Package org.jmol.jvxl.readers
Class KinemageReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.SurfaceFileReader
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- org.jmol.jvxl.readers.PolygonFileReader
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- org.jmol.jvxl.readers.PmeshReader
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- org.jmol.jvxl.readers.KinemageReader
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- All Implemented Interfaces:
VertexDataServer
class KinemageReader extends PmeshReader
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Field Summary
Fields Modifier and Type Field Description private String
findString
private String
lastAtom
private int
nDots
private static int
POINTS_ALL
private static int
POINTS_HETS
private static int
POINTS_MCMC
private static int
POINTS_MCSC
private static int
POINTS_SCSC
private int
pointType
private float
vMax
private float
vMin
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Fields inherited from class org.jmol.jvxl.readers.PmeshReader
fixedCount, isClosedFace, iToken, nPolygons, onePerLine, pmeshError, tokens, type, vertexBase, vertexMap
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Fields inherited from class org.jmol.jvxl.readers.PolygonFileReader
nTriangles, nVertices
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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 KinemageReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private float
assignValueFromGapColorForKin(String color)
C++ code gives these as " value > x.x ? "xxxxx", etc., so technically we are off by a smidgeon.private int
getColor(String color)
private int
getPoint(String line, int i, int[] retColor, boolean checkType)
(package private) void
init2(SurfaceGenerator sg, BufferedReader br)
private void
readDots()
protected boolean
readPolygons()
private void
readVectors()
protected boolean
readVertices()
protected boolean
readVolumeParameters(boolean isMapData)
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Methods inherited from class org.jmol.jvxl.readers.PmeshReader
checkBinary, getSurfaceData, init2PR, readBinaryHeader, readPolygonsPM, readVerticesAndPolygons, readVerticesPM, setHeader
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Methods inherited from class org.jmol.jvxl.readers.PolygonFileReader
init2PFR, readSurfaceData, readVolumeData
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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
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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 Detail
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POINTS_ALL
private static final int POINTS_ALL
- See Also:
- Constant Field Values
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POINTS_MCMC
private static final int POINTS_MCMC
- See Also:
- Constant Field Values
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POINTS_SCSC
private static final int POINTS_SCSC
- See Also:
- Constant Field Values
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POINTS_MCSC
private static final int POINTS_MCSC
- See Also:
- Constant Field Values
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POINTS_HETS
private static final int POINTS_HETS
- See Also:
- Constant Field Values
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nDots
private int nDots
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vMin
private float vMin
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vMax
private float vMax
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pointType
private int pointType
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findString
private String findString
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lastAtom
private String lastAtom
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Method Detail
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init2
void init2(SurfaceGenerator sg, BufferedReader br)
- Overrides:
init2
in classPmeshReader
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Overrides:
readVolumeParameters
in classPolygonFileReader
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readVertices
protected boolean readVertices() throws Exception
- Overrides:
readVertices
in classPmeshReader
- Throws:
Exception
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getPoint
private int getPoint(String line, int i, int[] retColor, boolean checkType)
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getColor
private int getColor(String color)
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assignValueFromGapColorForKin
private float assignValueFromGapColorForKin(String color)
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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