org.jmol.jvxl.readers
Class JaguarReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.SurfaceFileReader
          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, boundingBox, canDownsample, downsampleFactor, endOfData, isAngstroms, negativeAtomCount, nSurfaces, readerClosed, thePlane
 
Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next, os
 
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, 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
JaguarReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
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, getPlaneProcessed, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, initializeSurfaceData, nextVoxel, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, 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

extents

private float[] extents
Constructor Detail

JaguarReader

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

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