org.jmol.jvxl.readers.Dsn6BinaryReader

All Implemented Interfaces:: VertexDataServer

class Dsn6BinaryReader extends MapFileReader

Field Summary

Fields

Modifier and Type

Field

Description

private byte[]

brickLayer

private int

brickLayerByteCount

private int

brickLayerVoxelCount

private int

brickRowByteCount

private float

byteFactor

private int

nBrickX

private int

nBrickY

private int

pt

private int

xyCount

Fields inherited from class org.jmol.jvxl.readers.MapFileReader
a, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, n0, n1, n2, na, nb, nc, origin, p3, vectors, xIndex, xyzStart, yIndex, zIndex

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next, out

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader
allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isPeriodic, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlCutoffRange, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes
Constructor Summary

Constructors

Constructor

Description

Dsn6BinaryReader()
Method Summary

Modifier and Type

Method

Description

private float

getBrickValue(int pt)

(package private) void

init2(SurfaceGenerator sg, BufferedReader brNull)

protected float

nextVoxel()

private void

readBrickLayer()

protected void

readParameters()

protected void

skipData(int nPoints)

Methods inherited from class org.jmol.jvxl.readers.MapFileReader
checkInsideOut, getVectorsAndOrigin, init2MFR, setCutoffAutomatic

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getJVXLCutoff, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

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

Field Details
- byteFactor
  
  private float byteFactor
- xyCount
  
  private int xyCount
- nBrickX
  
  private int nBrickX
- nBrickY
  
  private int nBrickY
- brickLayerVoxelCount
  
  private int brickLayerVoxelCount
- brickLayerByteCount
  
  private int brickLayerByteCount
- brickRowByteCount
  
  private int brickRowByteCount
- brickLayer
  
  private byte[] brickLayer
- pt
  
  private int pt
Constructor Details
- Dsn6BinaryReader
  
  Dsn6BinaryReader()
Method Details
- init2
  
  void init2(SurfaceGenerator sg, BufferedReader brNull)
  
  Overrides:
  
  init2 in class MapFileReader
- readParameters
  
  protected void readParameters() throws Exception
  
  Specified by:
  
  readParameters in class VolumeFileReader
  
  Throws:
  
  Exception
- readBrickLayer
  
  private void readBrickLayer() throws Exception
  
  Throws:
  
  Exception
- getBrickValue
  
  private float getBrickValue(int pt)
- nextVoxel
  
  protected float nextVoxel() throws Exception
  
  Overrides:
  
  nextVoxel in class VolumeFileReader
  
  Throws:
  
  Exception
- skipData
  
  protected void skipData(int nPoints) throws Exception
  
  Overrides:
  
  skipData in class VolumeFileReader
  
  Throws:
  
  Exception

Class Dsn6BinaryReader

Field Summary

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

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

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

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

Constructor Summary

Method Summary

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

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

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

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

Methods inherited from class java.lang.Object

Field Details

byteFactor

xyCount

nBrickX

nBrickY

brickLayerVoxelCount

brickLayerByteCount

brickRowByteCount

brickLayer

pt

Constructor Details

Dsn6BinaryReader

Method Details

init2

readParameters

readBrickLayer

getBrickValue

nextVoxel

skipData