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.MrcBinaryReader

All Implemented Interfaces:

VertexDataServer

 class MrcBinaryReader
extends VolumeFileReader

Nested Class Summary

private class

MrcBinaryReader.MrcHeader

Field Summary

(package private) byte[]	b2
(package private) byte[]	b4
(package private) MrcBinaryReader.MrcHeader	mrcHeader

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

atomCount, canDownsample, 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	readAtomCountAndOrigin()
protected void	readTitleLines()
protected void	readVoxelVector(int voxelVectorIndex)
protected void	skipData(int nPoints)

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader

getNextVoxelValue, getVoxelBitSet, gotoData, readExtraLine, readSurfaceData, readVolumeData, readVolumeParameters, readVolumetricHeader, 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

mrcHeader

MrcBinaryReader.MrcHeader mrcHeader

b2

byte[] b2

b4

byte[] b4

Constructor Detail

MrcBinaryReader

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

Method Detail

readTitleLines

protected void readTitleLines()
                       throws java.lang.Exception

Overrides:

readTitleLines in class VolumeFileReader

Throws:

java.lang.Exception

readAtomCountAndOrigin

protected void readAtomCountAndOrigin()

Overrides:

readAtomCountAndOrigin in class VolumeFileReader

readVoxelVector

protected void readVoxelVector(int voxelVectorIndex)

Overrides:

readVoxelVector in class VolumeFileReader

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