Uses of Interface
org.episteme.natural.chemistry.loaders.cml.AbstractCMLDocument

Packages that use AbstractCMLDocument

Package	Description
org.episteme.natural.chemistry.loaders.cml	Provides the org.episteme.natural.chemistry.loaders.cml module.
org.episteme.natural.chemistry.loaders.cml.cmlimpl	Provides the org.episteme.natural.chemistry.loaders.cml.cmlimpl module.

Uses of AbstractCMLDocument in org.episteme.natural.chemistry.loaders.cml

Subclasses with type arguments of type AbstractCMLDocument in org.episteme.natural.chemistry.loaders.cml

Modifier and Type	Class	Description
class	CMLReader	Chemical Markup Language (CML) Reader.

Methods in org.episteme.natural.chemistry.loaders.cml that return AbstractCMLDocument

Modifier and Type	Method	Description
AbstractCMLDocument	CMLDocumentFactory.createDocument()	create document with current documentClassName
AbstractCMLDocument	AbstractBase.getCMLDocument()	get owner document as CMLDocument.
AbstractCMLDocument	Workflow.getCMLDocument()	Gets the CMLDocument for object creation.
protected AbstractCMLDocument	CMLReader.loadFromInputStream(InputStream is, String id)
protected AbstractCMLDocument	CMLReader.loadFromSource(String resourceId)
AbstractCMLDocument	CMLDocumentFactory.parseSAX(InputSource is)	Parses an XML document into the DOM, creating a new owner document (debug is false).
AbstractCMLDocument	CMLDocumentFactory.parseSAX(InputSource is, boolean debug)	Parses an XML document into the DOM, creating a new owner document.
AbstractCMLDocument	CMLDocumentFactory.parseString(String xmlString)	convenience method; parses a string representing a well-formed XML document
AbstractCMLDocument	CMLReader.read(File file)	Reads a CML document from a file.
AbstractCMLDocument	CMLReader.read(InputStream input)	Reads a CML document from an input stream.
AbstractCMLDocument	CMLReader.read(URL url)	Reads a CML document from a URL.
AbstractCMLDocument	CMLReader.readFromString(String cml)	Reads a CML document from a string.

Methods in org.episteme.natural.chemistry.loaders.cml that return types with arguments of type AbstractCMLDocument

Modifier and Type	Method	Description
Class<AbstractCMLDocument>	CMLReader.getResourceType()

Methods in org.episteme.natural.chemistry.loaders.cml with parameters of type AbstractCMLDocument

Modifier and Type	Method	Description
AbstractBase	AbstractBase.deepCopy(AbstractCMLDocument document)	deep clones an element including subclassing
BaseTool	BaseTool.getTestInstance(AbstractCMLDocument doc, int serial)	a standard instance for testing. returns null unless subclassed
Element	CMLDocumentFactory.parseSAX(InputSource is, AbstractCMLDocument doc)	parses XML document into existing DOM The new document must be well-formed with a single root element the application will probably wish to relocate this in the DOM. debug is set to false
Element	CMLDocumentFactory.parseSAX(InputSource is, AbstractCMLDocument doc, boolean debug)	parses XML document into existing DOM The new document must be well-formewd with a single root element the application will probably wish to relocate this in the DOM.
int	BaseTool.processCommandLine(String[] args, int offset, List<Object> argVector, AbstractCMLDocument doc)	process the commandline from main routines. normally subclassed

Uses of AbstractCMLDocument in org.episteme.natural.chemistry.loaders.cml.cmlimpl

Classes in org.episteme.natural.chemistry.loaders.cml.cmlimpl that implement AbstractCMLDocument

Modifier and Type	Class	Description
class	AbstractCMLDocumentImpl	The base class for any CML Document objects

Fields in org.episteme.natural.chemistry.loaders.cml.cmlimpl declared as AbstractCMLDocument

Modifier and Type	Field	Description
protected AbstractCMLDocument	BaseToolImpl.document
protected AbstractCMLDocument	CMLBaseImpl.ownerDocument

Methods in org.episteme.natural.chemistry.loaders.cml.cmlimpl that return AbstractCMLDocument

Modifier and Type	Method	Description
AbstractCMLDocument	DocumentFactoryImpl.createDocument()	Creates a CMLDocument instance using the current documentClassName.
AbstractCMLDocument	DocumentFactoryImpl.createDocument(String documentClassName)	Creates a CMLDocument instance using the specified class name.
static AbstractCMLDocument	DocumentFactoryImpl.createNewDocument()	Creates a new CMLDocument this creates Documents of the subclassed documentClassName NOTE: The default class will create Elements of type CMLBaseImpl, subclassed to fit the schema.
AbstractCMLDocument	BaseToolImpl.getCMLDocument()
AbstractCMLDocument	CMLBaseImpl.getCMLDocument()
AbstractCMLDocument	DocumentFactoryImpl.parseSAX(InputSource is)	Parses an XML document via SAX (whitespace is ignored).
AbstractCMLDocument	DocumentFactoryImpl.parseSAX(InputSource is, boolean debug)	Parses an XML document via SAX with optional debugging (whitespace is ignored).
AbstractCMLDocument	DocumentFactoryImpl.parseString(String xmlString)	Convenience method to parse an XML string into a CMLDocument.

Methods in org.episteme.natural.chemistry.loaders.cml.cmlimpl with parameters of type AbstractCMLDocument

Modifier and Type	Method	Description
AbstractBase	CMLBaseImpl.deepCopy(AbstractCMLDocument document)	deep clones an element including subclassing
BaseTool	BaseToolImpl.getTestInstance(AbstractCMLDocument doc, int serial)	a standard instance for testing. returns null unless subclassed
Element	DocumentFactoryImpl.parseSAX(InputSource is, AbstractCMLDocument doc)	Parses an XML document via SAX into an existing DOM (whitespace is ignored).
Element	DocumentFactoryImpl.parseSAX(InputSource is, AbstractCMLDocument doc, boolean debug)	Description of the Method whitespace is ignored
int	BaseToolImpl.processCommandLine(String[] args, int offset, List<Object> argVector, AbstractCMLDocument doc)	process the commandline from main routines. normally subclassed
static AbstractBase	AbstractCMLDocumentImpl.transferOwnerDocument(AbstractCMLDocument doc, AbstractBase elem)

Constructors in org.episteme.natural.chemistry.loaders.cml.cmlimpl with parameters of type AbstractCMLDocument

Modifier	Constructor	Description
	BaseToolImpl(AbstractCMLDocument document)	new BaseTool containing a new AbstractBase.
protected	CMLBaseImpl(String tagName, AbstractCMLDocument document)	used when creating new nodes in a DOM
	SaxHandlerImpl(AbstractCMLDocument d, boolean debug)	Creates a new SaxHandlerImpl object.