org.jmol.jvxl.readers
Class VolumeFileReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.SurfaceFileReader
          extended by org.jmol.jvxl.readers.VolumeFileReader
All Implemented Interfaces:
VertexDataServer
Direct Known Subclasses:
ApbsReader, CubeReader, JaguarReader, JvxlReader, MrcBinaryReader, PltFormattedReader, XplorReader

abstract class VolumeFileReader
extends SurfaceFileReader


Field Summary
protected  int atomCount
           
protected  boolean canDownsample
           
private  int[] downsampleRemainders
           
protected  boolean endOfData
           
protected  boolean isAngstroms
           
protected  boolean negativeAtomCount
           
private  int nSurfaces
           
 
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
VolumeFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
private  int countData(java.lang.String str)
           
protected  float getNextVoxelValue()
           
protected  java.util.BitSet getVoxelBitSet(int nPoints)
           
protected  void gotoData(int n, int nPoints)
           
protected  float nextVoxel()
           
protected  void readAtomCountAndOrigin()
           
protected  int readExtraLine()
           
protected  void readSurfaceData(boolean isMapData)
           
protected  void readTitleLines()
           
(package private)  boolean readVolumeData(boolean isMapData)
           
(package private)  boolean readVolumeParameters()
           
protected  int readVolumetricHeader()
           
protected  void readVoxelVector(int voxelVectorIndex)
           
protected  java.lang.String skipComments(boolean allowBlankLines)
           
protected  void skipData(int nPoints)
           
private  void skipVoxels(int n)
           
 
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

endOfData

protected boolean endOfData

negativeAtomCount

protected boolean negativeAtomCount

atomCount

protected int atomCount

nSurfaces

private int nSurfaces

isAngstroms

protected boolean isAngstroms

canDownsample

protected boolean canDownsample

downsampleRemainders

private int[] downsampleRemainders
Constructor Detail

VolumeFileReader

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

readVolumeParameters

boolean readVolumeParameters()
Specified by:
readVolumeParameters in class SurfaceReader

readVolumeData

boolean readVolumeData(boolean isMapData)
Specified by:
readVolumeData in class SurfaceReader

readVolumetricHeader

protected int readVolumetricHeader()

readTitleLines

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

skipComments

protected java.lang.String skipComments(boolean allowBlankLines)
                                 throws java.lang.Exception
Throws:
java.lang.Exception

readAtomCountAndOrigin

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

readVoxelVector

protected void readVoxelVector(int voxelVectorIndex)
                        throws java.lang.Exception
Throws:
java.lang.Exception

readExtraLine

protected int readExtraLine()
                     throws java.lang.Exception
Throws:
java.lang.Exception

readSurfaceData

protected void readSurfaceData(boolean isMapData)
                        throws java.lang.Exception
Specified by:
readSurfaceData in class SurfaceReader
Throws:
java.lang.Exception

skipVoxels

private void skipVoxels(int n)
                 throws java.lang.Exception
Throws:
java.lang.Exception

getVoxelBitSet

protected java.util.BitSet getVoxelBitSet(int nPoints)
                                   throws java.lang.Exception
Throws:
java.lang.Exception

getNextVoxelValue

protected float getNextVoxelValue()
                           throws java.lang.Exception
Throws:
java.lang.Exception

nextVoxel

protected float nextVoxel()
                   throws java.lang.Exception
Throws:
java.lang.Exception

gotoData

protected void gotoData(int n,
                        int nPoints)
                 throws java.lang.Exception
Overrides:
gotoData in class SurfaceReader
Throws:
java.lang.Exception

skipData

protected void skipData(int nPoints)
                 throws java.lang.Exception
Throws:
java.lang.Exception

countData

private int countData(java.lang.String str)