org.jmol.jvxl.readers
Class CastepDensityReader

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.CastepDensityReader
All Implemented Interfaces:
VertexDataServer

 class CastepDensityReader
extends VolumeFileReader


Field Summary
private  int nFilePoints
           
private  int nSkip
           
 
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
CastepDensityReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
protected  void gotoData(int n, int nPoints)
           
protected  void readParameters()
           
protected  void readSurfaceData(boolean isMapData)
           
private  void skipPoints(int n)
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSurfacePointAndFraction, getValue, getVoxelBitSet, initializeSurfaceData, nextVoxel, 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

nFilePoints

private int nFilePoints

nSkip

private int nSkip
Constructor Detail

CastepDensityReader

CastepDensityReader(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

gotoData

protected void gotoData(int n,
                        int nPoints)
                 throws java.lang.Exception
Overrides:
gotoData in class VolumeFileReader
Throws:
java.lang.Exception

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception
Overrides:
readSurfaceData in class VolumeFileReader
Throws:
java.lang.Exception

skipPoints

private void skipPoints(int n)