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

All Implemented Interfaces:

javajs.api.GenericLineReader
```
public class XmlArgusReader
extends XmlReader
```
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/ Use this reader as a template for adding new XML readers.

Field Summary

Fields
Modifier and Type	Field	Description
`private static int`	`ATOM`
`private java.lang.String`	`atomName1`
`private java.lang.String`	`atomName2`
`private static int`	`BOND`
`private int`	`bondOrder`
`private int`	`elementContext`
`private static java.lang.String[]`	`keepCharsList`
`private static int`	`MOLECULE`
`private int`	`ptTrans`
`private float[]`	`trans`
`private static int`	`TRANSFORMMAT`
`private static int`	`UNSET`

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader
atom, atts, chars, keepChars, 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

XmlArgusReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private int`	`parseBondToken(java.lang.String str)`
`(package private) void`	`processEndElement(java.lang.String localName)`
`void`	`processStartElement(java.lang.String localName, java.lang.String nodeName)`

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader
applySymmetryAndSetTrajectory, createDomNodeJS, endDocument, initCML, initializeReader, processDOM, processXml, processXml2, setKeepChars

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

keepCharsList

private static java.lang.String[] keepCharsList

atomName1
```
private java.lang.String atomName1
```

atomName2
```
private java.lang.String atomName2
```

bondOrder
```
private int bondOrder
```

elementContext
```
private int elementContext
```

UNSET
```
private static final int UNSET
```
See Also:

Constant Field Values

MOLECULE
```
private static final int MOLECULE
```
See Also:

Constant Field Values

ATOM
```
private static final int ATOM
```
See Also:

Constant Field Values

BOND
```
private static final int BOND
```
See Also:

Constant Field Values

TRANSFORMMAT
```
private static final int TRANSFORMMAT
```
See Also:

Constant Field Values

trans
```
private float[] trans
```

ptTrans
```
private int ptTrans
```

Constructor Detail
- XmlArgusReader
```
public XmlArgusReader()
```

Method Detail

processStartElement

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

Overrides:: processStartElement in class XmlReader; nodeName - TODO

parseBondToken

private int parseBondToken(java.lang.String str)

processEndElement
```
void processEndElement(java.lang.String localName)
```
Overrides:

processEndElement in class XmlReader

Class XmlArgusReader

Field Summary

Fields inherited from class org.jmol.adapter.readers.xml.XmlReader

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

Constructor Summary

Method Summary

Methods inherited from class org.jmol.adapter.readers.xml.XmlReader

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

Methods inherited from class java.lang.Object

Field Detail

keepCharsList

atomName1

atomName2

bondOrder

elementContext

UNSET

MOLECULE

ATOM

BOND

TRANSFORMMAT

trans

ptTrans

Constructor Detail

XmlArgusReader

Method Detail

processStartElement

parseBondToken

processEndElement