org.jmol.jvxl.readers
Class ApbsReader

java.lang.Object
  org.jmol.jvxl.readers.VoxelReader
      org.jmol.jvxl.readers.VolumeFileReader
          org.jmol.jvxl.readers.ApbsReader

All Implemented Interfaces:

VertexDataServer

 class ApbsReader
extends VolumeFileReader

Field Summary

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

atomCount, br, canDownsample, endOfData, isAngstroms, line, negativeAtomCount, next

Fields inherited from class org.jmol.jvxl.readers.VoxelReader

ANGSTROMS_PER_BOHR, cJvxlEdgeNaN, colorEncoder, colorFractionBase, colorFractionRange, contourVertexCount, defaultColorFractionBase, defaultColorFractionRange, defaultCutoff, defaultEdgeFractionBase, defaultEdgeFractionRange, defaultMappedDataMax, defaultMappedDataMin, edgeFractionBase, edgeFractionRange, fractionData, fReturn, isApbsDx, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, marchingSquares, meshData, meshDataServer, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData

Constructor Summary

ApbsReader(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

protected void	readAtomCountAndOrigin()
protected void	readTitleLines()
protected void	readVoxelVector(int voxelVectorIndex)

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader

determineFileType, discardTempData, getNextVoxelValue, getTokens, gotoData, nextVoxel, parseFloat, parseFloat, parseFloatNext, parseInt, parseInt, parseInt, parseIntNext, readExtraLine, readVolumeData, readVolumeParameters, readVolumetricHeader, readVoxelData, skipComments

Methods inherited from class org.jmol.jvxl.readers.VoxelReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, getCalcPoint, getColorIndexFromPalette, getColorPhaseIndex, getMaxMappedValue, getMinMappedValue, getSurfacePointIndex, gotoAndReadVoxelData, initializeVolumetricData, isInside, jvxlUpdateInfo, readColorData, readSurfacePoint, resetIsosurface, selectPocket, setVolumeData, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ApbsReader

ApbsReader(SurfaceGenerator sg,
           java.io.BufferedReader br)

Method Detail

readTitleLines

protected void readTitleLines()
                       throws java.lang.Exception

Overrides:

readTitleLines in class VolumeFileReader

Throws:

java.lang.Exception

readAtomCountAndOrigin

protected void readAtomCountAndOrigin()
                               throws java.lang.Exception

Overrides:

readAtomCountAndOrigin in class VolumeFileReader

Throws:

java.lang.Exception

readVoxelVector

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

Overrides:

readVoxelVector in class VolumeFileReader

Throws:

java.lang.Exception