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

 class IsoIntersectReader
extends AtomDataReader

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.BitSet[][]	bsAtomMinMax
private java.lang.Object[]	func
private int	funcType
private java.util.BitSet	myBsA
private java.util.BitSet	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

Fields inherited from class org.jmol.jvxl.readers.AtomDataReader

atomCount, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyz, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, havePlane, margin, maxDistance, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptXyzTemp, ptY0, ptZ0, thisAtomSet, thisPlane, thisX, validSpheres, voxelSource

Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader

allowMapData, atomDataServer, 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, 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

Constructor Summary

Constructors

Constructor and Description
IsoIntersectReader(SurfaceGenerator sg)

Method Summary

Methods

Modifier and Type	Method and Description
float[]	getPlane(int x)
private float	getValue(float va, float vb)
float	getValueAtPoint(javax.vecmath.Point3f pt)
private float	getValueAtPoint(javax.vecmath.Point3f pt, java.util.BitSet bs)
protected void	postProcessVertices()
protected boolean	readVolumeParameters(boolean isMapData)
protected void	setup(boolean isMapData)
private boolean	setVoxels()

Methods inherited from class org.jmol.jvxl.readers.AtomDataReader

fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeData, setVolumeForPlane, setVoxel, unsetVoxelData

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader

closeReader, generateCube, readSurfaceData, readVolumeData, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

TYPE_FUNCTION

private static final int TYPE_FUNCTION

See Also:

Constant Field Values

TYPE_SUM

private static final int TYPE_SUM

See Also:

Constant Field Values

TYPE_DIFF

private static final int TYPE_DIFF

See Also:

Constant Field Values

TYPE_MAX

private static final int TYPE_MAX

See Also:

Constant Field Values

TYPE_DIFF_PAIR

private static final int TYPE_DIFF_PAIR

See Also:

Constant Field Values

myBsA

private final java.util.BitSet myBsA

myBsB

private final java.util.BitSet myBsB

bsAtomMinMax

private java.util.BitSet[][] bsAtomMinMax

func

private java.lang.Object[] func

funcType

private int funcType

thisPlaneB

private float[] thisPlaneB

values

private final float[] values

Constructor Detail

IsoIntersectReader

IsoIntersectReader(SurfaceGenerator sg)

Method Detail

readVolumeParameters

protected boolean readVolumeParameters(boolean isMapData)

Overrides:

readVolumeParameters in class VolumeDataReader

setup

protected void setup(boolean isMapData)

Overrides:

setup in class AtomDataReader

getPlane

public float[] getPlane(int x)

Specified by:

getPlane in interface VertexDataServer

Overrides:

getPlane in class SurfaceReader

postProcessVertices

protected void postProcessVertices()

Overrides:

postProcessVertices in class SurfaceReader

setVoxels

private boolean setVoxels()

getValue

private float getValue(float va,
             float vb)

getValueAtPoint

public float getValueAtPoint(javax.vecmath.Point3f pt)

Overrides:

getValueAtPoint in class SurfaceReader

Returns:

value

getValueAtPoint

private float getValueAtPoint(javax.vecmath.Point3f pt,
                    java.util.BitSet bs)