org.jmol.adapter.readers.xml
Class XmlArgusReader

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.XmlArgusReader

public class XmlArgusReader
extends XmlReader

A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.


Nested Class Summary
(package private)  class XmlArgusReader.ArgusHandler
           
 
Nested classes/interfaces inherited from class org.jmol.adapter.readers.xml.XmlReader
XmlReader.DummyResolver, XmlReader.JmolXmlHandler
 
Field Summary
private  java.lang.String[] argusImplementedAttributes
           
private static int ATOM
           
private  java.lang.String atomName1
           
private  java.lang.String atomName2
           
private static int BOND
           
private  int bondOrder
           
private  int elementContext
           
private  java.lang.String[] keepCharsList
           
private static int MOLECULE
           
private  int ptTrans
           
private  float[] trans
           
private static int TRANSFORMMAT
           
private static int UNSET
           
 
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
XmlArgusReader()
           
 
Method Summary
(package private)  int parseBondToken(java.lang.String str)
           
 void processEndElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
           
 void processStartElement(java.lang.String namespaceURI, java.lang.String localName, java.lang.String qName, java.util.Map atts)
           
protected  void processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, netscape.javascript.JSObject DOMNode)
           
protected  void processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, org.xml.sax.XMLReader xmlReader)
           
 
Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
initializeReader, parseReaderXML, processStartElement, readAtomSetCollectionFromDOM, setKeepChars
 
Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, applySymmetryAndSetTrajectory, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearLatticeParameters, cloneLastAtomSet, createSpaceGroup, 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

argusImplementedAttributes

private java.lang.String[] argusImplementedAttributes

keepCharsList

private java.lang.String[] keepCharsList

atomName1

private java.lang.String atomName1

atomName2

private java.lang.String atomName2

bondOrder

private int bondOrder

elementContext

private int elementContext

UNSET

private static final int UNSET
See Also:
Constant Field Values

MOLECULE

private static final int MOLECULE
See Also:
Constant Field Values

ATOM

private static final int ATOM
See Also:
Constant Field Values

BOND

private static final int BOND
See Also:
Constant Field Values

TRANSFORMMAT

private static final int TRANSFORMMAT
See Also:
Constant Field Values

trans

private float[] trans

ptTrans

private int ptTrans
Constructor Detail

XmlArgusReader

XmlArgusReader()
Method Detail

processXml

protected void processXml(XmlReader parent,
                          AtomSetCollection atomSetCollection,
                          java.io.BufferedReader reader,
                          org.xml.sax.XMLReader xmlReader)
Overrides:
processXml in class XmlReader

processXml

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

processStartElement

public void processStartElement(java.lang.String namespaceURI,
                                java.lang.String localName,
                                java.lang.String qName,
                                java.util.Map atts)

parseBondToken

int parseBondToken(java.lang.String str)

processEndElement

public void processEndElement(java.lang.String uri,
                              java.lang.String localName,
                              java.lang.String qName)
Overrides:
processEndElement in class XmlReader