org.jmol.jvxl.readers
Class MrcBinaryReader

java.lang.Object
  org.jmol.jvxl.readers.SurfaceReader
      org.jmol.jvxl.readers.SurfaceFileReader
          org.jmol.jvxl.readers.VolumeFileReader
              org.jmol.jvxl.readers.MapFileReader
                  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, 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, java.lang.String fileName, java.lang.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 java.lang.String[] labels

b8

private static byte[] b8

Constructor Detail

MrcBinaryReader

MrcBinaryReader(SurfaceGenerator sg,
                java.lang.String fileName,
                java.lang.String data)

Method Detail

readParameters

protected void readParameters()
                       throws java.lang.Exception

Specified by:

readParameters in class VolumeFileReader

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