org.jmol.jvxl.readers
Class SurfaceFileReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.SurfaceFileReader
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
PolygonFileReader, VolumeFileReader

abstract class SurfaceFileReader
extends SurfaceReader


Field Summary
protected  BinaryDocument binarydoc
           
protected  BufferedReader br
           
protected  String line
           
protected  int[] next
           
protected  OutputStream 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
SurfaceFileReader(SurfaceGenerator sg, BufferedReader br)
           
 
Method Summary
protected  void closeReader()
           
(package private)  void discardTempData(boolean discardAll)
           
protected  String getNextQuotedString()
           
protected  String[] getTokens()
           
protected  float parseFloat()
           
protected  float parseFloat(String s)
           
protected  float[] parseFloatArray()
           
protected  float[] parseFloatArray(String s)
           
protected  int parseInt()
           
protected  int parseInt(String s)
           
protected  int parseIntNext(String s)
           
protected  String readLine()
           
protected  void setOutputStream(OutputStream os)
           
protected  void skipTo(String info, String what)
           
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readSurfaceData, readTheVolumeData, readVolumeData, readVolumeParameters, 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

br

protected BufferedReader br

binarydoc

protected BinaryDocument binarydoc

os

protected OutputStream os

line

protected String line

next

protected int[] next
Constructor Detail

SurfaceFileReader

SurfaceFileReader(SurfaceGenerator sg,
                  BufferedReader br)
Method Detail

setOutputStream

protected void setOutputStream(OutputStream os)
Overrides:
setOutputStream in class SurfaceReader

closeReader

protected void closeReader()
Specified by:
closeReader in class SurfaceReader

discardTempData

void discardTempData(boolean discardAll)
Overrides:
discardTempData in class SurfaceReader

getTokens

protected String[] getTokens()

parseFloat

protected float parseFloat()

parseFloat

protected float parseFloat(String s)

parseInt

protected int parseInt()

parseInt

protected int parseInt(String s)

parseIntNext

protected int parseIntNext(String s)

parseFloatArray

protected float[] parseFloatArray(String s)

parseFloatArray

protected float[] parseFloatArray()

getNextQuotedString

protected String getNextQuotedString()

skipTo

protected void skipTo(String info,
                      String what)
               throws Exception
Throws:
Exception

readLine

protected String readLine()
                   throws Exception
Throws:
Exception