org.jmol.jvxl.readers
Class XplorReader

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.MapFileReader
                  extended by org.jmol.jvxl.readers.XplorReader
All Implemented Interfaces:
VertexDataServer

 class XplorReader
extends MapFileReader


Field Summary
private  int linePt
           
private  int nBlock
           
private  int nRead
           
 
Fields inherited from class org.jmol.jvxl.readers.MapFileReader
a, adjustment, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors
 
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
XplorReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
private  java.lang.String getLine()
           
protected  float nextVoxel()
           
protected  void readParameters()
           
 
Methods inherited from class org.jmol.jvxl.readers.MapFileReader
getVectorsAndOrigin, setCutoffAutomatic
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, initializeSurfaceData, 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

nBlock

private int nBlock

linePt

private int linePt

nRead

private int nRead
Constructor Detail

XplorReader

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

readParameters

protected void readParameters()
                       throws java.lang.Exception
Specified by:
readParameters in class VolumeFileReader
Throws:
java.lang.Exception

getLine

private java.lang.String getLine()
                          throws java.lang.Exception
Throws:
java.lang.Exception

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception
Overrides:
nextVoxel in class VolumeFileReader
Throws:
java.lang.Exception