Package org.jmol.jvxl.readers
Class Pmesh4Reader
- 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.Pmesh4Reader
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- All Implemented Interfaces:
VertexDataServer
class Pmesh4Reader extends PolygonFileReader
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Field Summary
Fields Modifier and Type Field Description private intcolorprivate intiTokenprivate intnPolygonsprivate intnXprivate intnYprivate java.lang.StringpmeshErrorprivate java.lang.String[]tokens(package private) floattransparencyprivate java.lang.Stringtype-
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 Pmesh4Reader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private voidcreateMesh()private floatgetFloat()private intgetInt()(package private) voidgetSurfaceData()(package private) voidinit2(SurfaceGenerator sg, java.io.BufferedReader br)private java.lang.StringnextToken()private voidreadColor()private booleanreadVertices()private booleanreadVerticesAndPolygons()-
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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Method Detail
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init2
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
- Overrides:
init2in classSurfaceFileReader
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getSurfaceData
void getSurfaceData() throws java.lang.Exception- Specified by:
getSurfaceDatain classPolygonFileReader- Throws:
java.lang.Exception
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readVerticesAndPolygons
private boolean readVerticesAndPolygons()
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readColor
private void readColor() throws java.lang.Exception- Throws:
java.lang.Exception
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readVertices
private boolean readVertices() throws java.lang.Exception- Throws:
java.lang.Exception
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createMesh
private void createMesh()
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nextToken
private java.lang.String nextToken() throws java.lang.Exception- Throws:
java.lang.Exception
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getInt
private int getInt() throws java.lang.Exception- Throws:
java.lang.Exception
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getFloat
private float getFloat() throws java.lang.Exception- Throws:
java.lang.Exception
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