XmlReader

java.lang.Object
- org.jmol.adapter.smarter.AtomSetCollectionReader
- - org.jmol.adapter.readers.xml.XmlReader

All Implemented Interfaces:

javajs.api.GenericLineReader

Direct Known Subclasses:

XmlArgusReader, XmlChem3dReader, XmlCmlReader, XmlMagResReader, 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. 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. XmlHandler extends DefaultHandler is the generic interface to both reader and DOM element parsing. XmlCmlReader extends XmlReader XmlMolproReader extends XmlCmlReader. If you feel like expanding on that, feel free. XmlChem3dReader extends XmlReader. That one is simple; no need to expand on it at this time. XmlOdysseyReader extends XmlReader. That one is simple; no need to expand on it at this time. 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] Test files: molpro: vib.xml odyssey: water.xodydata cml: a wide variety of files in data-files. -Bob Hanson

Field Summary

Fields
Modifier and Type	Field	Description
`protected Atom`	`atom`
`private java.lang.Object[]`	`attArgs`
`private java.lang.Object[]`	`attribs`
`java.util.Map<java.lang.String,java.lang.String>`	`atts`
`protected javajs.util.SB`	`chars`
`private java.lang.Object[]`	`domObj`
`protected boolean`	`keepChars`
`private java.lang.Object[]`	`nullObj`
`protected XmlReader`	`parent`

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

Constructors
Constructor Description

XmlReader()

Constructors
Constructor	Description
`XmlReader()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`applySymmetryAndSetTrajectory()`
`(package private) void`	`createDomNodeJS(java.lang.String id, java.lang.Object data)`
`void`	`endDocument()`
`private java.lang.String`	`fixLocal(java.lang.String name)`
`private void`	`getDOMAttributesA(java.lang.Object[] attributes)`
`protected void`	`initCML()`
`void`	`initializeReader()`
`private java.lang.Object`	`jsObjectCall(java.lang.Object[] jsObject, java.lang.String method, java.lang.Object[] args)`
`private java.lang.Object`	`jsObjectGetMember(java.lang.Object[] jsObject, java.lang.String name)`
`private java.lang.String`	`parseXML()`
`protected void`	`processDOM(java.lang.Object DOMNode)`
`(package private) void`	`processEndElement(java.lang.String localName)`
`protected void`	`processStartElement(java.lang.String localName, java.lang.String nodeName)`
`protected void`	`processXml(XmlReader parent, java.lang.Object saxReader)`
`protected void`	`processXml2(XmlReader parent, java.lang.Object saxReader)`
`private java.lang.String`	`selectReaderAndGo(java.lang.Object saxReader)`
`protected void`	`setKeepChars(boolean TF)`
`private void`	`setMyError(java.lang.String err)`
`private void`	`walkDOMTree()`

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atom
```
protected Atom atom
```

parent
```
protected XmlReader parent
```

atts

public java.util.Map<java.lang.String,java.lang.String> atts

keepChars
```
protected boolean keepChars
```

chars
```
protected javajs.util.SB chars
```

domObj
```
private java.lang.Object[] domObj
```

attribs
```
private java.lang.Object[] attribs
```

attArgs
```
private java.lang.Object[] attArgs
```

nullObj
```
private java.lang.Object[] nullObj
```

Constructor Detail
- XmlReader
```
public XmlReader()
```

Method Detail

initializeReader
```
public void initializeReader()
                      throws java.lang.Exception
```
Overrides:

initializeReader in class AtomSetCollectionReader

Throws:

java.lang.Exception

initCML
```
protected void initCML()
```

setMyError

private void setMyError(java.lang.String err)

parseXML
```
private java.lang.String parseXML()
```

selectReaderAndGo

private java.lang.String selectReaderAndGo(java.lang.Object saxReader)

processXml

protected void processXml(XmlReader parent,
                          java.lang.Object saxReader)
                   throws java.lang.Exception

Parameters:: parent -; saxReader -
Throws:: java.lang.Exception

processXml2

protected void processXml2(XmlReader parent,
                           java.lang.Object saxReader)
                    throws java.lang.Exception

Throws:: java.lang.Exception

createDomNodeJS

void createDomNodeJS(java.lang.String id,
                     java.lang.Object data)

Parameters:: id -; data -

applySymmetryAndSetTrajectory
```
public void applySymmetryAndSetTrajectory()
```
Overrides:

applySymmetryAndSetTrajectory in class AtomSetCollectionReader

processDOM
```
protected void processDOM(java.lang.Object DOMNode)
```
Overrides:

processDOM in class AtomSetCollectionReader

processStartElement

protected void processStartElement(java.lang.String localName,
                                   java.lang.String nodeName)

Parameters:: localName -; nodeName - TODO

setKeepChars

protected void setKeepChars(boolean TF)

processEndElement

void processEndElement(java.lang.String localName)

Parameters:: localName -

walkDOMTree
```
private void walkDOMTree()
```

fixLocal

private java.lang.String fixLocal(java.lang.String name)

getDOMAttributesA

private void getDOMAttributesA(java.lang.Object[] attributes)

jsObjectCall

private java.lang.Object jsObjectCall(java.lang.Object[] jsObject,
                                      java.lang.String method,
                                      java.lang.Object[] args)

Parameters:: jsObject -; method -; args -
Returns:: object

jsObjectGetMember

private java.lang.Object jsObjectGetMember(java.lang.Object[] jsObject,
                                           java.lang.String name)

endDocument
```
public void endDocument()
```

Class XmlReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

atom

parent

atts

keepChars

chars

domObj

attribs

attArgs

nullObj

Constructor Detail

XmlReader

Method Detail

initializeReader

initCML

setMyError

parseXML

selectReaderAndGo

processXml

processXml2

createDomNodeJS

applySymmetryAndSetTrajectory

processDOM

processStartElement

setKeepChars

processEndElement

walkDOMTree

fixLocal

getDOMAttributesA

jsObjectCall

jsObjectGetMember

endDocument