org.jmol.jvxl.readers
Class JvxlReader

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.JvxlXmlReader
                  extended by org.jmol.jvxl.readers.JvxlReader
All Implemented Interfaces:
VertexDataServer

public class JvxlReader
extends JvxlXmlReader


Field Summary
 
Fields inherited from class org.jmol.jvxl.readers.JvxlXmlReader
bsVoxelBitSet, colorDataCount, edgeDataCount, haveContourData, haveReadColorData, isXmlFile, JVXL_VERSION, surfaceDataCount, tempDataXml, thisInside
 
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
JvxlReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
private  int countData(java.lang.String str)
           
protected  void gotoData(int n, int nPoints)
           
protected  java.lang.String jvxlReadData(java.lang.String type, int nPoints)
           
private  void jvxlReadDefinitionLine(boolean showMsg)
           
protected  void jvxlSkipData(int nPoints, boolean doSkipColorData)
           
private  void jvxlSkipDataBlock(int nPoints, boolean isInt)
           
protected  void readParameters()
           
protected  void readSurfaceData(boolean isMapDataIgnored)
           
 
Methods inherited from class org.jmol.jvxl.readers.JvxlXmlReader
getEncodedVertexData, getSurfacePointAndFraction, getVoxelBitSet, gotoAndReadVoxelData, jvxlDecodeContourData, jvxlDecodeTriangleData, jvxlDecodeVertexData, jvxlReadSurfaceInfo, jvxlSetColorRanges, postProcessVertices, readColorData, readSurfaceData, readVector, readVolumeData, readVolumeFileSurfaceData
 
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getValue, nextVoxel, 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, getSurfacePointIndexAndFraction, getValueAtPoint, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, 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
 

Constructor Detail

JvxlReader

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

readParameters

protected void readParameters()
                       throws java.lang.Exception
Overrides:
readParameters in class JvxlXmlReader
Throws:
java.lang.Exception

jvxlReadData

protected java.lang.String jvxlReadData(java.lang.String type,
                                        int nPoints)
Overrides:
jvxlReadData in class JvxlXmlReader

gotoData

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

jvxlReadDefinitionLine

private void jvxlReadDefinitionLine(boolean showMsg)
                             throws java.lang.Exception
Throws:
java.lang.Exception

readSurfaceData

protected void readSurfaceData(boolean isMapDataIgnored)
                        throws java.lang.Exception
Overrides:
readSurfaceData in class JvxlXmlReader
Throws:
java.lang.Exception

jvxlSkipData

protected void jvxlSkipData(int nPoints,
                            boolean doSkipColorData)
                     throws java.lang.Exception
Overrides:
jvxlSkipData in class JvxlXmlReader
Throws:
java.lang.Exception

jvxlSkipDataBlock

private void jvxlSkipDataBlock(int nPoints,
                               boolean isInt)
                        throws java.lang.Exception
Throws:
java.lang.Exception

countData

private int countData(java.lang.String str)