org.jmol.jvxl.readers
Class Dsn6BinaryReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.SurfaceFileReader
          extended by org.jmol.jvxl.readers.VolumeFileReader
              extended by org.jmol.jvxl.readers.MapFileReader
                  extended by org.jmol.jvxl.readers.Dsn6BinaryReader
All Implemented Interfaces:
VertexDataServer

 class Dsn6BinaryReader
extends MapFileReader


Field Summary
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, adjustment, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors
 
Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
atomCount, boundingBox, canDownsample, downsampleFactor, endOfData, isAngstroms, negativeAtomCount, nSurfaces, readerClosed, thePlane
 
Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next, os
 
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, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, 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
Dsn6BinaryReader(SurfaceGenerator sg, java.lang.String fileName, java.lang.String data)
           
 
Method Summary
private  float getBrickValue(int pt)
           
protected  float nextVoxel()
           
private  void readBrickLayer()
           
protected  void readParameters()
           
protected  void skipData(int nPoints)
           
 
Methods inherited from class org.jmol.jvxl.readers.MapFileReader
getVectorsAndOrigin, setCutoffAutomatic
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, initializeSurfaceData, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelVector, recordData, skipComments
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

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 Detail

Dsn6BinaryReader

Dsn6BinaryReader(SurfaceGenerator sg,
                 java.lang.String fileName,
                 java.lang.String data)
Method Detail

readParameters

protected void readParameters()
                       throws java.lang.Exception
Specified by:
readParameters in class VolumeFileReader
Throws:
java.lang.Exception

readBrickLayer

private void readBrickLayer()
                     throws java.lang.Exception
Throws:
java.lang.Exception

getBrickValue

private float getBrickValue(int pt)

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception
Overrides:
nextVoxel in class VolumeFileReader
Throws:
java.lang.Exception

skipData

protected void skipData(int nPoints)
                 throws java.lang.Exception
Overrides:
skipData in class VolumeFileReader
Throws:
java.lang.Exception