XmlCmlReader

A CML2 Reader - If passed a bufferedReader (from a file or inline string), we generate a SAX parser and use callbacks to construct an AtomSetCollection. If passed a JSObject (from LiveConnect) we treat it as a JS DOM tree, and walk the tree, (using the same processing as the SAX parser) to construct the AtomSetCollection. symmetry added by Bob Hanson: setSpaceGroupName() setUnitCellItem() setFractionalCoordinates() setAtomCoord() applySymmetry()

Nested Class Summary
class	XmlCmlReader.CmlHandler

Field Summary
Atom[]	atomArray
int	atomCount
Properties	atomIdNames
Bond[]	bondArray
int	bondCount
String	cellParameterType
String[]	cmlImplementedAttributes
protected int	CML state constants
protected int	CRYSTAL state constants
protected int	CRYSTAL_SCALAR state constants
protected int	CRYSTAL_SYMMETRY state constants
protected int	CRYSTAL_SYMMETRY_TRANSFORM3 state constants
boolean	embeddedCrystal
boolean	haveMolecule
int	latticeVectorPtr
String	localSpaceGroupName
protected int	LATTICE_VECTOR state constants
int	moduleNestingLevel
int	moleculeNesting
protected int	MODULE state constants
protected int	MOLECULE state constants
protected int	MOLECULE_ATOM state constants
protected int	MOLECULE_ATOM_ARRAY state constants
protected int	MOLECULE_ATOM_BUILTIN state constants
protected int	MOLECULE_ATOM_SCALAR state constants
protected int	MOLECULE_BOND state constants
protected int	MOLECULE_BOND_ARRAY state constants
protected int	MOLECULE_BOND_BUILTIN state constants
protected int	MOLECULE_FORMULA state constants
int	nModules
boolean	processing
String	scalarDictRef
String	scalarDictValue
String	scalarTitle
protected int	state the current state
protected int	START state constants
protected int	SYMMETRY state constants
int	tokenCount
String[]	tokens

Constructor Summary
	XmlCmlReader()
	XmlCmlReader(XmlReader parent, AtomSetCollection atomSetCollection, BufferedReader reader, XMLReader xmlReader)
	XmlCmlReader(XmlReader parent, AtomSetCollection atomSetCollection, JSObject DOMNode)

Method Summary
void	applySymmetry()
void	breakOutAtomTokens(String str)
void	breakOutBondTokens(String str)
void	breakOutTokens(String str)
void	checkAtomArrayLength(int newAtomCount)
void	checkBondArrayLength(int newBondCount)
void	createNewAtomSet(HashMap atts)
void	getDictRefValue(HashMap atts)
int	parseBondToken(String str)
void	processEndElement(String uri, String name, String qName)
void	processStartElement(String uri, String name, String qName, HashMap atts)

XmlCmlReader(XmlReader parent, AtomSetCollection atomSetCollection, BufferedReader reader, XMLReader xmlReader)

Class XmlCmlReader