public class XmlReader extends AtomSetCollectionReader
Modifier and Type | Class and Description |
---|---|
static class |
XmlReader.DummyResolver |
class |
XmlReader.JmolXmlHandler |
Modifier and Type | Field and Description |
---|---|
protected Atom |
atom |
protected java.lang.String |
chars |
protected java.lang.String[] |
implementedAttributes |
protected boolean |
keepChars |
protected XmlReader |
parent |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, next, notionalUnitCell, os, prevline, ptLine, ptSupercell, reader, readerName, readMolecularOrbitals, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
XmlReader() |
Modifier and Type | Method and Description |
---|---|
void |
applySymmetryAndSetTrajectory() |
protected XmlReader.JmolXmlHandler |
getHandler(java.lang.Object xmlReader) |
protected java.lang.String[] |
getImplementedAttributes() |
private java.lang.Object |
getXmlReader() |
private org.xml.sax.XMLReader |
getXMLReader() |
void |
initializeReader() |
protected void |
parseReaderXML(org.xml.sax.XMLReader xmlReader) |
protected void |
processEndElement(java.lang.String uri,
java.lang.String localName,
java.lang.String qName) |
protected void |
processStartElement(java.lang.String namespaceURI,
java.lang.String localName,
java.lang.String qName,
java.util.Map<java.lang.String,java.lang.String> atts) |
protected void |
processXml(java.lang.Object DOMNode) |
private java.lang.Object |
processXml(org.xml.sax.XMLReader xmlReader) |
protected void |
processXml(XmlReader parent,
AtomSetCollection atomSetCollection,
java.io.BufferedReader reader,
java.lang.Object xmlReader,
XmlReader.JmolXmlHandler handler) |
protected void |
setKeepChars(boolean TF) |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, checkFilter, checkLastModel, checkLine, checkLineForScript, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, fillDataBlock, fillDataBlock, fillFloatArray, fillFrequencyData, filterAtom, finalizeReader, getElementSymbol, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokens, getTokens, getTokensFloat, initializeSymmetry, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloat, parseFloat, parseInt, parseInt, parseInt, parseInt, parseStringInfestedFloatArray, parseToken, parseToken, parseToken, parseTokenNext, parseTrimmed, parseTrimmed, processBinaryDocument, read3Vectors, readData, readLine, readLines, set2D, setAtomCoord, setAtomCoord, setElementAndIsotope, setFilter, setFractionalCoordinates, setIsPDB, setMOData, setPdb, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem
protected Atom atom
protected java.lang.String[] implementedAttributes
protected XmlReader parent
protected boolean keepChars
protected java.lang.String chars
public void initializeReader() throws java.lang.Exception
initializeReader
in class AtomSetCollectionReader
java.lang.Exception
private org.xml.sax.XMLReader getXMLReader()
private java.lang.Object processXml(org.xml.sax.XMLReader xmlReader) throws java.lang.Exception
java.lang.Exception
private java.lang.Object getXmlReader()
protected void processXml(XmlReader parent, AtomSetCollection atomSetCollection, java.io.BufferedReader reader, java.lang.Object xmlReader, XmlReader.JmolXmlHandler handler)
parent
- atomSetCollection
- reader
- xmlReader
- handler
- protected void parseReaderXML(org.xml.sax.XMLReader xmlReader)
protected void processXml(java.lang.Object DOMNode)
processXml
in class AtomSetCollectionReader
protected java.lang.String[] getImplementedAttributes()
protected void processStartElement(java.lang.String namespaceURI, java.lang.String localName, java.lang.String qName, java.util.Map<java.lang.String,java.lang.String> atts)
namespaceURI
- localName
- qName
- atts
- protected void setKeepChars(boolean TF)
protected void processEndElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
uri
- localName
- qName
- public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
protected XmlReader.JmolXmlHandler getHandler(java.lang.Object xmlReader)