JaguarReader

java.lang.Object
- org.jmol.jvxl.readers.SurfaceReader
- - org.jmol.jvxl.readers.SurfaceFileReader
  - - org.jmol.jvxl.readers.VolumeFileReader
    - - org.jmol.jvxl.readers.JaguarReader

All Implemented Interfaces:: VertexDataServer

class JaguarReader
extends VolumeFileReader

Field Summary

Fields
Modifier and Type Field Description

private float[] extents
- Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
  ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces
- Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
  binarydoc, br, line, next, out
- 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

JaguarReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`(package private) void`	`init2(SurfaceGenerator sg, java.io.BufferedReader br)`
`private void`	`readExtents(int voxelVectorIndex)`	read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data
`protected void`	`readParameters()`	nothing much here

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - extents
```
private float[] extents
```
- Constructor Detail
  - JaguarReader
```
JaguarReader()
```
- Method Detail
  - init2
```
void init2(SurfaceGenerator sg,
           java.io.BufferedReader br)
```
    Overrides:
    
    init2 in class VolumeFileReader
  - readParameters
```
protected void readParameters()
                       throws java.lang.Exception
```
    nothing much here
    
    Specified by:
    
    readParameters in class VolumeFileReader
    
    Throws:
    
    java.lang.Exception - -- generally a reader issue
  - readExtents
```
private void readExtents(int voxelVectorIndex)
                  throws java.lang.Exception
```
    read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data
    
    Parameters:
    
    voxelVectorIndex - 0, 1, or 2
    
    Throws:
    
    java.lang.Exception - -- generally a reader issue