org.jmol.adapter.readers.xml

Class XmlReader

java.lang.Object

org.jmol.adapter.smarter.AtomSetCollectionReader

org.jmol.adapter.readers.xml.XmlReader

Direct Known Subclasses:

XmlArgusReader, XmlChem3dReader, XmlCmlReader, XmlOdysseyReader, XmlQEReader, XmlVaspReader, XmlXsdReader

public class XmlReader
extends AtomSetCollectionReader

A generic XML reader template -- by itself, does nothing. The actual readers are XmlCmlReader, XmlMolproReader (which is an extension of XmlCmlReader, XmlChem3dReader, and XmlOdysseyReader, which is wholely different. XmlReader takes all XML streams, whether from a file reader or from DOM. This class functions as a resolver, since it: (1) identifying the specific strain of XML to be handled, and (2) passing the responsibility on to the correct format-specific XML readers. There are parallel entry points and handler methods for reader and DOM. Each format-specific XML reader then assigns its own handler to manage the parsing of elements. In addition, this class handles generic XML tag parsing. XmlReader.JmolXmlHandler extends DefaultHandler is the generic interface to both reader and DOM element parsing. XmlCmlReader extends XmlReader and is where I'd like Andrew to take charge. XmlCmlReader.CmlHandler extends XmlReader.JmolXmlHandler is generic XmlMolproReader extends XmlCmlReader. If you feel like expanding on that, feel free. XmlMolproReader.MolprolHandler extends XmlCmlReader.CmlHandler adds Molpro-specific XML tag processing XmlChem3dReader extends XmlReader. That one is simple; no need to expand on it at this time. XmlChem3dReader.Chem3dHandler extends XmlReader.JmolXmlHandler is generic XmlOdysseyReader extends XmlReader. That one is simple; no need to expand on it at this time. XmlOdysseyReader.OdysseyHandler extends XmlReader.JmolXmlHandler is generic Note that the tag processing routines are shared between SAX and DOM processors. This means that attributes must be transformed from either Attributes (SAX) or JSObjects (DOM) to Hashtable name:value pairs. This is taken care of in JmolXmlHandler for all readers. TODO 27/8/06: Several aspects of CifReader are NOT YET implemented here. These include loading a specific model when there are several, applying the symmetry, and loading fractional coordinates. [DONE for CML reader 2/2007 RMH] The DOM reader is NOT CHECKED OVER, and I do not think that it supports reading characters between start/end tags: characters If you work on this, please read formats other than CML into DOM so that we can see that that works as well. Test files: molpro: vib.xml odyssey: water.xodydata cml: a wide variety of files in data-files. Feel free to prune if some are not of use. -Bob Hanson

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	XmlReader.DummyResolver
class	XmlReader.JmolXmlHandler

Field Summary

Fields

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

Fields inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

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 Summary

Constructors

Constructor and Description
XmlReader()

Method Summary

Methods

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)

Methods inherited from class org.jmol.adapter.smarter.AtomSetCollectionReader

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atom

protected Atom atom

implementedAttributes

protected java.lang.String[] implementedAttributes

parent

protected XmlReader parent

keepChars

protected boolean keepChars

chars

protected java.lang.String chars

Constructor Detail

XmlReader

public XmlReader()

Method Detail

initializeReader

public void initializeReader()
                      throws java.lang.Exception

Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

getXMLReader

private org.xml.sax.XMLReader getXMLReader()

processXml

private java.lang.Object processXml(org.xml.sax.XMLReader xmlReader)
                             throws java.lang.Exception

Throws:

java.lang.Exception

getXmlReader

private java.lang.Object getXmlReader()

processXml

protected void processXml(XmlReader parent,
              AtomSetCollection atomSetCollection,
              java.io.BufferedReader reader,
              java.lang.Object xmlReader,
              XmlReader.JmolXmlHandler handler)

Parameters:

parent -

atomSetCollection -

reader -

xmlReader -

handler -

parseReaderXML

protected void parseReaderXML(org.xml.sax.XMLReader xmlReader)

processXml

protected void processXml(java.lang.Object DOMNode)

Overrides:

processXml in class AtomSetCollectionReader

getImplementedAttributes

protected java.lang.String[] getImplementedAttributes()

processStartElement

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)

Parameters:

namespaceURI -

localName -

qName -

atts -

setKeepChars

protected void setKeepChars(boolean TF)

processEndElement

protected void processEndElement(java.lang.String uri,
                     java.lang.String localName,
                     java.lang.String qName)

Parameters:

uri -

localName -

qName -

applySymmetryAndSetTrajectory

public void applySymmetryAndSetTrajectory()

Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

getHandler

protected XmlReader.JmolXmlHandler getHandler(java.lang.Object xmlReader)