org.jmol.jvxl.readers
Class IsoIntersectReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.VolumeDataReader
          extended by org.jmol.jvxl.readers.AtomDataReader
              extended by org.jmol.jvxl.readers.IsoIntersectReader
All Implemented Interfaces:
VertexDataServer

 class IsoIntersectReader
extends AtomDataReader


Field Summary
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, 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
IsoIntersectReader(SurfaceGenerator sg)
           
 
Method Summary
 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)