org.jmol.jvxl.readers
Class XplorReader

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.XplorReader
All Implemented Interfaces:
VertexDataServer

 class XplorReader
extends VolumeFileReader


Field Summary
(package private)  int linePt
           
(package private)  int nBlock
           
(package private)  int nRead
           
 
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
XplorReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
private  java.lang.String getLine()
           
protected  float nextVoxel()
           
protected  void readAtomCountAndOrigin()
           
protected  void readTitleLines()
           
protected  int readVolumetricHeader()
           
protected  void readVoxelVectors()
           
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
getNextVoxelValue, getVoxelBitSet, gotoData, readExtraLine, readSurfaceData, 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

nBlock

int nBlock

linePt

int linePt

nRead

int nRead
Constructor Detail

XplorReader

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

readVolumetricHeader

protected int readVolumetricHeader()
Overrides:
readVolumetricHeader in class VolumeFileReader

readTitleLines

protected void readTitleLines()
                       throws java.lang.Exception
Overrides:
readTitleLines in class VolumeFileReader
Throws:
java.lang.Exception

readVoxelVectors

protected void readVoxelVectors()
                         throws java.lang.Exception
Throws:
java.lang.Exception

readAtomCountAndOrigin

protected void readAtomCountAndOrigin()
                               throws java.lang.Exception
Overrides:
readAtomCountAndOrigin in class VolumeFileReader
Throws:
java.lang.Exception

getLine

private java.lang.String getLine()
                          throws java.io.IOException
Throws:
java.io.IOException

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception
Overrides:
nextVoxel in class VolumeFileReader
Throws:
java.lang.Exception