org.jmol.jvxl.readers
Class VolumeDataReader

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

 class VolumeDataReader
extends SurfaceReader


Field Summary
protected  boolean allowMapData
           
protected  AtomDataServer atomDataServer
           
protected  int dataType
           
protected  int maxGrid
           
protected  javax.vecmath.Point3f point
           
protected  boolean precalculateVoxelData
           
protected  float ptsPerAngstrom
           
protected  boolean 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
VolumeDataReader(SurfaceGenerator sg)
           
 
Method Summary
protected  void closeReader()
           
protected  void generateCube()
           
protected  void readSurfaceData(boolean isMapData)
           
protected  boolean readVolumeData(boolean isMapData)
           
protected  boolean readVolumeParameters(boolean isMapData)
           
protected  void readVoxelDataIndividually(boolean isMapData)
           
(package private)  void setup(boolean isMapData)
           
protected  void setVolumeData()
           
protected  boolean setVolumeDataParams()
           
protected  int setVoxelRange(int index, float min, float max, float ptsPerAngstrom, int gridMax)
           
protected  void showGridInfo()
           
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, 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

dataType

protected int dataType

precalculateVoxelData

protected boolean precalculateVoxelData

allowMapData

protected boolean allowMapData

point

protected javax.vecmath.Point3f point

ptsPerAngstrom

protected float ptsPerAngstrom

maxGrid

protected int maxGrid

atomDataServer

protected AtomDataServer atomDataServer

useOriginStepsPoints

protected boolean useOriginStepsPoints
Constructor Detail

VolumeDataReader

VolumeDataReader(SurfaceGenerator sg)
Method Detail

setup

void setup(boolean isMapData)
Parameters:
isMapData -

readVolumeParameters

protected boolean readVolumeParameters(boolean isMapData)
Specified by:
readVolumeParameters in class SurfaceReader

readVolumeData

protected boolean readVolumeData(boolean isMapData)
Specified by:
readVolumeData in class SurfaceReader

readVoxelDataIndividually

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

setVolumeData

protected void setVolumeData()

setVolumeDataParams

protected boolean setVolumeDataParams()

showGridInfo

protected void showGridInfo()

setVoxelRange

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

readSurfaceData

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

generateCube

protected void generateCube()

closeReader

protected void closeReader()
Specified by:
closeReader in class SurfaceReader