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[][]bsAtomMinMaxprivate java.lang.Object[]funcprivate intfuncTypeprivate BSmyBsAprivate BSmyBsBprivate float[]thisPlaneBprivate static intTYPE_DIFFprivate static intTYPE_DIFF_PAIRprivate static intTYPE_FUNCTIONprivate static intTYPE_MAXprivate static intTYPE_SUMprivate float[]values-
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 floatgetValueAB(float va, float vb)floatgetValueAtPoint(javajs.util.T3 pt, boolean getSource)private floatgetValueAtPoint2(javajs.util.T3 pt, BS bs)(package private) voidinit(SurfaceGenerator sg)implemented in SurfaceFileReader andprotected booleanreadVolumeParameters(boolean isMapData)protected voidsetup(boolean isMapData)private booleansetVoxels()-
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: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()
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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:
getValueAtPointin classSurfaceReadergetSource- TODO- Returns:
- value
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getValueAtPoint2
private float getValueAtPoint2(javajs.util.T3 pt, BS bs)
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