Package org.jmol.jvxl.readers
Class IsoFxyReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.VolumeDataReader
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- org.jmol.jvxl.readers.AtomDataReader
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- org.jmol.jvxl.readers.IsoFxyReader
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- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
IsoFxyzReader
class IsoFxyReader extends AtomDataReader
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Field Summary
Fields Modifier and Type Field Description private float[][]
data
private java.lang.Object[]
func
private boolean
isPlanarMapping
private float[]
values
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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
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Fields inherited from class org.jmol.jvxl.readers.VolumeDataReader
allowMapData, dataType, maxGrid, point, precalculateVoxelData, ptsPerAngstrom, useOriginStepsPoints
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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, 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
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Constructor Summary
Constructors Constructor Description IsoFxyReader()
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Method Summary
All Methods Instance Methods Concrete Methods 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 onlyfloat
getValueAtPoint(javajs.util.T3 pt, boolean getSource)
(package private) void
init(SurfaceGenerator sg)
implemented in SurfaceFileReader andprotected void
initIFR(SurfaceGenerator sg)
protected void
readSurfaceData(boolean isMapData)
private void
setPlane(int x, float[] plane)
protected void
setup(boolean isMapData)
protected void
setupType(java.lang.String type)
protected void
setVolumeData()
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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
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Methods inherited from class org.jmol.jvxl.readers.VolumeDataReader
closeReader, generateCube, initVDR, readSurfaceDataVDR, readVolumeData, readVolumeParameters, readVoxelDataIndividually, setVolumeDataParams, setVoxelRange, showGridInfo
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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
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Method Detail
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init
void init(SurfaceGenerator sg)
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Overrides:
init
in classVolumeDataReader
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initIFR
protected void initIFR(SurfaceGenerator sg)
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setup
protected void setup(boolean isMapData)
- Overrides:
setup
in classAtomDataReader
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setupType
protected void setupType(java.lang.String type)
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setVolumeData
protected void setVolumeData()
- Overrides:
setVolumeData
in classAtomDataReader
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readSurfaceData
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
- Overrides:
readSurfaceData
in classVolumeDataReader
- Throws:
java.lang.Exception
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getPlane
public float[] getPlane(int x)
- Specified by:
getPlane
in interfaceVertexDataServer
- Overrides:
getPlane
in classSurfaceReader
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setPlane
private void setPlane(int x, float[] plane)
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getValue
public float getValue(int x, int y, int z, int pxyz)
Description copied from interface:VertexDataServer
for readers only- Specified by:
getValue
in interfaceVertexDataServer
- Overrides:
getValue
in classSurfaceReader
- Returns:
- value[x][y][z]
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getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)
- Overrides:
getValueAtPoint
in classSurfaceReader
getSource
- TODO- Returns:
- value
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evaluateValue
protected float evaluateValue(int x, int y, int z)
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