org.jmol.jvxl.readers
Class MapFileReader

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
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
Dsn6BinaryReader, MrcBinaryReader, XplorReader

abstract class MapFileReader
extends VolumeFileReader


Field Summary
protected  float a
           
protected  javax.vecmath.Point3f adjustment
           
protected  float alpha
           
protected  float b
           
protected  float beta
           
protected  float c
           
protected  float dmax
           
protected  float dmean
           
protected  float dmin
           
protected  float drange
           
protected  float gamma
           
protected  int mapc
           
protected  int mapr
           
protected  int maps
           
protected  int mode
           
protected  int na
           
protected  int nb
           
protected  int nc
           
protected  int nx
           
protected  int[] nxyzStart
           
protected  int ny
           
protected  int nz
           
protected  javax.vecmath.Point3f origin
           
protected  javax.vecmath.Point3f[] 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
MapFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
protected  void getVectorsAndOrigin()
           
protected  void setCutoffAutomatic()
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getValue, getVoxelBitSet, gotoData, nextVoxel, readParameters, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData
 
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

dmin

protected float dmin

dmax

protected float dmax

dmean

protected float dmean

drange

protected float drange

mapc

protected int mapc

mapr

protected int mapr

maps

protected int maps

nx

protected int nx

ny

protected int ny

nz

protected int nz

mode

protected int mode

nxyzStart

protected int[] nxyzStart

na

protected int na

nb

protected int nb

nc

protected int nc

a

protected float a

b

protected float b

c

protected float c

alpha

protected float alpha

beta

protected float beta

gamma

protected float gamma

origin

protected javax.vecmath.Point3f origin

adjustment

protected javax.vecmath.Point3f adjustment

vectors

protected javax.vecmath.Point3f[] vectors
Constructor Detail

MapFileReader

MapFileReader(SurfaceGenerator sg,
              java.io.BufferedReader br)
Method Detail

getVectorsAndOrigin

protected void getVectorsAndOrigin()

setCutoffAutomatic

protected void setCutoffAutomatic()