org.jmol.jvxl.readers
Class IsoFxyReader

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.IsoFxyReader
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
IsoFxyzReader

 class IsoFxyReader
extends AtomDataReader


Field Summary
private  float[][] data
           
private  java.lang.Object[] func
           
private  boolean isPlanarMapping
           
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
IsoFxyReader(SurfaceGenerator sg)
           
 
Method Summary
protected  float evaluateValue(int x, int y, int z)
           
 float[] getPlane(int x)
           
private  void getPlane(int x, float[] plane)
           
protected  float getValue(int x, int y, int z)
           
 float getValueAtPoint(javax.vecmath.Point3f pt)
           
protected  void readSurfaceData(boolean isMapData)
           
protected  void setup(boolean isMapData)
           
protected  void setup(java.lang.String type)
           
protected  void setVolumeData()
           
 
Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
fixTitleLine, getAtomMinMax, getAtoms, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRanges, setVertexSource, setVolumeForPlane, setVoxel, unsetVoxelData
 
Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, readVolumeData, readVolumeParameters, 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, postProcessVertices, 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

data

private float[][] data

isPlanarMapping

private boolean isPlanarMapping

func

private java.lang.Object[] func

values

private final float[] values
Constructor Detail

IsoFxyReader

IsoFxyReader(SurfaceGenerator sg)
Method Detail

setup

protected void setup(boolean isMapData)
Overrides:
setup in class AtomDataReader

setup

protected void setup(java.lang.String type)

setVolumeData

protected void setVolumeData()
Overrides:
setVolumeData in class AtomDataReader

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception
Overrides:
readSurfaceData in class VolumeDataReader
Throws:
java.lang.Exception

getPlane

public float[] getPlane(int x)
Specified by:
getPlane in interface VertexDataServer
Overrides:
getPlane in class SurfaceReader

getPlane

private void getPlane(int x,
                      float[] plane)

getValue

protected float getValue(int x,
                         int y,
                         int z)

getValueAtPoint

public float getValueAtPoint(javax.vecmath.Point3f pt)
Overrides:
getValueAtPoint in class SurfaceReader
Returns:
value

evaluateValue

protected float evaluateValue(int x,
                              int y,
                              int z)