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

Version:

$Rev: 1639 $

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 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_L3V1Core` The namespace URI of SBML Level 3 Version 1.

Fields inherited from class org.sbml.jsbml.AbstractSBase
ignoredExtensions, ignoredXMLElements, lv

Fields inherited from class org.sbml.jsbml.AbstractTreeNode
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

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

Methods
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/).
`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.
`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 `SBMLError`s reflecting problems in the overall data structure of this `SBMLDocument`.
`SBMLErrorLog`	`getListOfErrors()` Returns a collection of all `SBMLError`s 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()`
`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`.
`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.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)` If the attribute is an id or name attribute, it will set the id or name of this object with the value of the XML attribute ('value').
`(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`.
`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()`
`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()`

Methods inherited from class org.sbml.jsbml.AbstractSBase
addCVTerm, addDeclaredNamespace, addExtension, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getExtension, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregister, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

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 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_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
  - 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 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.
    
    Parameters:
    sb -
  - 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 -
    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. This is a helper method until the methods enablePackage() are implemented.
    
    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
  - 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 @em 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
  - 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
    
    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.
    
    Parameters:
    metaid - - the metaid of SBase to find
    
    Returns:
    the SBase with the given metaid or null
    See Also:
    findSBase(String)
  - getError
```
public SBMLError getError(int i)
```
    Returns the ith error or warning encountered during consistency checking.
    
    Parameters:
    i - - the index of the SBMLError to get
    
    Returns:
    the ith 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()
```
    Specified by:
    
    hashCode in interface SBase
    
    Overrides:
    
    hashCode in class AbstractSBase
    
    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.
    
    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.
  - 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
    
    If the attribute is an id or name attribute, it will set the id or name of this object with the value of the XML attribute ('value').
    
    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.
  - 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 CHECK_CATEGORYH enumeration. The following are the possible choices:
  - 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.
  - 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.
  - 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.
  - 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.
  - 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.
  - OVERDETERMINED_MODEL: Static analysis of whether the system of equations implied by a model is mathematically overdetermined. With respect to the SBML specification, this is validation rule #10601 in the SBML Level 2 Versions 2, 3 and 4 specifications.
  - 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(int, 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(int, 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()
```
Specified by:

toString in class AbstractSBase

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()
```
Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:
a Map containing the XML attributes of this object.

Class SBMLDocument

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

Constructor Summary

Method Summary

Methods inherited from class org.sbml.jsbml.AbstractSBase

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

Methods inherited from class java.lang.Object

Methods inherited from interface org.sbml.jsbml.SBase

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

Methods inherited from interface javax.swing.tree.TreeNode

Field Detail

serialVersionUID

URI_NAMESPACE_L1

URI_NAMESPACE_L2V1

URI_NAMESPACE_L2V2

URI_NAMESPACE_L2V3

URI_NAMESPACE_L2V4

URI_NAMESPACE_L3V1Core

checkConsistencyParameters

listOfErrors

logger

mappingFromMetaId2SBase

model

enabledPackageMap

SBMLDocumentAttributes

Constructor Detail

SBMLDocument

SBMLDocument

SBMLDocument

Method Detail

addNamespace

addPackageDeclaration

checkConsistency

checkMetaId

clone

collectMetaIds

containsMetaId

createModel

createModel

disablePackage

enablePackage

enablePackage

equals

findSBase

getAllowsChildren

getChildAt

getChildCount

getDefaultLevel

getDefaultVersion

getElementName

getElementByMetaId

getError

getErrorCount

getErrorLog

getListOfErrors

getModel

getNumErrors

getPackageRequired

getPkgRequired

getSBMLDocumentAttributes

getSBMLDocumentNamespaces

hashCode

initDefaults

isIgnoredPackage

isIgnoredPkg

isPackageEnabled

isSetListOfErrors

isSetModel

isSetPackageRequired

isSetPkgRequired

nextMetaId

printErrors

readAttribute

registerMetaId

registerMetaIds

setConsistencyChecks

setLevelAndVersion

setLevelAndVersion