Package org.jmol.jvxl.readers
Class IsoIntersectReader
- 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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- org.jmol.jvxl.readers.AtomDataReader
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- org.jmol.jvxl.readers.IsoIntersectReader
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- All Implemented Interfaces:
VertexDataServer
class IsoIntersectReader extends AtomDataReader
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Field Summary
Fields Modifier and Type Field Description private BS[][]
bsAtomMinMax
private java.lang.Object[]
func
private int
funcType
private BS
myBsA
private BS
myBsB
private float[]
thisPlaneB
private static int
TYPE_DIFF
private static int
TYPE_DIFF_PAIR
private static int
TYPE_FUNCTION
private static int
TYPE_MAX
private static int
TYPE_SUM
private float[]
values
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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, voxelSource
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Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, 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 IsoIntersectReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description float[]
getPlane(int x)
private float
getValueAB(float va, float vb)
float
getValueAtPoint(javajs.util.T3 pt, boolean getSource)
private float
getValueAtPoint2(javajs.util.T3 pt, BS bs)
(package private) void
init(SurfaceGenerator sg)
implemented in SurfaceFileReader andprotected boolean
readVolumeParameters(boolean isMapData)
protected void
setup(boolean isMapData)
private boolean
setVoxels()
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Methods 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, unsetVoxelData2
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Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, 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, 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 Detail
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TYPE_FUNCTION
private static final int TYPE_FUNCTION
- See Also:
- Constant Field Values
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TYPE_SUM
private static final int TYPE_SUM
- See Also:
- Constant Field Values
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TYPE_DIFF
private static final int TYPE_DIFF
- See Also:
- Constant Field Values
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TYPE_MAX
private static final int TYPE_MAX
- See Also:
- Constant Field Values
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TYPE_DIFF_PAIR
private static final int TYPE_DIFF_PAIR
- See Also:
- Constant Field Values
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myBsA
private final BS myBsA
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myBsB
private final BS myBsB
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bsAtomMinMax
private BS[][] bsAtomMinMax
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func
private java.lang.Object[] func
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funcType
private int funcType
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thisPlaneB
private float[] thisPlaneB
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values
private final float[] values
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Method Detail
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init
void init(SurfaceGenerator sg)
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Overrides:
init
in classVolumeDataReader
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Overrides:
readVolumeParameters
in classVolumeDataReader
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setup
protected void setup(boolean isMapData)
- Overrides:
setup
in classAtomDataReader
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getPlane
public float[] getPlane(int x)
- Specified by:
getPlane
in interfaceVertexDataServer
- Overrides:
getPlane
in classSurfaceReader
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setVoxels
private boolean setVoxels()
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getValueAB
private float getValueAB(float va, float vb)
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getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
- Overrides:
getValueAtPoint
in classSurfaceReader
getSource
- TODO- Returns:
- value
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getValueAtPoint2
private float getValueAtPoint2(javajs.util.T3 pt, BS bs)
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