public class XmlReader extends AtomSetCollectionReader
Modifier and Type | Field and Description |
---|---|
protected Atom |
atom |
private Object[] |
attArgs |
private Object[] |
attribs |
Map<String,String> |
atts |
protected String |
chars |
protected String[] |
domAttributes |
private Object[] |
domObj |
protected boolean |
keepChars |
private Object[] |
nullObj |
protected XmlReader |
parent |
addVibrations, ANGSTROMS_PER_BOHR, applySymmetryToBonds, atomSetCollection, bsFilter, bsModels, calculationType, continuing, desiredModelNumber, desiredVibrationNumber, doApplySymmetry, doc, doCentralize, doCheckUnitCell, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, fileName, fileOffset, filePath, fileScaling, filter, filterHetero, forcePacked, getHeader, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isSequential, isTrajectory, latticeCells, line, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, notionalUnitCell, out, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, spaceGroup, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, trajectorySteps, useAltNames, vibrationNumber, viewer
Constructor and Description |
---|
XmlReader() |
Modifier and Type | Method and Description |
---|---|
void |
applySymmetryAndSetTrajectory() |
protected String[] |
getDOMAttributes() |
private void |
getDOMAttributesA(Object[] attributes) |
void |
initializeReader() |
private Object |
jsObjectCall(Object[] jsObject,
String method,
Object[] args) |
private Object |
jsObjectGetMember(Object[] jsObject,
String name) |
private String |
parseXML() |
protected void |
processDOM(Object DOMNode) |
(package private) void |
processEndElement(String localName) |
protected void |
processStartElement(String localName) |
protected void |
processXml(XmlReader parent,
Object saxReader) |
protected void |
PX(XmlReader parent,
Object saxReader) |
private String |
selectReaderAndGo(Object saxReader) |
protected void |
setKeepChars(boolean TF) |
private void |
setMyError(String err) |
private void |
walkDOMTree() |
addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReader, finalizeReaderASCR, getElementSymbol, getFilter, getFortranFormatLengths, getStrings, getSymmetry, getTokens, getTokensAt, getTokensFloat, getTokensStr, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseStringInfestedFloatArray, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, parseTrimmedAt, parseTrimmedRange, processBinaryDocument, read3Vectors, readDataObject, readLine, readLines, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setSpaceGroupName, setSymmetryOperator, setTransform, setU, setUnitCell, setUnitCellItem, setup, setupASCR
protected Atom atom
protected String[] domAttributes
protected XmlReader parent
protected boolean keepChars
protected String chars
private Object[] domObj
private Object[] attribs
private Object[] attArgs
private Object[] nullObj
public void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
private void setMyError(String err)
private String parseXML()
protected void processXml(XmlReader parent, Object saxReader) throws Exception
parent
- saxReader
- Exception
public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
protected void processDOM(Object DOMNode)
processDOM
in class AtomSetCollectionReader
protected String[] getDOMAttributes()
protected void processStartElement(String localName)
localName
- protected void setKeepChars(boolean TF)
void processEndElement(String localName)
localName
- private void walkDOMTree()
private void getDOMAttributesA(Object[] attributes)