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, IsoFxyReader, IsoFxyzReader, IsoShapeReader

 class VolumeDataReader
extends SurfaceReader


Field Summary
protected  boolean allowMapData
           
protected  int dataType
           
protected  Point3f point
           
protected  boolean precalculateVoxelData
           
 
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, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin
 
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()
           
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.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, 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 Point3f point
Constructor Detail

VolumeDataReader

VolumeDataReader(SurfaceGenerator sg)
Method Detail

setup

void setup()

readVolumeParameters

protected boolean readVolumeParameters()
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 Exception
Throws:
Exception

setVoxelRange

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

readSurfaceData

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

generateCube

protected void generateCube()

closeReader

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