org.jmol.jvxl.readers
Class XplorReader

java.lang.Object
  org.jmol.jvxl.readers.SurfaceReader
      org.jmol.jvxl.readers.SurfaceFileReader
          org.jmol.jvxl.readers.VolumeFileReader
              org.jmol.jvxl.readers.MapFileReader
                  org.jmol.jvxl.readers.XplorReader

All Implemented Interfaces:

VertexDataServer

 class XplorReader
extends MapFileReader

Field Summary

private int	linePt
private int	nBlock
private int	nRead

Fields inherited from class org.jmol.jvxl.readers.MapFileReader

a, adjustment, alpha, b, beta, c, gamma, mapc, mapr, maps, mode, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

atomCount, canDownsample, downsampleRemainders, endOfData, isAngstroms, negativeAtomCount

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

binarydoc, br, line, next

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vContours, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData

Constructor Summary

XplorReader(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

private java.lang.String	getLine()
protected float	nextVoxel()
protected void	readParameters()

Methods inherited from class org.jmol.jvxl.readers.MapFileReader

getVectorsAndOrigin, readVolumetricHeader

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader

getNextVoxelValue, getVoxelBitSet, gotoData, readAtomCountAndOrigin, readExtraLine, readSurfaceData, readTitleLines, readVolumeData, readVolumeParameters, readVoxelVector, skipComments, skipData

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

determineFileType, discardTempData, getTokens, parseFloat, parseFloat, parseInt, parseInt, parseIntNext, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getArgbFromPalette, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, initializeVolumetricData, jvxlUpdateInfo, readColorData, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

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

Field Detail

nBlock

private int nBlock

linePt

private int linePt

nRead

private int nRead

Constructor Detail

XplorReader

XplorReader(SurfaceGenerator sg,
            java.io.BufferedReader br)

Method Detail

readParameters

protected void readParameters()
                       throws java.lang.Exception

Specified by:

readParameters in class MapFileReader

Throws:

java.lang.Exception

getLine

private java.lang.String getLine()
                          throws java.io.IOException

Throws:

java.io.IOException

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception

Overrides:

nextVoxel in class VolumeFileReader

Throws:

java.lang.Exception