Package org.jmol.jvxl.readers
Class PolygonFileReader
- 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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- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
EfvetReader
,NffReader
,Pmesh4Reader
,PmeshReader
,Ras3DReader
abstract class PolygonFileReader extends SurfaceFileReader
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Field Summary
Fields Modifier and Type Field Description protected int
nTriangles
protected int
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 PolygonFileReader()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description (package private) abstract void
getSurfaceData()
protected void
init2PFR(SurfaceGenerator sg, java.io.BufferedReader br)
protected void
readSurfaceData(boolean isMapData)
protected boolean
readVolumeData(boolean isMapData)
protected boolean
readVolumeParameters(boolean isMapData)
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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, 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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Method Detail
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init2PFR
protected void init2PFR(SurfaceGenerator sg, java.io.BufferedReader br)
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readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Specified by:
readVolumeParameters
in classSurfaceReader
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readVolumeData
protected boolean readVolumeData(boolean isMapData)
- Specified by:
readVolumeData
in classSurfaceReader
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readSurfaceData
protected void readSurfaceData(boolean isMapData) throws java.lang.Exception
- Specified by:
readSurfaceData
in classSurfaceReader
- Throws:
java.lang.Exception
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getSurfaceData
abstract void getSurfaceData() throws java.lang.Exception
- Throws:
java.lang.Exception
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