Package org.jmol.jvxl.readers
Class VolumeDataReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.VolumeDataReader
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- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
AtomDataReader
,IsoShapeReader
class VolumeDataReader extends SurfaceReader
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Field Summary
Fields Modifier and Type Field Description protected boolean
allowMapData
protected int
dataType
protected int
maxGrid
protected javajs.util.P3
point
protected boolean
precalculateVoxelData
protected float
ptsPerAngstrom
protected boolean
useOriginStepsPoints
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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 VolumeDataReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
closeReader()
protected void
generateCube()
(package private) void
init(SurfaceGenerator sg)
implemented in SurfaceFileReader andprotected void
initVDR(SurfaceGenerator sg)
protected void
readSurfaceData(boolean isMapData)
protected void
readSurfaceDataVDR(boolean isMapData)
protected boolean
readVolumeData(boolean isMapData)
protected boolean
readVolumeParameters(boolean isMapData)
protected void
readVoxelDataIndividually(boolean isMapData)
(package private) void
setup(boolean isMapData)
protected void
setVolumeData()
protected boolean
setVolumeDataParams()
protected int
setVoxelRange(int index, float min, float max, float ptsPerAngstrom, int gridMax, float minPointsPerAngstrom)
protected void
showGridInfo()
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Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Detail
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dataType
protected int dataType
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precalculateVoxelData
protected boolean precalculateVoxelData
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allowMapData
protected boolean allowMapData
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point
protected javajs.util.P3 point
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ptsPerAngstrom
protected float ptsPerAngstrom
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maxGrid
protected int maxGrid
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useOriginStepsPoints
protected boolean useOriginStepsPoints
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Method Detail
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init
void init(SurfaceGenerator sg)
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Specified by:
init
in classSurfaceReader
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initVDR
protected void initVDR(SurfaceGenerator sg)
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setup
void setup(boolean isMapData)
- Parameters:
isMapData
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Specified by:
readVolumeParameters
in classSurfaceReader
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readVolumeData
protected boolean readVolumeData(boolean isMapData)
- Specified by:
readVolumeData
in classSurfaceReader
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readVoxelDataIndividually
protected void readVoxelDataIndividually(boolean isMapData) throws Exception
- Throws:
Exception
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setVolumeData
protected void setVolumeData()
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setVolumeDataParams
protected boolean setVolumeDataParams()
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showGridInfo
protected void showGridInfo()
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setVoxelRange
protected int setVoxelRange(int index, float min, float max, float ptsPerAngstrom, int gridMax, float minPointsPerAngstrom)
- Parameters:
index
-min
-max
-ptsPerAngstrom
-gridMax
-minPointsPerAngstrom
- -- added, but not necessary- Returns:
- number of grid points total
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readSurfaceData
protected void readSurfaceData(boolean isMapData) throws Exception
- Specified by:
readSurfaceData
in classSurfaceReader
- Throws:
Exception
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readSurfaceDataVDR
protected void readSurfaceDataVDR(boolean isMapData) throws Exception
- Throws:
Exception
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generateCube
protected void generateCube()
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closeReader
protected void closeReader()
- Specified by:
closeReader
in classSurfaceReader
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