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org.xmlcml.cml
Class AbstractAtomImpl

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
                                            |
                                            +--org.xmlcml.cml.AbstractBuiltinContainerImpl
                                                  |
                                                  +--org.xmlcml.cml.AbstractAtomImpl
Direct Known Subclasses:
AtomArrayImpl, AtomImpl
public abstract class AbstractAtomImpl
extends AbstractBuiltinContainerImpl
implements AbstractAtom

See Also:
Serialized Form

Field Summary
protected  double count
           
 
Fields inherited from class org.xmlcml.cml.AbstractBuiltinContainerImpl
builtinValues, nonBuiltinTable
 
Fields inherited from class org.xmlcml.cml.CMLBaseImpl
conventionName, conventionTable, dictRef, id, title, 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.AbstractAtom
ATOM_BUILTIN_COUNT, ATOM_FLOATVAL_COUNT, ATOM_FLOATVAL_END, ATOM_FLOATVAL_START, ATOM_ID, ATOM_INTEGERVAL_COUNT, ATOM_INTEGERVAL_END, ATOM_INTEGERVAL_START, ATOM_PARITY_FLOAT, ATOM_PARITY_INT, ATOM_STRINGVAL_COUNT, ATOM_STRINGVAL_END, ATOM_STRINGVAL_START, ELEMENT_TYPE, FORMAL_CHARGE_FLOAT, FORMAL_CHARGE_INT, HYDROGEN_COUNT_FLOAT, HYDROGEN_COUNT_INT, ISOTOPE_FLOAT, ISOTOPE_INT, NON_HYDROGEN_COUNT_FLOAT, NON_HYDROGEN_COUNT_INT, OCCUPANCY, RESIDUE_ID, RESIDUE_TYPE, SMILESATOMS, SP, SP2, SP3, spTypeStrings, valences, X2, X3, XFRACT, Y2, Y3, YFRACT, Z3, ZFRACT
 
Fields inherited from interface org.xmlcml.cml.AbstractBuiltinContainer
NONUNIQUE, UNIQUE
 
Fields inherited from interface org.xmlcml.cml.HasCount
COUNT
 
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
AbstractAtomImpl()
           
AbstractAtomImpl(org.w3c.dom.Element element)
           
AbstractAtomImpl(java.lang.String tagName, org.w3c.dom.Document document)
           
 
Method Summary
 int getBuiltinCount()
           
static int getBuiltinFloatValCount()
           
static java.lang.String[] getBuiltinFloatValNames()
           
static int getBuiltinIntegerValCount()
           
static java.lang.String[] getBuiltinIntegerValNames()
           
static java.lang.String[] getBuiltinNames()
           
static int getBuiltinStringValCount()
           
static java.lang.String[] getBuiltinStringValNames()
           
 double getCount()
           
 Validity getValidity()
          Determines whether node is valid (class specific).
 void setCount(double count)
           
static void showBuiltinNames()
           
 void updateDOM()
           
 void updateDOMHasCount()
           
 
Methods inherited from class org.xmlcml.cml.AbstractBuiltinContainerImpl
addBuiltinChildWithFloatValue, addBuiltinChildWithIntegerValue, addBuiltinChildWithStringValue, checkBuiltins, deleteNonBuiltinVal, getBuiltinChildElements, getBuiltinChildFloatValue, getBuiltinChildIntegerValue, getBuiltinChildStringValue, getBuiltinVal, getNonBuiltinVal, setBuiltinVal, setNonBuiltinVal
 
Methods inherited from class org.xmlcml.cml.CMLBaseImpl
addValidity, convertToSubclass, debug, getConventionName, getDictRef, getId, getSubClassedElement, getTitle, help, isValid, main, processDOM, setConventionName, setDictRef, setId, setTitle, showElementNames, test1, updateDOMHasConvention, updateDOMHasConvention, updateDOMHasCount, updateDOMHasDictRef, updateDOMHasDictRef, updateDOMHasId, updateDOMHasId, updateDOMHasTitle, updateDOMHasTitle, updateDOMHasUnits
 
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

count

protected double count
Constructor Detail

AbstractAtomImpl

public AbstractAtomImpl()

AbstractAtomImpl

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

AbstractAtomImpl

public AbstractAtomImpl(org.w3c.dom.Element element)
Method Detail

getBuiltinFloatValNames

public static java.lang.String[] getBuiltinFloatValNames()

getBuiltinFloatValCount

public static int getBuiltinFloatValCount()

getBuiltinIntegerValNames

public static java.lang.String[] getBuiltinIntegerValNames()

getBuiltinIntegerValCount

public static int getBuiltinIntegerValCount()

getBuiltinStringValNames

public static java.lang.String[] getBuiltinStringValNames()

getBuiltinStringValCount

public static int getBuiltinStringValCount()

getBuiltinNames

public static java.lang.String[] getBuiltinNames()

getBuiltinCount

public int getBuiltinCount()
Overrides:
getBuiltinCount in class AbstractBuiltinContainerImpl

showBuiltinNames

public static void showBuiltinNames()

setCount

public void setCount(double count)
Specified by:
setCount in interface AbstractAtom

getCount

public double getCount()
Specified by:
getCount in interface AbstractAtom

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 CMLBaseImpl

updateDOMHasCount

public void updateDOMHasCount()

updateDOM

public void updateDOM()
               throws CMLException
Overrides:
updateDOM in class CMLBaseImpl
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