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 javajs.util.SB |
chars |
private Object[] |
domObj |
protected boolean |
keepChars |
private Object[] |
nullObj |
protected XmlReader |
parent |
addedData, addedDataKey, addVibrations, allowPDBFilter, ANGSTROMS_PER_BOHR, applySymmetryToBonds, asc, baseAtomIndex, binaryDoc, bsFilter, bsModels, calculationType, continuing, debugging, desiredModelNumber, desiredSpaceGroupIndex, desiredVibrationNumber, doApplySymmetry, doCentralize, doCheckUnitCell, doConvertToFractional, doPackUnitCell, doProcessLines, doReadMolecularOrbitals, dssr, fileName, fileOffset, filePath, fileScaling, fillRange, filter, filterHetero, fixJavaFloat, forcePacked, getHeader, haveAtomFilter, haveModel, havePartialChargeFilter, htParams, ignoreFileSpaceGroupName, ignoreFileSymmetryOperators, ignoreFileUnitCell, ignoreStructure, iHaveFractionalCoordinates, iHaveSymmetryOperators, iHaveUnitCell, isBinary, isConcatenated, isDSSP1, isFinalized, isMolecular, isSequential, isTrajectory, latticeCells, latticeScaling, line, lstNCS, matUnitCellOrientation, modelNumber, ms, mustFinalizeModelSet, next, out, packingError, prevline, ptLine, ptSupercell, reader, readerName, reverseModels, sgName, stateScriptVersionInt, strSupercell, symmetry, templateAtomCount, thisBiomolecule, trajectorySteps, unitCellOffset, unitCellParams, useAltNames, useFileModelNumbers, validation, vibrationNumber, vibsFractional, vwr
Constructor and Description |
---|
XmlReader() |
Modifier and Type | Method and Description |
---|---|
void |
applySymmetryAndSetTrajectory() |
(package private) void |
createDomNodeJS(String id,
Object data) |
void |
endDocument() |
private String |
fixLocal(String name) |
private void |
getDOMAttributesA(Object[] attributes) |
protected void |
initCML() |
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,
String nodeName) |
protected void |
processXml(XmlReader parent,
Object saxReader) |
protected void |
processXml2(XmlReader parent,
Object saxReader) |
private String |
selectReaderAndGo(Object saxReader) |
protected void |
setKeepChars(boolean TF) |
private void |
setMyError(String err) |
private void |
walkDOMTree() |
addAtomXYZSymName, addJmolScript, addPrimitiveLatticeVector, addSites, addSiteScript, appendLoadNote, appendUunitCellInfo, applySymTrajASCR, checkCurrentLineForScript, checkFilterKey, checkLastModel, checkLine, checkLineForScript, clearUnitCell, cloneLastAtomSet, discardLinesUntilBlank, discardLinesUntilContains, discardLinesUntilContains2, discardLinesUntilNonBlank, discardLinesUntilStartsWith, discardPreviousAtoms, doGetModel, doGetVibration, doPreSymmetry, fillDataBlock, fillDataBlockFixed, fillFloatArray, fillFrequencyData, filterAtom, filterReject, finalizeMOData, finalizeModelSet, finalizeReaderASCR, finalizeSubclassReader, finalizeSubclassSymmetry, forceSymmetry, fractionalizeCoordinates, getElementSymbol, getFilter, getFortranFormatLengths, getInterface, getNewSymmetry, getStrings, getSymmetry, getTokens, getTokensFloat, initializeSymmetry, initializeSymmetryOptions, initializeTrajectoryFile, isLastModel, newAtomSet, parseFloat, parseFloatRange, parseFloatStr, parseInt, parseIntAt, parseIntRange, parseIntStr, parseToken, parseTokenNext, parseTokenRange, parseTokenStr, processBinaryDocument, rd, read3Vectors, readDataObject, readLines, readNextLine, rejectAtomName, RL, set2D, setAtomCoord, setAtomCoordScaled, setAtomCoordTokens, setAtomCoordXYZ, setChainID, setElementAndIsotope, setFilter, setFilterAtomTypeStr, setFractionalCoordinates, setIsPDB, setLoadNote, setModelPDB, setSpaceGroupName, setSymmetryOperator, setTransform, setUnitCell, setUnitCellItem, setup, setupASCR
protected Atom atom
protected XmlReader parent
protected boolean keepChars
protected javajs.util.SB chars
private Object[] domObj
private Object[] attribs
private Object[] attArgs
private Object[] nullObj
public void initializeReader() throws Exception
initializeReader
in class AtomSetCollectionReader
Exception
protected void initCML()
private void setMyError(String err)
private String parseXML()
protected void processXml(XmlReader parent, Object saxReader) throws Exception
parent
- saxReader
- Exception
protected void processXml2(XmlReader parent, Object saxReader) throws Exception
Exception
public void applySymmetryAndSetTrajectory()
applySymmetryAndSetTrajectory
in class AtomSetCollectionReader
protected void processDOM(Object DOMNode)
processDOM
in class AtomSetCollectionReader
protected void processStartElement(String localName, String nodeName)
localName
- nodeName
- TODOprotected void setKeepChars(boolean TF)
void processEndElement(String localName)
localName
- private void walkDOMTree()
private void getDOMAttributesA(Object[] attributes)
private Object jsObjectCall(Object[] jsObject, String method, Object[] args)
jsObject
- method
- args
- public void endDocument()