org.jmol.adapter.readers.xml
Class XmlOdysseyReader

java.lang.Object
  extended by org.jmol.adapter.smarter.AtomSetCollectionReader
      extended by org.jmol.adapter.readers.xml.XmlReader
          extended by org.jmol.adapter.readers.xml.XmlOdysseyReader

public class XmlOdysseyReader
extends XmlReader

An Odyssey xodydata reader


Nested Class Summary
(package private)  class XmlOdysseyReader.OdysseyHandler
           
 
Nested classes/interfaces inherited from class org.jmol.adapter.readers.xml.XmlReader
XmlReader.DummyResolver, XmlReader.JmolXmlHandler
 
Field Summary
(package private)  String formula
           
(package private)  String modelName
           
(package private)  String[] odysseyImplementedAttributes
           
(package private)  String phase
           
 
Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, chars, implementedAttributes, keepChars, parent
 
Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doCheckUnitCell, doProcessLines, filter, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveSymmetryOperators, iHaveUnitCell, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, reader, readerName, readMolecularOrbitals, spaceGroup, symmetry, templateAtomCount, vibrationNumber, viewer
 
Constructor Summary
XmlOdysseyReader()
           
 
Method Summary
 void applySymmetryAndSetTrajectory()
           
(package private)  int parseBondToken(String str)
           
protected  void processEndElement(String uri, String localName, String qName)
           
protected  void processStartElement(String namespaceURI, String localName, String qName, HashMap atts)
           
protected  void processXml(XmlReader parent, AtomSetCollection atomSetCollection, BufferedReader reader, netscape.javascript.JSObject DOMNode)
           
protected  void processXml(XmlReader parent, AtomSetCollection atomSetCollection, BufferedReader reader, XMLReader xmlReader)
           
 
Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
initializeReader, parseReaderXML, readAtomSetCollectionFromDOM, setKeepChars
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, discardLines, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, readData, readLine, set2D, setAtomCoord, setAtomCoord, setFilter, setFractionalCoordinates, setMOData, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

odysseyImplementedAttributes

String[] odysseyImplementedAttributes

modelName

String modelName

formula

String formula

phase

String phase
Constructor Detail

XmlOdysseyReader

XmlOdysseyReader()
Method Detail

processXml

protected void processXml(XmlReader parent,
                          AtomSetCollection atomSetCollection,
                          BufferedReader reader,
                          XMLReader xmlReader)
Overrides:
processXml in class XmlReader

processXml

protected void processXml(XmlReader parent,
                          AtomSetCollection atomSetCollection,
                          BufferedReader reader,
                          netscape.javascript.JSObject DOMNode)
Overrides:
processXml in class XmlReader

processStartElement

protected void processStartElement(String namespaceURI,
                                   String localName,
                                   String qName,
                                   HashMap atts)
Overrides:
processStartElement in class XmlReader

applySymmetryAndSetTrajectory

public void applySymmetryAndSetTrajectory()
Overrides:
applySymmetryAndSetTrajectory in class AtomSetCollectionReader

parseBondToken

int parseBondToken(String str)

processEndElement

protected void processEndElement(String uri,
                                 String localName,
                                 String qName)
Overrides:
processEndElement in class XmlReader