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  java.lang.String[] labels
           
 
Fields inherited from class org.jmol.jvxl.readers.MapFileReader
a, adjustment, alpha, b, beta, c, gamma, mapc, mapr, maps, mode, na, nb, nc, nx, nxyzStart, ny, nz, origin, vectors
 
Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
atomCount, canDownsample, downsampleRemainders, endOfData, isAngstroms, negativeAtomCount
 
Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next
 
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader
ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vContours, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData
 
Constructor Summary
MrcBinaryReader(SurfaceGenerator sg, java.lang.String fileName, boolean isBigEndian)
           
 
Method Summary
protected  float nextVoxel()
           
protected  void readParameters()
           
protected  void skipData(int nPoints)
           
 
Methods inherited from class org.jmol.jvxl.readers.MapFileReader
getVectorsAndOrigin, readVolumetricHeader
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
getNextVoxelValue, getVoxelBitSet, gotoData, readAtomCountAndOrigin, readExtraLine, readSurfaceData, readTitleLines, readVolumeData, readVolumeParameters, readVoxelVector, skipComments
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
determineFileType, discardTempData, getTokens, parseFloat, parseFloat, parseInt, parseInt, parseIntNext, skipTo
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getArgbFromPalette, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, gotoAndReadVoxelData, initializeVolumetricData, jvxlUpdateInfo, readColorData, 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

labels

protected java.lang.String[] labels

b8

private static byte[] b8
Constructor Detail

MrcBinaryReader

MrcBinaryReader(SurfaceGenerator sg,
                java.lang.String fileName,
                boolean isBigEndian)
Method Detail

readParameters

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

nextVoxel

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

skipData

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