Package org.jmol.jvxl.readers
Class IsoFxyReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.VolumeDataReader
org.jmol.jvxl.readers.AtomDataReader
org.jmol.jvxl.readers.IsoFxyReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
IsoFxyzReader
-
Field Summary
FieldsModifier and TypeFieldDescriptionprivate float[][]
private Object[]
private boolean
private final float[]
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 -
Method Summary
Modifier and TypeMethodDescriptionprotected 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
protected void
readSurfaceData
(boolean isMapData) private void
setPlane
(int x, float[] plane) protected void
setup
(boolean isMapData) protected void
protected void
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
-
Field Details
-
data
private float[][] data -
isPlanarMapping
private boolean isPlanarMapping -
func
-
values
private final float[] values
-
-
Constructor Details
-
IsoFxyReader
IsoFxyReader()
-
-
Method Details
-
init
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Overrides:
init
in classVolumeDataReader
-
initIFR
-
setup
protected void setup(boolean isMapData) - Overrides:
setup
in classAtomDataReader
-
setupType
-
setVolumeData
protected void setVolumeData()- Overrides:
setVolumeData
in classAtomDataReader
-
readSurfaceData
- Overrides:
readSurfaceData
in classVolumeDataReader
- Throws:
Exception
-
getPlane
public float[] getPlane(int x) - Specified by:
getPlane
in interfaceVertexDataServer
- Overrides:
getPlane
in classSurfaceReader
-
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 interfaceVertexDataServer
- Overrides:
getValue
in classSurfaceReader
- Returns:
- value[x][y][z]
-
getValueAtPoint
public float getValueAtPoint(javajs.util.T3 pt, boolean getSource) - Overrides:
getValueAtPoint
in classSurfaceReader
getSource
- TODO- Returns:
- value
-
evaluateValue
protected float evaluateValue(int x, int y, int z)
-