Package org.jmol.jvxl.readers
Class IsoIntersectReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.VolumeDataReader
org.jmol.jvxl.readers.AtomDataReader
org.jmol.jvxl.readers.IsoIntersectReader
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VertexDataServer
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate javajs.util.BS[][]private Object[]private intprivate final javajs.util.BSprivate final javajs.util.BSprivate float[]private static final intprivate static final intprivate static final intprivate static final intprivate static final intprivate final float[]Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyzTruncated, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, haveOneProperty, havePlane, margin, maxDistance, maxRS, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptV, ptY0, ptZ0, rs, rs2, sr, theProperty, thisAtomSet, thisPlane, thisX, validSpheres, vl0, vl1, vl2, voxelSourceFields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPointsFields 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 -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfloat[]getPlane(int x) private floatgetValueAB(float va, float vb) floatgetValueAtPoint(javajs.util.T3 pt, boolean getSource) private floatgetValueAtPoint2(javajs.util.T3 pt, javajs.util.BS bs) (package private) voidinit(SurfaceGenerator sg) implemented in SurfaceFileReader andprotected booleanreadVolumeParameters(boolean isMapData) protected voidsetup(boolean isMapData) private booleanMethods inherited from class org.jmol.jvxl.readers.AtomDataReader
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeData, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfoMethods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, 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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TYPE_FUNCTION
private static final int TYPE_FUNCTION- See Also:
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TYPE_SUM
private static final int TYPE_SUM- See Also:
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TYPE_DIFF
private static final int TYPE_DIFF- See Also:
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TYPE_MAX
private static final int TYPE_MAX- See Also:
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TYPE_DIFF_PAIR
private static final int TYPE_DIFF_PAIR- See Also:
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myBsA
private final javajs.util.BS myBsA -
myBsB
private final javajs.util.BS myBsB -
bsAtomMinMax
private javajs.util.BS[][] bsAtomMinMax -
func
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funcType
private int funcType -
thisPlaneB
private float[] thisPlaneB -
values
private final float[] values
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Constructor Details
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IsoIntersectReader
IsoIntersectReader()
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Method Details
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init
Description copied from class:SurfaceReaderimplemented in SurfaceFileReader and- Overrides:
initin classVolumeDataReader
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData) - Overrides:
readVolumeParametersin classVolumeDataReader
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setup
protected void setup(boolean isMapData) - Overrides:
setupin classAtomDataReader
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getPlane
public float[] getPlane(int x) - Specified by:
getPlanein interfaceVertexDataServer- Overrides:
getPlanein classSurfaceReader
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setVoxels
private boolean setVoxels() -
getValueAB
private float getValueAB(float va, float vb) -
getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource) - Overrides:
getValueAtPointin classSurfaceReadergetSource- TODO- Returns:
- value
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getValueAtPoint2
private float getValueAtPoint2(javajs.util.T3 pt, javajs.util.BS bs)
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