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[][]dataprivate java.lang.Object[]funcprivate booleanisPlanarMappingprivate 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
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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 floatevaluateValue(int x, int y, int z)float[]getPlane(int x)protected floatgetValue(int x, int y, int z)floatgetValueAtPoint(javajs.util.T3 pt, boolean getSource)(package private) voidinit(SurfaceGenerator sg)implemented in SurfaceFileReader andprotected voidinitIFR(SurfaceGenerator sg)protected voidreadSurfaceData(boolean isMapData)private voidsetPlane(int x, float[] plane)protected voidsetup(boolean isMapData)protected voidsetupType(java.lang.String type)protected voidsetVolumeData()-
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, getValue, 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:SurfaceReaderimplemented in SurfaceFileReader and- Overrides:
initin classVolumeDataReader
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initIFR
protected void initIFR(SurfaceGenerator sg)
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setup
protected void setup(boolean isMapData)
- Overrides:
setupin classAtomDataReader
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setupType
protected void setupType(java.lang.String type)
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setVolumeData
protected void setVolumeData()
- Overrides:
setVolumeDatain classAtomDataReader
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readSurfaceData
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception- Overrides:
readSurfaceDatain classVolumeDataReader- Throws:
java.lang.Exception
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getPlane
public float[] getPlane(int x)
- Specified by:
getPlanein interfaceVertexDataServer- Overrides:
getPlanein classSurfaceReader
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setPlane
private void setPlane(int x, float[] plane)
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getValue
protected float getValue(int x, int y, int z)
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getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource)- Overrides:
getValueAtPointin classSurfaceReadergetSource- TODO- Returns:
- value
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evaluateValue
protected float evaluateValue(int x, int y, int z)
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