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, IsoShapeReader

abstract class VolumeDataReader
extends SurfaceReader

Field Summary

Fields

Modifier and Type	Field and Description
protected boolean	allowMapData
protected AtomDataServer	atomDataServer
protected int	dataType
protected int	maxGrid
protected P3	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, jvxlDataIsColorDensity, 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

Constructors

Constructor and Description
VolumeDataReader()

Method Summary

Methods

Modifier and Type	Method and Description
protected void	closeReader()
protected void	generateCube()
protected void	initVDR(SurfaceGenerator sg)
protected void	readSurfaceData(boolean isMapData)
protected void	readSurfaceDataVDR(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, float minPointsPerAngstrom)
protected void	showGridInfo()

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlane2, getSpanningVectors, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, init, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputStream, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, 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 P3 point

ptsPerAngstrom

protected float ptsPerAngstrom

maxGrid

protected int maxGrid

atomDataServer

protected AtomDataServer atomDataServer

useOriginStepsPoints

protected boolean useOriginStepsPoints

Constructor Detail

VolumeDataReader

VolumeDataReader()

Method Detail

initVDR

protected void initVDR(SurfaceGenerator sg)

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,
                float minPointsPerAngstrom)

Parameters:

index -

min -

max -

ptsPerAngstrom -

gridMax -

minPointsPerAngstrom - -- added, but not necessary

Returns:

number of grid points total

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception

Specified by:

readSurfaceData in class SurfaceReader

Throws:

java.lang.Exception

readSurfaceDataVDR

protected void readSurfaceDataVDR(boolean isMapData)
                           throws java.lang.Exception

Throws:

java.lang.Exception

generateCube

protected void generateCube()

closeReader

protected void closeReader()

Specified by:

closeReader in class SurfaceReader