Package org.jmol.jvxl.readers
Class Dsn6BinaryReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.SurfaceFileReader
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- org.jmol.jvxl.readers.VolumeFileReader
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- org.jmol.jvxl.readers.MapFileReader
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- org.jmol.jvxl.readers.Dsn6BinaryReader
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- All Implemented Interfaces:
VertexDataServer
class Dsn6BinaryReader extends MapFileReader
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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
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Fields inherited from class org.jmol.jvxl.readers.MapFileReader
a, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors
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Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces
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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, 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
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Constructor Summary
Constructors Constructor Description Dsn6BinaryReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private float
getBrickValue(int pt)
(package private) void
init2(SurfaceGenerator sg, java.io.BufferedReader brNull)
protected float
nextVoxel()
private void
readBrickLayer()
protected void
readParameters()
protected void
skipData(int nPoints)
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Methods inherited from class org.jmol.jvxl.readers.MapFileReader
getVectorsAndOrigin, init2MFR, setCutoffAutomatic
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Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipDataVFR, swapXZ
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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
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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
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Field Detail
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byteFactor
private float byteFactor
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xyCount
private int xyCount
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nBrickX
private int nBrickX
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nBrickY
private int nBrickY
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brickLayerVoxelCount
private int brickLayerVoxelCount
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brickLayerByteCount
private int brickLayerByteCount
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brickRowByteCount
private int brickRowByteCount
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brickLayer
private byte[] brickLayer
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pt
private int pt
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Method Detail
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init2
void init2(SurfaceGenerator sg, java.io.BufferedReader brNull)
- Overrides:
init2
in classMapFileReader
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readParameters
protected void readParameters() throws java.lang.Exception
- Specified by:
readParameters
in classVolumeFileReader
- Throws:
java.lang.Exception
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readBrickLayer
private void readBrickLayer() throws java.lang.Exception
- Throws:
java.lang.Exception
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getBrickValue
private float getBrickValue(int pt)
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nextVoxel
protected float nextVoxel() throws java.lang.Exception
- Overrides:
nextVoxel
in classVolumeFileReader
- Throws:
java.lang.Exception
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skipData
protected void skipData(int nPoints) throws java.lang.Exception
- Overrides:
skipData
in classVolumeFileReader
- Throws:
java.lang.Exception
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