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
- All Implemented Interfaces:
VertexDataServer
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate javajs.util.BS[][]
private Object[]
private int
private final javajs.util.BS
private final javajs.util.BS
private float[]
private static final int
private static final int
private static final int
private static final int
private static final int
private 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, voxelSource
Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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 TypeMethodDescriptionfloat[]
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, javajs.util.BS bs) (package private) void
init
(SurfaceGenerator sg) implemented in SurfaceFileReader andprotected boolean
readVolumeParameters
(boolean isMapData) protected void
setup
(boolean isMapData) private boolean
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
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, initVDR, readSurfaceData, readSurfaceDataVDR, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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 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:SurfaceReader
implemented in SurfaceFileReader and- Overrides:
init
in classVolumeDataReader
- Parameters:
sg
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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
- Parameters:
isMapData
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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() -
getValueAB
private float getValueAB(float va, float vb) -
getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource) - Overrides:
getValueAtPoint
in classSurfaceReader
- Parameters:
pt
-getSource
- TODO- Returns:
- value
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getValueAtPoint2
private float getValueAtPoint2(javajs.util.T3 pt, javajs.util.BS bs)
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