Package org.jmol.jvxl.readers
Class MsmsReader
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- All Implemented Interfaces:
VertexDataServer
class MsmsReader extends PmeshReader
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Field Summary
Fields Modifier and Type Field Description private String
fileName
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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 MsmsReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) void
init2(SurfaceGenerator sg, BufferedReader br)
protected boolean
readPolygons()
protected boolean
readVertices()
private void
skipHeader()
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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, readVolumeParameters
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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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fileName
private String fileName
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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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readVertices
protected boolean readVertices() throws Exception
- Overrides:
readVertices
in classPmeshReader
- Throws:
Exception
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readPolygons
protected boolean readPolygons() throws Exception
- Overrides:
readPolygons
in classPmeshReader
- Throws:
Exception
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