other element within this SBMLDocument.

printErrors

public void printErrors(java.io.PrintStream stream)

Prints all the errors or warnings encountered trying to check this SBML document.

Parameters:

stream - the stream where to print the SBMLDocument errors.

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.

registerMetaId

boolean registerMetaId(SBase sbase,
                       boolean add)

Saves or removes the given meta identifier in this SBMLDocument's mappingFromMetaId2SBase.

Parameters:

sbase - the element whose meta identifier is to be registered (if it is set).

add - if true this will add the given meta identifier to this SBMLDocument's mappingFromMetaId2SBase. Otherwise, the given identifier will be removed from this set.

Returns:

• if add is true, then this method returns true if this set did not already contain the specified element, false otherwise.
• if add is not true, this method returns true if this set contained the specified element, false otherwise.
• This method also returns false if the given SBase does not have a defined metaId

registerMetaIds

void registerMetaIds(SBase sbase,
                     boolean recursively,
                     boolean delete)

Collects all meta identifiers of this AbstractSBase and all of its sub-elements if recursively is true. It can also be used to delete meta identifiers from the given Set.

Parameters:

sbase - The SBase whose meta identifier is to be registered and from which we maybe have to recursively go through all of its children.

recursively - if true, this method will also consider all sub-elements of this AbstractSBase.

delete - if true the purpose of this method will be to delete the meta identifier from the given Set. Otherwise, it will try to add it to the set.

Throws:

java.lang.IllegalArgumentException - However, duplications are not legal and an IllegalArgumentException will be thrown in such cases.

metaIds

public java.util.Collection<java.lang.String> metaIds()

Provides access to all registered metaIds in this SBMLDocument. The given collection is unmodifiable. Modifications made to the values has hence no effect. This method is helpful to iterate through all metaIds in the document and to query elements based on the metaId.

Returns:

An unmodifiable collection of Strings as a view of the actual metaIds within this SBMLDocument. Hence, modifying any of the values returned by this method does not have any effect for the content of this document.

setConsistencyChecks

public void setConsistencyChecks(SBMLValidator.CHECK_CATEGORY category,
                                 boolean apply)

Controls the consistency checks that are performed when checkConsistency() is called.

This method works by adding or subtracting consistency checks from the set of all possible checks that checkConsistency() knows how to perform. This method may need to be called multiple times in order to achieve the desired combination of checks. The first argument (category) in a call to this method indicates the category of consistency/error checks that are to be turned on or off, and the second argument (apply, a boolean) indicates whether to turn it on (value of true) or off (value of false).

The possible categories (values to the argument category) are the set of values from the SBMLValidator.CHECK_CATEGORY enumeration. The following are the possible choices:

• SBMLValidator.CHECK_CATEGORY.GENERAL_CONSISTENCY : Correctness and consistency of specific SBML language constructs. Performing this set of checks is highly recommended. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2, 3 and 4 specifications.
• SBMLValidator.CHECK_CATEGORY.IDENTIFIER_CONSISTENCY : Correctness and consistency of identifiers used for model entities. An example of inconsistency would be using a species identifier in a reaction rate formula without first having declared the species. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2, 3 and 4 specifications.
• SBMLValidator.CHECK_CATEGORY.UNITS_CONSISTENCY : Consistency of measurement units associated with quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2, 3 and 4 specifications.
• SBMLValidator.CHECK_CATEGORY.MATHML_CONSISTENCY : Syntax of MathML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2, 3 and 4 specifications.
• SBMLValidator.CHECK_CATEGORY.SBO_CONSISTENCY : Consistency and validity of SBO identifiers (if any) used in the model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2, 3 and 4 specifications.
• SBMLValidator.CHECK_CATEGORY.OVERDETERMINED_MODEL : Static analysis of whether the system of equations implied by a model is mathematically over-determined. With respect to the SBML specification, this is validation rule #10601 in the SBML Level 2 Versions 2, 3 and 4 specifications.
• SBMLValidator.CHECK_CATEGORY.MODELING_PRACTICE : Additional checks for recommended good modeling practice. (These are tests performed by libSBML and do not have equivalent SBML validation rules.)

By default, all validation checks are applied to the model in an SBMLDocument object unless SBMLDocument#setConsistencyChecks(CHECK_CATEGORY, boolean) is called to indicate that only a subset should be applied. Further, this default (i.e., performing all checks) applies separately to each new SBMLDocument object created. In other words, each time a model is read using SBMLReader.readSBML(String) , SBMLReader.readSBMLFromString(String), a new SBMLDocument is created and for that document, a call to checkConsistency() will default to applying all possible checks. Calling programs must invoke SBMLDocument#setConsistencyChecks(CHECK_CATEGORY, boolean) for each such new model if they wish to change the consistency checks applied.

Parameters:

category - a value drawn from JSBML#JSBML.SBML_VALIDATOR_* indicating the consistency checking/validation to be turned on or off

apply - a boolean indicating whether the checks indicated by category should be applied or not.

See Also:

checkConsistency()

setLevelAndVersion

public boolean setLevelAndVersion(int level,
                                  int version)

Sets the SBML Level and Version of this SBMLDocument instance, without attempting to convert the model.

Parameters:

level - the desired SBML Level

version - the desired Version within the SBML Level

Returns:

true if 'level' and 'version' are valid.

See Also:

setLevelAndVersion(int, int, boolean)

setLevelAndVersion

public boolean setLevelAndVersion(int level,
                                  int version,
                                  boolean strict)

Sets the SBML Level and Version of this SBMLDocument instance, attempting to convert the model as needed.

This method is the principal way in JSBML to convert models between Levels and Versions of SBML. Generally, models can be converted upward without difficulty (e.g., from SBML Level 1 to Level 2, or from an earlier Version of Level 2 to the latest Version of Level 2). Sometimes models can be translated downward as well, if they do not use constructs specific to more advanced Levels of SBML.

Calling this method will not necessarily lead to a successful conversion. If the conversion fails, it will be logged in the error list associated with this SBMLDocument. Callers should consult getErrorCount() to find out if the conversion succeeded without problems. For conversions from Level 2 to Level 1, callers can also check the Level of the model after calling this method to find out whether it is Level 1. (If the conversion to Level 1 failed, the Level of this model will be left unchanged.)

Overrides:

setLevelAndVersion in class AbstractSBase

Parameters:

level - the desired SBML Level

version - the desired Version within the SBML Level

strict - boolean indicating whether to check consistency of both the source and target model when performing conversion (defaults to true)

Returns:

true if 'level' and 'version' are valid.

setModel

public void setModel(Model model)

Sets the Model for this SBMLDocument to the given Model.

Parameters:

model -

setPackageRequired

public boolean setPackageRequired(java.lang.String nameOrUri,
                                  boolean flag)

Sets the required attribute value of the given package extension (does nothing in fact!).

Parameters:

nameOrUri - the name or URI of the package extension.

flag - boolean value indicating whether the package is required.

Returns:

true

setPkgRequired

@Deprecated
public boolean setPkgRequired(java.lang.String pckage,
                                          boolean flag)

Deprecated. use setPackageRequired(String, boolean)

Sets the value of the required attribute for the given package (does nothing in fact!).

Parameters:

pckage - the name or URI of the package extension.

flag - a Boolean value indicating whether the package is required.

Returns:

true

setSBMLDocumentAttributes

public void setSBMLDocumentAttributes(java.util.Map<java.lang.String,java.lang.String> attributes)

Sets the SBMLDocumentAttributes.

Parameters:

attributes -

toString

public java.lang.String toString()

Description copied from class: AbstractSBase

Returns a String representing this SBase with all the attributes that are defined.

Overrides:

toString in class AbstractSBase

Returns:

a String representing this SBase with all its attributes

unsetModel

public boolean unsetModel()

Sets the Model of this SBMLDocument to null and notifies all TreeNodeChangeListener about changes.

Returns:

true if calling this method changed the properties of this element.

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.