org.jmol.jvxl.readers.IsoFxyReader

All Implemented Interfaces:: VertexDataServer

Direct Known Subclasses:: IsoFxyzReader

class IsoFxyReader extends AtomDataReader

Field Summary

Fields

Modifier and Type

Field

Description

private float[][]

data

private Object[]

func

private boolean

isPlanarMapping

private final float[]

values

Fields inherited from class org.jmol.jvxl.readers.AtomDataReader
ac, atomData, atomIndex, atomNo, atomProp, atomRadius, atomXyzTruncated, bsMyIgnored, bsMySelected, bsNearby, bsSurfaceVoxels, contactPair, doAddHydrogens, doUseIterator, fileDotModel, fileName, firstNearbyAtom, haveOneProperty, havePlane, margin, maxDistance, maxRS, modelIndex, myAtomCount, myIndex, nearbyAtomCount, noFaceSpheres, pt0, pt1, ptV, ptY0, ptZ0, rs, rs2, sr, theProperty, thisAtomSet, thisPlane, thisX, validSpheres, vl0, vl1, vl2, voxelSource

Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints

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

IsoFxyReader()
Method Summary

Modifier and Type

Method

Description

protected float

evaluateValue(int x, int y, int z)

float[]

getPlane(int x)

float

getValue(int x, int y, int z, int pxyz)

for readers only

float

getValueAtPoint(javajs.util.T3 pt, boolean getSource)

(package private) void

init(SurfaceGenerator sg)

implemented in SurfaceFileReader and

protected void

initIFR(SurfaceGenerator sg)

protected void

readSurfaceData(boolean isMapData)

private void

setPlane(int x, float[] plane)

protected void

setup(boolean isMapData)

protected void

setupType(String type)

protected void

setVolumeData()

Methods inherited from class org.jmol.jvxl.readers.AtomDataReader
getAtomMinMax, getAtoms, initADR, markPlaneVoxels, markSphereVoxels, resetPlane, resetVoxelData, setGridLimitsForAtom, setHeader, setRadii, setRanges, setup2, setVertexSource, setVolumeDataADR, setVolumeForPlane, setVoxel, unsetVoxelData, unsetVoxelData2

Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, initVDR, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempData, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue2, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setOutputChannel, 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
- data
  
  private float[][] data
- isPlanarMapping
  
  private boolean isPlanarMapping
- func
  
  private Object[] func
- values
  
  private final float[] values
Constructor Details
- IsoFxyReader
  
  IsoFxyReader()
Method Details
- init
  
  void init(SurfaceGenerator sg)
  
  Description copied from class: SurfaceReader
  
  implemented in SurfaceFileReader and
  
  Overrides:
  
  init in class VolumeDataReader
- initIFR
  
  protected void initIFR(SurfaceGenerator sg)
- setup
  
  protected void setup(boolean isMapData)
  
  Overrides:
  
  setup in class AtomDataReader
- setupType
  
  protected void setupType(String type)
- setVolumeData
  
  protected void setVolumeData()
  
  Overrides:
  
  setVolumeData in class AtomDataReader
- readSurfaceData
  
  protected void readSurfaceData(boolean isMapData) throws Exception
  
  Overrides:
  
  readSurfaceData in class VolumeDataReader
  
  Throws:
  
  Exception
- getPlane
  
  public float[] getPlane(int x)
  
  Specified by:
  
  getPlane in interface VertexDataServer
  
  Overrides:
  
  getPlane in class SurfaceReader
- setPlane
  
  private void setPlane(int x, float[] plane)
- getValue
  
  public float getValue(int x, int y, int z, int pxyz)
  
  Description copied from interface: VertexDataServer
  
  for readers only
  
  Specified by:
  
  getValue in interface VertexDataServer
  
  Overrides:
  
  getValue in class SurfaceReader
  
  Returns:
  
  value[x][y][z]
- getValueAtPoint
  
  public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
  
  Overrides:
  
  getValueAtPoint in class SurfaceReader
  
  getSource - TODO
  
  Returns:
  
  value
- evaluateValue
  
  protected float evaluateValue(int x, int y, int z)

Class IsoFxyReader

Field Summary

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

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

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

Constructor Summary

Method Summary

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

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

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

Methods inherited from class java.lang.Object

Field Details

data

isPlanarMapping

func

values

Constructor Details

IsoFxyReader

Method Details

init

initIFR

setup

setupType

setVolumeData

readSurfaceData

getPlane

setPlane

getValue

getValueAtPoint

evaluateValue