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.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