org.jmol.jvxl.readers
Class JaguarReader

java.lang.Object
  extended by org.jmol.jvxl.readers.VoxelReader
      extended by org.jmol.jvxl.readers.VolumeFileReader
          extended by 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