org.jmol.jvxl.readers
Class VolumeDataReader

java.lang.Object
  extended by org.jmol.jvxl.readers.VoxelReader
      extended by org.jmol.jvxl.readers.VolumeDataReader
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
AtomDataReader, IsoFxyReader, IsoShapeReader

 class VolumeDataReader
extends VoxelReader


Field Summary
protected  boolean allowMapData
           
protected  float[] anisotropy
           
protected  javax.vecmath.Point3f center
           
protected  int dataType
           
protected  javax.vecmath.Matrix3f eccentricityMatrix
           
protected  javax.vecmath.Matrix3f eccentricityMatrixInverse
           
protected  float eccentricityRatio
           
protected  float eccentricityScale
           
protected  boolean isAnisotropic
           
protected  boolean isEccentric
           
protected  javax.vecmath.Point3f point
           
protected  boolean precalculateVoxelData
           
 
Fields inherited from class org.jmol.jvxl.readers.VoxelReader
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultColorFractionBase, defaultColorFractionRange, defaultCutoff, defaultEdgeFractionBase, defaultEdgeFractionRange, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, fReturn, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData
 
Constructor Summary
VolumeDataReader(SurfaceGenerator sg)
           
 
Method Summary
protected  void generateCube()
           
protected  float getValue(int x, int y, int z)
           
(package private)  void readVolumeData(boolean isMapData)
           
(package private)  void readVolumeParameters()
           
protected  void readVoxelData(boolean isMapData)
           
protected  void readVoxelDataIndividually(boolean isMapData)
           
(package private)  void setup()
           
protected  int setVoxelRange(int index, float min, float max, float ptsPerAngstrom, int gridMax)
           
 
Methods inherited from class org.jmol.jvxl.readers.VoxelReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, getCalcPoint, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointIndex, gotoAndReadVoxelData, gotoData, initializeVolumetricData, isInside, jvxlUpdateInfo, readColorData, readSurfacePoint, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

dataType

protected int dataType

precalculateVoxelData

protected boolean precalculateVoxelData

allowMapData

protected boolean allowMapData

center

protected javax.vecmath.Point3f center

point

protected javax.vecmath.Point3f point

anisotropy

protected float[] anisotropy

isAnisotropic

protected boolean isAnisotropic

eccentricityMatrix

protected javax.vecmath.Matrix3f eccentricityMatrix

eccentricityMatrixInverse

protected javax.vecmath.Matrix3f eccentricityMatrixInverse

isEccentric

protected boolean isEccentric

eccentricityScale

protected float eccentricityScale

eccentricityRatio

protected float eccentricityRatio
Constructor Detail

VolumeDataReader

VolumeDataReader(SurfaceGenerator sg)
Method Detail

setup

void setup()

readVolumeParameters

void readVolumeParameters()
Specified by:
readVolumeParameters in class VoxelReader

readVolumeData

void readVolumeData(boolean isMapData)
Specified by:
readVolumeData in class VoxelReader

readVoxelDataIndividually

protected void readVoxelDataIndividually(boolean isMapData)
                                  throws java.lang.Exception
Throws:
java.lang.Exception

getValue

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

setVoxelRange

protected int setVoxelRange(int index,
                            float min,
                            float max,
                            float ptsPerAngstrom,
                            int gridMax)

readVoxelData

protected void readVoxelData(boolean isMapData)
                      throws java.lang.Exception
Specified by:
readVoxelData in class VoxelReader
Throws:
java.lang.Exception

generateCube

protected void generateCube()