org.jmol.jvxl.readers.IsoIntersectGridReader

All Implemented Interfaces:: VertexDataServer

class IsoIntersectGridReader extends VolumeFileReader

A class to read a linear combination of cube file data. readerData is Object[] { VolumeFileReader[], float[] }

Field Summary

Fields

Modifier and Type

Field

Description

private float[]

factors

private VolumeFileReader[]

readers

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader
binarydoc, br, line, next, out

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, isPeriodic, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlCutoffRange, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, 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

Constructors

Constructor

Description

IsoIntersectGridReader()
Method Summary

Modifier and Type

Method

Description

protected void

closeReader()

protected float

getNextVoxelValue()

protected void

init(SurfaceGenerator sg)

implemented in SurfaceFileReader and

protected void

readParameters()

protected boolean

readVolumeParameters(boolean isMapData)

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, getJVXLCutoff, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- readers
  
  private VolumeFileReader[] readers
- factors
  
  private float[] factors
Constructor Details
- IsoIntersectGridReader
  
  public IsoIntersectGridReader()
Method Details
- init
  
  protected void init(SurfaceGenerator sg)
  
  Description copied from class: SurfaceReader
  
  implemented in SurfaceFileReader and
  
  Overrides:
  
  init in class SurfaceFileReader
- readVolumeParameters
  
  protected boolean readVolumeParameters(boolean isMapData)
  
  Overrides:
  
  readVolumeParameters in class VolumeFileReader
- getNextVoxelValue
  
  protected float getNextVoxelValue() throws Exception
  
  Overrides:
  
  getNextVoxelValue in class VolumeFileReader
  
  Throws:
  
  Exception
- closeReader
  
  protected void closeReader()
  
  Overrides:
  
  closeReader in class VolumeFileReader
- readParameters
  
  protected void readParameters() throws Exception
  
  Specified by:
  
  readParameters in class VolumeFileReader
  
  Throws:
  
  Exception

Class IsoIntersectGridReader

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Details

readers

factors

Constructor Details

IsoIntersectGridReader

Method Details

init

readVolumeParameters

getNextVoxelValue

closeReader

readParameters