org.xmlcml.cml
Interface AtomArray

All Known Implementing Classes:

AtomArrayImpl

public interface AtomArray

extends AbstractAtom, HasBuiltinArrayNames

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

Method Summary

void	add(Atom atom) when an Atom is added then it is split over the various StringArrays
AbstractBuiltinContainer	createArrayElement(org.w3c.dom.Document document)
void	delete(Atom atom)
void	deleteNonBuiltinArray(java.lang.String name)
Atom	elementAt(int index) when an Atom is extracted then it is combined from the various StringArrays
StringArray	getBuiltinArray(int builtinId) this is slightly tricky/ucky since AtomArray is subclassed from Atom and StringArray from StringVal we can extract the array object as scalars and simply cast them
StringArray	getNonBuiltinArray(java.lang.String name)
void	setBuiltinArray(int builtinId, StringArray array)
void	setNonBuiltinArray(java.lang.String name, StringArray array)
int	size()

Methods inherited from interface org.xmlcml.cml.AbstractAtom

getCount, setCount

Methods inherited from interface org.xmlcml.cml.AbstractBuiltinContainer

addBuiltinChildWithFloatValue, addBuiltinChildWithIntegerValue, addBuiltinChildWithStringValue, checkBuiltins, deleteNonBuiltinVal, getBuiltinChildElements, getBuiltinChildFloatValue, getBuiltinChildIntegerValue, getBuiltinChildStringValue, getBuiltinCount, getBuiltinVal, getNonBuiltinVal, setBuiltinVal, setNonBuiltinVal

Methods inherited from interface org.xmlcml.cml.HasCount

updateDOMHasCount

Methods inherited from interface org.xmlcml.cml.CMLBase

addValidity, debug, isValid, processDOM, updateDOM

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

appendTo, getValidity, processDescendants, setProcessFlag, setTagName

Methods inherited from interface org.xmlcml.cml.HasTitle

getTitle, setTitle, updateDOMHasTitle

Methods inherited from interface org.xmlcml.cml.HasDictRef

getDictRef, setDictRef, updateDOMHasDictRef

Methods inherited from interface org.xmlcml.cml.HasId

getId, setId, updateDOMHasId

Methods inherited from interface org.xmlcml.cml.HasConvention

getConventionName, setConventionName, updateDOMHasConvention

Methods inherited from interface org.w3c.dom.Element

getAttribute, getAttributeNode, getAttributeNodeNS, getAttributeNS, getElementsByTagName, getElementsByTagNameNS, getTagName, hasAttribute, hasAttributeNS, removeAttribute, removeAttributeNode, removeAttributeNS, setAttribute, setAttributeNode, setAttributeNodeNS, setAttributeNS

Method Detail

add

public void add(Atom atom)

when an Atom is added then it is split over the various StringArrays

size

public int size()

elementAt

public Atom elementAt(int index)

when an Atom is extracted then it is combined from the various StringArrays

delete

public void delete(Atom atom)

getBuiltinArray

public StringArray getBuiltinArray(int builtinId)

this is slightly tricky/ucky since AtomArray is subclassed from Atom and StringArray from StringVal we can extract the array object as scalars and simply cast them

Specified by:

getBuiltinArray in interface HasBuiltinArrayNames

setBuiltinArray

public void setBuiltinArray(int builtinId,
                            StringArray array)

Specified by:

setBuiltinArray in interface HasBuiltinArrayNames

getNonBuiltinArray

public StringArray getNonBuiltinArray(java.lang.String name)

Specified by:

getNonBuiltinArray in interface HasBuiltinArrayNames

setNonBuiltinArray

public void setNonBuiltinArray(java.lang.String name,
                               StringArray array)

Specified by:

setNonBuiltinArray in interface HasBuiltinArrayNames

deleteNonBuiltinArray

public void deleteNonBuiltinArray(java.lang.String name)

Specified by:

deleteNonBuiltinArray in interface HasBuiltinArrayNames

createArrayElement

public AbstractBuiltinContainer createArrayElement(org.w3c.dom.Document document)

Specified by:

createArrayElement in interface HasBuiltinArrayNames