org.jmol.jvxl.readers
Class JaguarReader

java.lang.Object
  org.jmol.jvxl.readers.VoxelReader
      org.jmol.jvxl.readers.VolumeFileReader
          org.jmol.jvxl.readers.JaguarReader

All Implemented Interfaces:

VertexDataServer

 class JaguarReader
extends VolumeFileReader

Field Summary

private float[]

extents

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

atomCount, br, canDownsample, endOfData, isAngstroms, line, negativeAtomCount, next

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

ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultColorFractionBase, defaultColorFractionRange, defaultCutoff, defaultEdgeFractionBase, defaultEdgeFractionRange, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, fReturn, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData

Constructor Summary

JaguarReader(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

protected float	nextVoxel() read one value per line
protected void	readAtomCountAndOrigin() skip initial stuff and read the origin= line
protected void	readTitleLines() nothing much here
protected void	readVoxelVector(int voxelVectorIndex) read the extentx=, extenty=, extentz= lines and cache them then read the npts= line and construct the necessary data

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

determineFileType, discardTempData, getNextVoxelValue, getTokens, gotoData, parseFloat, parseFloat, parseFloatNext, parseInt, parseInt, parseInt, parseIntNext, readExtraLine, readVolumeData, readVolumeParameters, readVolumetricHeader, readVoxelData, skipComments

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

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getCalcPoint, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointIndex, gotoAndReadVoxelData, initializeVolumetricData, isInside, jvxlUpdateInfo, readColorData, readSurfacePoint, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles

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(SurfaceGenerator sg,
             java.io.BufferedReader br)

Method Detail

readTitleLines

protected void readTitleLines()
                       throws java.lang.Exception

nothing much here

Overrides:

readTitleLines in class VolumeFileReader

Throws:

java.lang.Exception - -- generally a reader issue

readAtomCountAndOrigin

protected void readAtomCountAndOrigin()
                               throws java.lang.Exception

skip initial stuff and read the origin= line

Overrides:

readAtomCountAndOrigin in class VolumeFileReader

Throws:

java.lang.Exception - -- generally a reader issue

readVoxelVector

protected void readVoxelVector(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

Overrides:

readVoxelVector in class VolumeFileReader

Parameters:

voxelVectorIndex - 0, 1, or 2

Throws:

java.lang.Exception - -- generally a reader issue

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception

read one value per line

Overrides:

nextVoxel in class VolumeFileReader

Returns:

the next floating point value

Throws:

java.lang.Exception - -- generally a reader issue