org.jmol.jvxl.readers

Class VolumeDataReader

java.lang.Object

org.jmol.jvxl.readers.SurfaceReader

org.jmol.jvxl.readers.VolumeDataReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

AtomDataReader, IsoFxyReader, IsoFxyzReader, IsoShapeReader

 class VolumeDataReader
extends SurfaceReader

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	allowMapData
protected int	dataType
protected javax.vecmath.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

Constructors

Constructor and Description
VolumeDataReader(SurfaceGenerator sg)

Method Summary

Methods

Modifier and Type	Method and Description
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 javax.vecmath.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 java.lang.Exception

Throws:

java.lang.Exception

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