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[]brickLayerprivate intbrickLayerByteCountprivate intbrickLayerVoxelCountprivate intbrickRowByteCountprivate floatbyteFactorprivate intnBrickXprivate intnBrickYprivate intptprivate intxyCount-
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 floatgetBrickValue(int pt)(package private) voidinit2(SurfaceGenerator sg, java.io.BufferedReader brNull)protected floatnextVoxel()private voidreadBrickLayer()protected voidreadParameters()protected voidskipData(int nPoints)-
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:
init2in classMapFileReader
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readParameters
protected void readParameters() throws java.lang.Exception- Specified by:
readParametersin 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:
nextVoxelin classVolumeFileReader- Throws:
java.lang.Exception
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skipData
protected void skipData(int nPoints) throws java.lang.Exception- Overrides:
skipDatain classVolumeFileReader- Throws:
java.lang.Exception
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