Package org.jmol.jvxl.readers
Class KinemageReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.PolygonFileReader
org.jmol.jvxl.readers.PmeshReader
org.jmol.jvxl.readers.KinemageReader
- All Implemented Interfaces:
VertexDataServer
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate String
private String
private int
private static final int
private static final int
private static final int
private static final int
private static final int
private int
private float
private float
Fields inherited from class org.jmol.jvxl.readers.PmeshReader
fixedCount, isClosedFace, iToken, nPolygons, onePerLine, pmeshError, tokens, type, vertexBase, vertexMap
Fields inherited from class org.jmol.jvxl.readers.PolygonFileReader
nTriangles, nVertices
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate float
C++ code gives these as " value > x.x ? "xxxxx", etc.private int
private int
(package private) void
init2
(SurfaceGenerator sg, BufferedReader br) private void
readDots()
protected boolean
private void
protected boolean
protected boolean
readVolumeParameters
(boolean isMapData) Methods inherited from class org.jmol.jvxl.readers.PmeshReader
checkBinary, getSurfaceData, init2PR, readBinaryHeader, readPolygonsPM, readVerticesAndPolygons, readVerticesPM, setHeader
Methods inherited from class org.jmol.jvxl.readers.PolygonFileReader
init2PFR, readSurfaceData, readVolumeData
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReader, closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, 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, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Details
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POINTS_ALL
private static final int POINTS_ALL- See Also:
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POINTS_MCMC
private static final int POINTS_MCMC- See Also:
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POINTS_SCSC
private static final int POINTS_SCSC- See Also:
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POINTS_MCSC
private static final int POINTS_MCSC- See Also:
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POINTS_HETS
private static final int POINTS_HETS- See Also:
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nDots
private int nDots -
vMin
private float vMin -
vMax
private float vMax -
pointType
private int pointType -
findString
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lastAtom
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Constructor Details
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KinemageReader
KinemageReader()
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Method Details
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init2
- Overrides:
init2
in classPmeshReader
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData) - Overrides:
readVolumeParameters
in classPolygonFileReader
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readVertices
- Overrides:
readVertices
in classPmeshReader
- Throws:
Exception
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readDots
- Throws:
Exception
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readVectors
- Throws:
Exception
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getPoint
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getColor
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assignValueFromGapColorForKin
C++ code gives these as " value > x.x ? "xxxxx", etc. so technically we are off by a smidgeon. But they are the reference numbers, so we will use them inclusively instead.- Parameters:
color
-- Returns:
- value or NaN if outsided desired range
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readPolygons
protected boolean readPolygons()- Overrides:
readPolygons
in classPmeshReader
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