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:
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 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, 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
MapFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
protected  void getVectorsAndOrigin()
           
protected abstract  void readParameters()
           
protected  int readVolumetricHeader()
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
getNextVoxelValue, getVoxelBitSet, gotoData, nextVoxel, readAtomCountAndOrigin, readExtraLine, readSurfaceData, readTitleLines, readVolumeData, readVolumeParameters, readVoxelVector, skipComments, skipData
 
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

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

readParameters

protected abstract void readParameters()
                                throws java.lang.Exception
Throws:
java.lang.Exception

readVolumetricHeader

protected int readVolumetricHeader()
Overrides:
readVolumetricHeader in class VolumeFileReader

getVectorsAndOrigin

protected void getVectorsAndOrigin()