Package org.jmol.jvxl.readers
Class PmeshReader
- 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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- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
KinemageReader,MsmsReader,ObjReader
class PmeshReader extends PolygonFileReader
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Field Summary
Fields Modifier and Type Field Description protected intfixedCountprivate booleanisBinaryprotected booleanisClosedFaceprotected intiTokenprotected intnPolygonsprotected booleanonePerLineprotected java.lang.StringpmeshErrorprotected java.lang.String[]tokensprotected java.lang.Stringtypeprotected intvertexBaseprotected int[]vertexMap-
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 PmeshReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected booleancheckBinary(java.lang.String fileName)private floatgetFloat()private intgetInt()(package private) voidgetSurfaceData()(package private) voidinit2(SurfaceGenerator sg, java.io.BufferedReader br)protected voidinit2PR(SurfaceGenerator sg, java.io.BufferedReader br)private java.lang.StringnextToken()(package private) booleanreadBinaryHeader()protected booleanreadPolygons()protected booleanreadPolygonsPM()protected booleanreadVertices()protected booleanreadVerticesAndPolygons()protected booleanreadVerticesPM()protected voidsetHeader()-
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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isBinary
private boolean isBinary
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nPolygons
protected int nPolygons
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pmeshError
protected java.lang.String pmeshError
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type
protected java.lang.String type
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isClosedFace
protected boolean isClosedFace
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fixedCount
protected int fixedCount
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onePerLine
protected boolean onePerLine
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vertexBase
protected int vertexBase
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vertexMap
protected int[] vertexMap
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tokens
protected java.lang.String[] tokens
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iToken
protected int iToken
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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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init2PR
protected void init2PR(SurfaceGenerator sg, java.io.BufferedReader br)
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setHeader
protected void setHeader()
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checkBinary
protected boolean checkBinary(java.lang.String fileName)
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getSurfaceData
void getSurfaceData() throws java.lang.Exception- Specified by:
getSurfaceDatain classPolygonFileReader- Throws:
java.lang.Exception
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readVerticesAndPolygons
protected boolean readVerticesAndPolygons()
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readBinaryHeader
boolean readBinaryHeader()
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readVertices
protected boolean readVertices() throws java.lang.Exception- Throws:
java.lang.Exception
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readVerticesPM
protected boolean readVerticesPM() throws java.lang.Exception- Throws:
java.lang.Exception
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readPolygons
protected boolean readPolygons() throws java.lang.Exception- Throws:
java.lang.Exception
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readPolygonsPM
protected boolean readPolygonsPM() throws java.lang.Exception- Throws:
java.lang.Exception
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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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