org.jmol.jvxl.readers
Class PolygonFileReader

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

abstract class PolygonFileReader
extends SurfaceFileReader


Field Summary
protected  int nTriangles
           
protected  int nVertices
           
 
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, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes
 
Constructor Summary
PolygonFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
(package private) abstract  void getSurfaceData()
           
protected  void readSurfaceData(boolean isMapData)
           
protected  boolean readVolumeData(boolean isMapData)
           
protected  boolean readVolumeParameters(boolean isMapData)
           
 
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReader, 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, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, 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

nVertices

protected int nVertices

nTriangles

protected int nTriangles
Constructor Detail

PolygonFileReader

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

readVolumeParameters

protected boolean readVolumeParameters(boolean isMapData)
Specified by:
readVolumeParameters in class SurfaceReader

readVolumeData

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

readSurfaceData

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

getSurfaceData

abstract void getSurfaceData()
                      throws java.lang.Exception
Throws:
java.lang.Exception