org.jscience.ml.cml.cmlimpl
Class AbstractCMLDocumentImpl

java.lang.Object
  org.jscience.ml.cml.dom.pmr.PMRNodeImpl
      org.jscience.ml.cml.dom.pmr.PMRDocumentImpl
          org.jscience.ml.cml.cmlimpl.AbstractCMLDocumentImpl

All Implemented Interfaces:

AbstractCMLDocument, CMLNode, PMRDocument, org.w3c.dom.Document, org.w3c.dom.Node

public class AbstractCMLDocumentImpl
extends PMRDocumentImpl
implements AbstractCMLDocument

The base class for any CML Document objects

Field Summary

protected boolean	arraySyntax
protected boolean	debug
static java.lang.String	DEFAULT_OUTPUT_DTD Description of the Field
static java.lang.String	DEFAULT_OUTPUT_ENCODING Description of the Field
protected java.lang.String	version

Fields inherited from class org.jscience.ml.cml.dom.pmr.PMRNodeImpl

childNodes, delegateNode, parentNode, pmrDocument, siblingNodes

Fields inherited from interface org.jscience.ml.cml.AbstractCMLDocument

DEFAULT_OUTPUT_NAMESPACE, NULL_DTD, NULL_NAMESPACE, PACKAGE_NAME

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_POSITION_CONTAINED_BY, DOCUMENT_POSITION_CONTAINS, DOCUMENT_POSITION_DISCONNECTED, DOCUMENT_POSITION_FOLLOWING, DOCUMENT_POSITION_IMPLEMENTATION_SPECIFIC, DOCUMENT_POSITION_PRECEDING, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

Fields inherited from interface org.jscience.ml.cml.CMLNode

ARRAY, CML1, CML2

Constructor Summary

	AbstractCMLDocumentImpl() create an Empty Document.
protected	AbstractCMLDocumentImpl(org.w3c.dom.Document doc) Constructor for the AbstractCMLDocumentImpl object

Method Summary

AbstractBase	clone(AbstractBase element) clone element in context of document.
AbstractBase	createAbstractBase() creates new AbstractBase
org.w3c.dom.Element	createSubclassedElement(java.lang.String tagName) Description of the Method
protected void	debug(java.lang.String s) output string if debug set
boolean	getDebug() debug status
org.w3c.dom.Element[]	getElementList(java.lang.String elementName) getElementList (cf AbstractBase) NOTE this will get subelements as well as toplevel ones (for example Molecules which have Molecule children)
java.util.Vector	getElementVector(java.lang.String elementName) getChildVector (cf AbstractBase)
org.w3c.dom.Element	getFirstElement(java.lang.String elementName) getFirstChild (cf AbstractBase)
static void	main(java.lang.String[] args) main
void	setArraySyntax(boolean syntax) set array syntax set CML array syntax (default false)
void	setDebug(boolean d) toggle debugging
void	setVersion(java.lang.String v) set CML version 1 or 2 at present (default 2)
org.w3c.dom.Element	subclass(org.w3c.dom.Element oldEl) DOCUMENT ME!
static AbstractBase	transferOwnerDocument(AbstractCMLDocument doc, AbstractBase elem)
void	updateDelegates() update delegates.
void	updateDOM() update DOM.
void	writeXML(java.io.Writer w) write XML use current control (version and syntax)
void	writeXML(java.io.Writer w, java.lang.String control) write the document in XML, using node-specific routines

Methods inherited from class org.jscience.ml.cml.dom.pmr.PMRDocumentImpl

adoptNode, createAttribute, createAttributeNS, createCDATASection, createComment, createDocumentFragment, createElement, createElementNS, createEntityReference, createProcessingInstruction, createTextNode, getDoctype, getDocumentElement, getDocumentURI, getDomConfig, getElementById, getElementsByTagName, getElementsByTagNameNS, getImplementation, getInputEncoding, getStrictErrorChecking, getXmlEncoding, getXmlStandalone, getXmlVersion, importNode, normalizeDocument, renameNode, setDocumentURI, setStrictErrorChecking, setXmlStandalone, setXmlVersion, test, test, toString

Methods inherited from class org.jscience.ml.cml.dom.pmr.PMRNodeImpl

appendChild, cloneNode, compareDocumentPosition, getAttributes, getBaseURI, getChildNodes, getDelegateNode, getDelegateParentNode, getFeature, getFirstChild, getLastChild, getLocalName, getNamespaceURI, getNextSibling, getNodeName, getNodeType, getNodeValue, getOwnerDocument, getParentNode, getPrefix, getPreviousSibling, getTextContent, getUserData, hasAttributes, hasChildNodes, insertBefore, isDefaultNamespace, isEqualNode, isSameNode, isSupported, lookupNamespaceURI, lookupPrefix, normalize, removeChild, replaceChild, setDelegateNode, setNodeValue, setOwnerDocument, setOwnerDocumentRecursively, setPrefix, setTextContent, setUserData, wrapRecursively

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.w3c.dom.Document

adoptNode, createAttribute, createAttributeNS, createCDATASection, createComment, createDocumentFragment, createElement, createElementNS, createEntityReference, createProcessingInstruction, createTextNode, getDoctype, getDocumentElement, getDocumentURI, getDomConfig, getElementById, getElementsByTagName, getElementsByTagNameNS, getImplementation, getInputEncoding, getStrictErrorChecking, getXmlEncoding, getXmlStandalone, getXmlVersion, importNode, normalizeDocument, renameNode, setDocumentURI, setStrictErrorChecking, setXmlStandalone, setXmlVersion

Methods inherited from interface org.w3c.dom.Node

appendChild, cloneNode, compareDocumentPosition, getAttributes, getBaseURI, getChildNodes, getFeature, getFirstChild, getLastChild, getLocalName, getNamespaceURI, getNextSibling, getNodeName, getNodeType, getNodeValue, getOwnerDocument, getParentNode, getPrefix, getPreviousSibling, getTextContent, getUserData, hasAttributes, hasChildNodes, insertBefore, isDefaultNamespace, isEqualNode, isSameNode, isSupported, lookupNamespaceURI, lookupPrefix, normalize, removeChild, replaceChild, setNodeValue, setPrefix, setTextContent, setUserData

Field Detail

DEFAULT_OUTPUT_ENCODING

public static final java.lang.String DEFAULT_OUTPUT_ENCODING

Description of the Field

See Also:

Constant Field Values

DEFAULT_OUTPUT_DTD

public static final java.lang.String DEFAULT_OUTPUT_DTD

Description of the Field

See Also:

Constant Field Values

version

protected java.lang.String version

arraySyntax

protected boolean arraySyntax

debug

protected boolean debug

Constructor Detail

AbstractCMLDocumentImpl

public AbstractCMLDocumentImpl()

create an Empty Document. probably should only be used when we need an instance of this class for introspection

AbstractCMLDocumentImpl

protected AbstractCMLDocumentImpl(org.w3c.dom.Document doc)

Constructor for the AbstractCMLDocumentImpl object

Parameters:

doc - Description of the Parameter

Method Detail

transferOwnerDocument

public static AbstractBase transferOwnerDocument(AbstractCMLDocument doc,
                                                 AbstractBase elem)

createSubclassedElement

public org.w3c.dom.Element createSubclassedElement(java.lang.String tagName)

Description of the Method

Specified by:

createSubclassedElement in interface AbstractCMLDocument

Parameters:

tagName - Description of the Parameter

Returns:

Description of the Return Value

subclass

public org.w3c.dom.Element subclass(org.w3c.dom.Element oldEl)

Description copied from interface: AbstractCMLDocument

DOCUMENT ME!

Specified by:

subclass in interface AbstractCMLDocument

Parameters:

oldEl - DOCUMENT ME!

Returns:

DOCUMENT ME!

createAbstractBase

public AbstractBase createAbstractBase()

creates new AbstractBase

Specified by:

createAbstractBase in interface AbstractCMLDocument

Returns:

the new element

getFirstElement

public org.w3c.dom.Element getFirstElement(java.lang.String elementName)

getFirstChild (cf AbstractBase)

Specified by:

getFirstElement in interface AbstractCMLDocument

Parameters:

elementName - Description of the Parameter

Returns:

the Element (null if none)

getElementList

public org.w3c.dom.Element[] getElementList(java.lang.String elementName)

getElementList (cf AbstractBase) NOTE this will get subelements as well as toplevel ones (for example Molecules which have Molecule children)

Specified by:

getElementList in interface AbstractCMLDocument

Parameters:

elementName - Description of the Parameter

Returns:

the Elements (null if none)

getElementVector

public java.util.Vector getElementVector(java.lang.String elementName)

getChildVector (cf AbstractBase)

Specified by:

getElementVector in interface AbstractCMLDocument

Parameters:

elementName - Description of the Parameter

Returns:

the Elements (empty list if none)

setDebug

public void setDebug(boolean d)

toggle debugging

Specified by:

setDebug in interface AbstractCMLDocument

Parameters:

d - debug

getDebug

public boolean getDebug()

debug status

Specified by:

getDebug in interface AbstractCMLDocument

Returns:

is debug set

debug

protected void debug(java.lang.String s)

output string if debug set

Parameters:

s - string to output

setVersion

public void setVersion(java.lang.String v)
                throws CMLException

set CML version

1 or 2 at present (default 2)

Specified by:

setVersion in interface CMLNode

Parameters:

v - version

Throws:

unsupported - version

CMLException

setArraySyntax

public void setArraySyntax(boolean syntax)

set array syntax

set CML array syntax (default false)

Specified by:

setArraySyntax in interface CMLNode

Parameters:

syntax -

writeXML

public void writeXML(java.io.Writer w)
              throws CMLException,
                     java.io.IOException

write XML use current control (version and syntax)

Specified by:

writeXML in interface CMLNode

Parameters:

w - - output

Throws:

CMLException

java.io.IOException

writeXML

public void writeXML(java.io.Writer w,
                     java.lang.String control)
              throws java.io.IOException,
                     CMLException

write the document in XML, using node-specific routines

Specified by:

writeXML in interface CMLNode

Parameters:

w - the writer

control - (cannot remember what this does!)

Throws:

java.io.IOException - Description of the Exception

CMLException - Description of the Exception

main

public static void main(java.lang.String[] args)

main

Parameters:

args - command line

clone

public AbstractBase clone(AbstractBase element)
                   throws CMLException

clone element in context of document.

Specified by:

clone in interface AbstractCMLDocument

Parameters:

element - to clone (may or may not be owned by this)

Returns:

the cloned element (owner is this)

Throws:

CMLException - cannot clone non-AbstractBase

updateDelegates

public void updateDelegates()

update delegates. updates documentElement delegates (content and attributes) then recurses through children

Specified by:

updateDelegates in interface AbstractCMLDocument

updateDOM

public void updateDOM()

update DOM. updates documentElement DOM (content and attributes) then recurses through children

Specified by:

updateDOM in interface AbstractCMLDocument