Package org.jmol.jvxl.readers
Class VolumeDataReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.VolumeDataReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
AtomDataReader
,IsoShapeReader
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
protected int
protected int
protected javajs.util.P3
protected boolean
protected float
protected boolean
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
protected void
(package private) void
init
(SurfaceGenerator sg) implemented in SurfaceFileReader andprotected void
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
protected boolean
protected int
setVoxelRange
(int index, float min, float max, float ptsPerAngstrom, int gridMax, float minPointsPerAngstrom) protected void
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 Details
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dataType
protected int dataType -
precalculateVoxelData
protected boolean precalculateVoxelData -
allowMapData
protected boolean allowMapData -
point
protected javajs.util.P3 point -
ptsPerAngstrom
protected float ptsPerAngstrom -
maxGrid
protected int maxGrid -
useOriginStepsPoints
protected boolean useOriginStepsPoints
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Constructor Details
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VolumeDataReader
VolumeDataReader()
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Method Details
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init
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Specified by:
init
in classSurfaceReader
- Parameters:
sg
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initVDR
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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
- Throws:
Exception
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setVolumeData
protected void setVolumeData() -
setVolumeDataParams
protected boolean setVolumeDataParams() -
showGridInfo
protected void showGridInfo() -
setVoxelRange
protected int setVoxelRange(int index, float min, float max, float ptsPerAngstrom, int gridMax, float minPointsPerAngstrom) - Parameters:
index
-min
-max
-ptsPerAngstrom
-gridMax
-minPointsPerAngstrom
- -- necessary for highly prolate models such a 6ef8- Returns:
- number of grid points total
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readSurfaceData
- Specified by:
readSurfaceData
in classSurfaceReader
- Throws:
Exception
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readSurfaceDataVDR
- Throws:
Exception
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generateCube
protected void generateCube() -
closeReader
protected void closeReader()- Specified by:
closeReader
in classSurfaceReader
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