org.jmol.jvxl.readers
Class MrcBinaryReader

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.MrcBinaryReader
All Implemented Interfaces:
VertexDataServer

 class MrcBinaryReader
extends MapFileReader


Field Summary
private static byte[] b8
           
protected  String[] labels
           
 
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, 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, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin
 
Constructor Summary
MrcBinaryReader(SurfaceGenerator sg, String fileName, String data)
           
 
Method Summary
protected  float nextVoxel()
           
protected  void readParameters()
           
protected  void skipData(int nPoints)
           
 
Methods inherited from class org.jmol.jvxl.readers.MapFileReader
getVectorsAndOrigin, setCutoffAutomatic
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getValue, getVoxelBitSet, gotoData, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelVector, recordData, skipComments
 
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, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, 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

labels

protected String[] labels

b8

private static byte[] b8
Constructor Detail

MrcBinaryReader

MrcBinaryReader(SurfaceGenerator sg,
                String fileName,
                String data)
Method Detail

readParameters

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

nextVoxel

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

skipData

protected void skipData(int nPoints)
                 throws Exception
Overrides:
skipData in class VolumeFileReader
Throws:
Exception