org.xmlcml.noncml
Class NonCMLDocumentImpl

java.lang.Object
  |
  +--org.apache.xerces.dom.NodeImpl
        |
        +--org.apache.xerces.dom.ParentNode
              |
              +--org.apache.xerces.dom.DocumentImpl
                    |
                    +--uk.co.demon.ursus.dom.AbstractDocumentImpl
                          |
                          +--uk.co.demon.ursus.dom.PMRDocumentImpl
                                |
                                +--org.xmlcml.cml.CMLDocumentImpl
                                      |
                                      +--org.xmlcml.noncml.NonCMLDocumentImpl

Direct Known Subclasses:

JMEImpl, MDLMolImpl, SDFImpl, SMILESImpl, XYZImpl

public abstract class NonCMLDocumentImpl

extends CMLDocumentImpl

implements NonCMLDocument

base class for all nonCML molecules

See Also:

Serialized Form

Field Summary

protected org.w3c.dom.NodeList	atomList general tools for input and output
protected CMLBase	atomParent
protected org.w3c.dom.NodeList	bondList
protected CMLBase	bondParent
protected java.io.BufferedReader	bReader most input requires a BufferedReader
protected CML	inputCML the CML object created from the input legacy
protected Molecule	inputCMLMolecule the molecule created from the input legacy
protected java.lang.String	line and uses a line as the container
protected int	natoms
protected int	nbonds
protected CML	outputCML a CML object to be output as legacy
protected Molecule	outputCMLMolecule a CML Molecule to be output as legacy

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

DEFAULT_PARSER_NAME, docElement

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

allowGrammarAccess, docElement, docType, errorChecking, identifiers, iterators, kidOK, ranges, treeWalkers, userData

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

changes, firstChild, nodeListIndex, nodeListLength, nodeListNode, ownerDocument

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.noncml.NonCMLDocument

JME, MDLMOL, SDF, SMILES, XYZ

Fields inherited from interface org.xmlcml.cml.CMLDocument

PACKAGE_NAME

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

PACKAGENAME

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

NonCMLDocumentImpl()

Method Summary

protected void	createCMLElement(java.lang.String convention, java.lang.String id)
protected void	createMoleculeElement(java.lang.String convention, java.lang.String id)

Methods inherited from class org.xmlcml.cml.CMLDocumentImpl

createCMLDocument, createCMLDocument, debug, getMolecule, main, test1

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

createDocument, createDocument, testBuild, testRead

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

adoptNode, clone, cloneNode, createAttribute, createAttributeNS, createCDATASection, createComment, createDocumentFragment, createDocumentType, createElement, createElementDefinition, createElementNS, createEntity, createEntityReference, createEvent, createNodeIterator, createNodeIterator, createNotation, createProcessingInstruction, createRange, createTextNode, createTreeWalker, createTreeWalker, getDoctype, getDocumentElement, getElementById, getElementsByTagName, getElementsByTagNameNS, getErrorChecking, getIdentifier, getIdentifiers, getImplementation, getNodeIterators, getNodeName, getNodeType, getOwnerDocument, getRanges, getTreeWalkers, getUserData, importNode, insertBefore, isKidOK, isXMLName, putIdentifier, removeChild, removeIdentifier, removeTreeWalker, setErrorChecking, setUserData

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

changed, changes, getChildNodes, getFirstChild, getLastChild, getLength, hasChildNodes, item, normalize, replaceChild, setReadOnly, synchronizeChildren, synchronizeChildren

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

addEventListener, appendChild, dispatchEvent, finalize, getAttributes, getLocalName, getNamespaceURI, getNextSibling, getNodeValue, getParentNode, getPrefix, getPreviousSibling, getReadOnly, getUserData, removeEventListener, setNodeValue, setPrefix, setUserData, supports, synchronizeData, toString

Methods inherited from class java.lang.Object

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

Field Detail

inputCML

protected CML inputCML

the CML object created from the input legacy

outputCML

protected CML outputCML

a CML object to be output as legacy

inputCMLMolecule

protected Molecule inputCMLMolecule

the molecule created from the input legacy

outputCMLMolecule

protected Molecule outputCMLMolecule

a CML Molecule to be output as legacy

bReader

protected java.io.BufferedReader bReader

most input requires a BufferedReader

line

protected java.lang.String line

and uses a line as the container

atomList

protected org.w3c.dom.NodeList atomList

general tools for input and output

bondList

protected org.w3c.dom.NodeList bondList

natoms

protected int natoms

nbonds

protected int nbonds

atomParent

protected CMLBase atomParent

bondParent

protected CMLBase bondParent

Constructor Detail

NonCMLDocumentImpl

public NonCMLDocumentImpl()

Method Detail

createMoleculeElement

protected void createMoleculeElement(java.lang.String convention,
                                     java.lang.String id)

createCMLElement

protected void createCMLElement(java.lang.String convention,
                                java.lang.String id)