Package org.jmol.jvxl.readers
Class SurfaceFileReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
PolygonFileReader
,VolumeFileReader
PolygonFileReader or VolumeFileReader
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected javajs.api.GenericBinaryDocument
protected BufferedReader
protected String
protected int[]
protected javajs.util.OC
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, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
protected void
(package private) void
discardTempData
(boolean discardAll) protected String
protected String[]
(package private) void
init
(SurfaceGenerator sg) implemented in SurfaceFileReader and(package private) void
init2
(SurfaceGenerator sg, BufferedReader br) (package private) void
init2SFR
(SurfaceGenerator sg, BufferedReader br) (package private) javajs.api.GenericBinaryDocument
protected float
protected float[]
parseFloatArray
(float[] a, String strStart, String strEnd) protected float[]
protected float
parseFloatRange
(String s, int iStart, int iEnd) protected float
protected int
parseInt()
protected int
protected int
protected String
rd()
protected void
setOutputChannel
(javajs.util.OC out) protected void
protected void
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, readSurfaceData, readVolumeData, readVolumeParameters, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
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Field Details
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br
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binarydoc
protected javajs.api.GenericBinaryDocument binarydoc -
out
protected javajs.util.OC out -
line
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next
protected int[] next
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Constructor Details
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SurfaceFileReader
SurfaceFileReader()
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Method Details
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setStream
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init
Description copied from class:SurfaceReader
implemented in SurfaceFileReader and- Specified by:
init
in classSurfaceReader
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init2
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init2SFR
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newBinaryDocument
javajs.api.GenericBinaryDocument newBinaryDocument() -
setOutputChannel
protected void setOutputChannel(javajs.util.OC out) - Overrides:
setOutputChannel
in classSurfaceReader
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closeReader
protected void closeReader()- Specified by:
closeReader
in classSurfaceReader
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closeReaderSFR
protected void closeReaderSFR() -
discardTempData
void discardTempData(boolean discardAll) - Overrides:
discardTempData
in classSurfaceReader
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getTokens
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parseFloat
protected float parseFloat() -
parseFloatStr
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parseFloatRange
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parseInt
protected int parseInt() -
parseIntStr
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parseIntNext
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parseFloatArrayStr
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parseFloatArray
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getQuotedStringNext
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skipTo
- Throws:
Exception
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rd
- Throws:
Exception
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