java.lang.Object
- org.jmol.jvxl.readers.SurfaceReader
- - org.jmol.jvxl.readers.VolumeDataReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

AtomDataReader, IsoShapeReader
```
class VolumeDataReader
extends SurfaceReader
```

Field Summary

Fields
Modifier and Type	Field	Description
`protected boolean`	`allowMapData`
`protected int`	`dataType`
`protected int`	`maxGrid`
`protected javajs.util.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, isPeriodic, 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 Description

VolumeDataReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`closeReader()`
`protected void`	`generateCube()`
`(package private) void`	`init(SurfaceGenerator sg)`	implemented in SurfaceFileReader and
`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, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, 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 javajs.util.P3 point
```

ptsPerAngstrom
```
protected float ptsPerAngstrom
```

maxGrid
```
protected int maxGrid
```

useOriginStepsPoints
```
protected boolean useOriginStepsPoints
```

Constructor Detail
- VolumeDataReader
```
VolumeDataReader()
```

Method Detail

init
```
void init(SurfaceGenerator sg)
```
Description copied from class: SurfaceReader

implemented in SurfaceFileReader and

Specified by:

init in class SurfaceReader

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

Class VolumeDataReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

dataType

precalculateVoxelData

allowMapData

point

ptsPerAngstrom

maxGrid

useOriginStepsPoints

Constructor Detail

VolumeDataReader

Method Detail

init

initVDR

setup

readVolumeParameters

readVolumeData

readVoxelDataIndividually

setVolumeData

setVolumeDataParams

showGridInfo

setVoxelRange

readSurfaceData

readSurfaceDataVDR

generateCube

closeReader