Package org.jmol.jvxl.readers
Class PolygonFileReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.PolygonFileReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
EfvetReader,NffReader,Pmesh4Reader,PmeshReader,Ras3DReader
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Field Summary
FieldsFields 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 TypeMethodDescription(package private) abstract voidprotected voidinit2PFR(SurfaceGenerator sg, BufferedReader br) protected voidreadSurfaceData(boolean isMapData) protected booleanreadVolumeData(boolean isMapData) protected booleanreadVolumeParameters(boolean isMapData) Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReader, closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipToMethods 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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nVertices
protected int nVertices -
nTriangles
protected int nTriangles
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Constructor Details
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PolygonFileReader
PolygonFileReader()
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Method Details
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init2PFR
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData) - Specified by:
readVolumeParametersin classSurfaceReader
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readVolumeData
protected boolean readVolumeData(boolean isMapData) - Specified by:
readVolumeDatain classSurfaceReader
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readSurfaceData
- Specified by:
readSurfaceDatain classSurfaceReader- Throws:
Exception
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getSurfaceData
- Throws:
Exception
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