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