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 java.lang.StringfindStringprivate java.lang.StringlastAtomprivate intnDotsprivate static intPOINTS_ALLprivate static intPOINTS_HETSprivate static intPOINTS_MCMCprivate static intPOINTS_MCSCprivate static intPOINTS_SCSCprivate intpointTypeprivate floatvMaxprivate floatvMin-
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 floatassignValueFromGapColorForKin(java.lang.String color)C++ code gives these as " value > x.x ? "xxxxx", etc.private intgetColor(java.lang.String color)private intgetPoint(java.lang.String line, int i, int[] retColor, boolean checkType)(package private) voidinit2(SurfaceGenerator sg, java.io.BufferedReader br)private voidreadDots()protected booleanreadPolygons()private voidreadVectors()protected booleanreadVertices()protected booleanreadVolumeParameters(boolean isMapData)-
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 java.lang.String findString
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lastAtom
private java.lang.String lastAtom
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Method Detail
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init2
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
- Overrides:
init2in classPmeshReader
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Overrides:
readVolumeParametersin classPolygonFileReader
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readVertices
protected boolean readVertices() throws java.lang.Exception- Overrides:
readVerticesin classPmeshReader- Throws:
java.lang.Exception
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readDots
private void readDots() throws java.lang.Exception- Throws:
java.lang.Exception
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readVectors
private void readVectors() throws java.lang.Exception- Throws:
java.lang.Exception
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getPoint
private int getPoint(java.lang.String line, int i, int[] retColor, boolean checkType)
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getColor
private int getColor(java.lang.String color)
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assignValueFromGapColorForKin
private float assignValueFromGapColorForKin(java.lang.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:
readPolygonsin classPmeshReader
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