org.xmlcml.cml
Class CMLBaseImpl

java.lang.Object
  |
  +--org.apache.xerces.dom.NodeImpl
        |
        +--org.apache.xerces.dom.ChildNode
              |
              +--org.apache.xerces.dom.ChildAndParentNode
                    |
                    +--org.apache.xerces.dom.ElementImpl
                          |
                          +--uk.co.demon.ursus.dom.AbstractElementImpl
                                |
                                +--uk.co.demon.ursus.dom.PMRElementImpl
                                      |
                                      +--org.xmlcml.cml.CMLBaseImpl

Direct Known Subclasses:

AbstractAtomRefImpl, AbstractBuiltinContainerImpl, AbstractStringValImpl, CMLImpl, ElectronImpl, ExecuteImpl, FeatureImpl, FormulaImpl, LinkImpl, ListImpl, MoleculeImpl, ReactionImpl, SequenceImpl

public abstract class CMLBaseImpl

extends PMRElementImpl

implements CMLBase

The base class for all elementObjects mentioned in the CML DTD.

Any CML element may have attributes:

• title
• id
• dictRef
• convention

and convenience get/set methods are provided for all, through the interfaces HasTitle, HasId and HasConvention.

An element (FOO) subclassed from a CMLBase may be constructed in the following ways:

• FOO(). Creates a new empty element with null values of the attributes. Required for newInstance(), but use carefully since it has no tagName and no document associated with it.
• FOO(String tagName, Document document). Creates an empty element with null attribute names.
• FOO(org.w3c.dom.Element element). Creates a subclassed Element with the same attribute values as the input Element. Used when a DOM has been created with non-CML-aware software. The routine makeAndProcessSubclass(Element element) will replace the current Element with the appropriate CML subclass.
• FOO(String title, String id, String dictRef, String conventionName). Makes subclassed Element and sets attribute values.

See Also:

Serialized Form

Field Summary

protected java.lang.String	conventionName
protected static java.util.Hashtable	conventionTable
protected java.lang.String	dictRef
protected java.lang.String	id
protected java.lang.String	title
protected CMLValidity	validity

Fields inherited from class uk.co.demon.ursus.dom.PMRElementImpl

CLASSNAME, processFlag

Fields inherited from class uk.co.demon.ursus.dom.AbstractElementImpl

CLASSNAME

Fields inherited from class org.apache.xerces.dom.ElementImpl

attributes, name

Fields inherited from class org.apache.xerces.dom.ChildAndParentNode

changes, firstChild, nodeListIndex, nodeListLength, nodeListNode, ownerDocument

Fields inherited from class org.apache.xerces.dom.ChildNode

nextSibling, previousSibling

Fields inherited from class org.apache.xerces.dom.NodeImpl

ELEMENT_DEFINITION_NODE, FIRSTCHILD, flags, IGNORABLEWS, MUTATION_AGGREGATE, MUTATION_ALL, MUTATION_LOCAL, MUTATION_NONE, MUTATIONEVENTS, OWNED, ownerNode, READONLY, SETVALUE, SPECIFIED, SYNCCHILDREN, SYNCDATA

Fields inherited from interface org.xmlcml.cml.CMLBase

ANGLE, ATOM, ATOMARRAY, BOND, BONDARRAY, BUILTIN, CML, CRYSTAL, ELECTRON, ELEMENT_COUNT, ELEMENT_NAMES, EXECUTE, FEATURE, FLOAT, FLOAT_TYPE, FLOATARRAY, FLOATMATRIX, FORMULA, INTEGER, INTEGER_TYPE, INTEGERARRAY, LINK, LIST, MOLECULE, PACKAGE_NAME, REACTION, SEQUENCE, STRING, STRING_TYPE, STRINGARRAY, TORSION, UNK, UNK_ELEM, UNKNOWN

Fields inherited from interface uk.co.demon.ursus.dom.PMRElement

CLASSNAME, LOCAL, QUALIFIED, UNIVERSAL

Fields inherited from interface org.xmlcml.cml.HasTitle

TITLE

Fields inherited from interface org.xmlcml.cml.HasDictRef

DICTREF

Fields inherited from interface org.xmlcml.cml.HasId

ID

Fields inherited from interface org.xmlcml.cml.HasConvention

CONVENTION

Fields inherited from interface uk.co.demon.ursus.dom.PMRNode

ATTRIBUTES, CONTENT, ELEMENTNAME, IDLIST, NESTED, NESTEDATTS, PACKAGENAME, PRETTY, SPLITFILES, STYLE, TAGGED, UNTAGGED, WHITESPACE, XMLCONTENT

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

Constructor Summary

CMLBaseImpl()
create a Node WITHOUT tagName OR document.

CMLBaseImpl(org.w3c.dom.Element element)
used when analysing a DOM

CMLBaseImpl(java.lang.String tagName, org.w3c.dom.Document document)
used when creating new nodes in a DOM

CMLBaseImpl(java.lang.String tagName, org.w3c.dom.Document document, java.lang.String title, java.lang.String id, java.lang.String dictRef, java.lang.String conventionName)

Method Summary

void	addValidity(CMLValidity v) potentially subclassable to determine whether a node is valid.
static PMRElement	convertToSubclass(org.w3c.dom.Element element) recursively process all nodes.
void	debug(java.io.Writer w) output debug info to Writer and return String equivalent (e.g.
java.lang.String	getConventionName()
java.lang.String	getDictRef()
java.lang.String	getId()
static PMRElement	getSubClassedElement(java.lang.String name, CMLDocument cmlDocument) create a PMRElement (usually a CMLBase) and processDOM() it.
java.lang.String	getTitle()
Validity	getValidity() Determines whether node is valid (class specific).
static void	help()
boolean	isValid() convenience to avoid analysing Validity
static void	main(java.lang.String[] args)
void	processDOM() subclassed if necessary
void	setConventionName(java.lang.String conventionName)
void	setDictRef(java.lang.String dictRef)
void	setId(java.lang.String id)
void	setTitle(java.lang.String title)
static void	showElementNames()
static void	test1(java.lang.String[] args)
void	updateDOM()
void	updateDOMHasConvention()
static void	updateDOMHasConvention(HasConvention element)
static void	updateDOMHasCount(HasCount element)
void	updateDOMHasDictRef()
static void	updateDOMHasDictRef(HasDictRef element)
void	updateDOMHasId()
static void	updateDOMHasId(HasId element)
void	updateDOMHasTitle()
static void	updateDOMHasTitle(HasTitle element)
static void	updateDOMHasUnits(HasUnits element)

Methods inherited from class uk.co.demon.ursus.dom.PMRElementImpl

appendTo, initialise, processDescendants, setProcessFlag

Methods inherited from class uk.co.demon.ursus.dom.AbstractElementImpl

setTagName

Methods inherited from class org.apache.xerces.dom.ElementImpl

cloneNode, getAttribute, getAttributeNode, getAttributeNodeNS, getAttributeNS, getAttributes, getElementsByTagName, getElementsByTagNameNS, getNodeName, getNodeType, getTagName, hasAttribute, hasAttributeNS, normalize, removeAttribute, removeAttributeNode, removeAttributeNS, setAttribute, setAttributeNode, setAttributeNodeNS, setAttributeNS, setReadOnly, setupDefaultAttributes, synchronizeData

Methods inherited from class org.apache.xerces.dom.ChildAndParentNode

changed, changes, getChildNodes, getFirstChild, getLastChild, getLength, getOwnerDocument, hasChildNodes, insertBefore, item, removeChild, replaceChild, synchronizeChildren, synchronizeChildren

Methods inherited from class org.apache.xerces.dom.ChildNode

getNextSibling, getParentNode, getPreviousSibling

Methods inherited from class org.apache.xerces.dom.NodeImpl

addEventListener, appendChild, dispatchEvent, finalize, getLocalName, getNamespaceURI, getNodeValue, getPrefix, getReadOnly, getUserData, removeEventListener, setNodeValue, setPrefix, setUserData, supports, toString

Methods inherited from class java.lang.Object

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

Field Detail

conventionTable

protected static java.util.Hashtable conventionTable

title

protected java.lang.String title

id

protected java.lang.String id

dictRef

protected java.lang.String dictRef

conventionName

protected java.lang.String conventionName

validity

protected CMLValidity validity

Constructor Detail

CMLBaseImpl

public CMLBaseImpl()

create a Node WITHOUT tagName OR document. Use with care

CMLBaseImpl

public CMLBaseImpl(java.lang.String tagName,
                   org.w3c.dom.Document document)

used when creating new nodes in a DOM

CMLBaseImpl

public CMLBaseImpl(org.w3c.dom.Element element)

used when analysing a DOM

CMLBaseImpl

public CMLBaseImpl(java.lang.String tagName,
                   org.w3c.dom.Document document,
                   java.lang.String title,
                   java.lang.String id,
                   java.lang.String dictRef,
                   java.lang.String conventionName)

Method Detail

showElementNames

public static final void showElementNames()

setTitle

public void setTitle(java.lang.String title)

getTitle

public java.lang.String getTitle()

setId

public void setId(java.lang.String id)

getId

public java.lang.String getId()

setDictRef

public void setDictRef(java.lang.String dictRef)

getDictRef

public java.lang.String getDictRef()

setConventionName

public void setConventionName(java.lang.String conventionName)

getConventionName

public java.lang.String getConventionName()

convertToSubclass

public static PMRElement convertToSubclass(org.w3c.dom.Element element)
                                    throws java.lang.Exception

recursively process all nodes. Assumes we have built a DOM and all Nodes are of type Element. They need to be converted to PMRElement or a subclass of it

getSubClassedElement

public static PMRElement getSubClassedElement(java.lang.String name,
                                              CMLDocument cmlDocument)
                                       throws java.lang.Exception

create a PMRElement (usually a CMLBase) and processDOM() it.

processDOM

public void processDOM()
                throws CMLException

subclassed if necessary

Specified by:

processDOM in interface CMLBase

Overrides:

processDOM in class PMRElementImpl

Tags copied from class: PMRElementImpl

Throws:

java.lang.Exception - these can be of many kinds and may include class-specific ones

addValidity

public void addValidity(CMLValidity v)

potentially subclassable to determine whether a node is valid. Validity objects are merged as they are added. Cleared by adding a null Validity.

Specified by:

addValidity in interface CMLBase

Tags copied from interface: CMLBase

Returns:

boolean truue by default

getValidity

public Validity getValidity()

Description copied from interface: PMRElement

Determines whether node is valid (class specific). Perhaps used in treeWalk mode

Overrides:

getValidity in class PMRElementImpl

isValid

public boolean isValid()

Description copied from interface: CMLBase

convenience to avoid analysing Validity

Specified by:

isValid in interface CMLBase

debug

public void debug(java.io.Writer w)
           throws java.io.IOException

output debug info to Writer and return String equivalent (e.g. with new StringWriter()

Specified by:

debug in interface CMLBase

Parameters:

Writer - w Writer to output to

Returns:

the String equivalent

help

public static void help()

updateDOMHasConvention

public static void updateDOMHasConvention(HasConvention element)

updateDOMHasDictRef

public static void updateDOMHasDictRef(HasDictRef element)

updateDOMHasCount

public static void updateDOMHasCount(HasCount element)

updateDOMHasId

public static void updateDOMHasId(HasId element)

updateDOMHasTitle

public static void updateDOMHasTitle(HasTitle element)

updateDOMHasUnits

public static void updateDOMHasUnits(HasUnits element)

updateDOMHasConvention

public void updateDOMHasConvention()

updateDOMHasDictRef

public void updateDOMHasDictRef()

updateDOMHasId

public void updateDOMHasId()

updateDOMHasTitle

public void updateDOMHasTitle()

updateDOM

public void updateDOM()
               throws CMLException

Specified by:

updateDOM in interface CMLBase

test1

public static void test1(java.lang.String[] args)
                  throws java.lang.Exception

main

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