Package org.jmol.jvxl.readers
Class JvxlReader
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- All Implemented Interfaces:
VertexDataServer
public class JvxlReader extends JvxlXmlReader
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Field Summary
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Fields inherited from class org.jmol.jvxl.readers.JvxlXmlReader
bsVoxelBitSet, colorDataCount, edgeDataCount, haveContourData, haveReadColorData, isXmlFile, JVXL_VERSION, surfaceDataCount, tempDataXml, thisInside
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Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
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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 JvxlReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description private int
countData(String str)
protected void
gotoData(int n, int nPoints)
(package private) void
init2(SurfaceGenerator sg, BufferedReader br)
private void
jvxlReadDefinitionLine(boolean showMsg)
protected String
jvxlReadFractionData(String type, int nPoints)
"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge.protected void
jvxlSkipData(int nPoints, boolean doSkipColorData)
private void
jvxlSkipDataBlock(int nPoints, boolean isInt)
protected void
readParameters()
protected void
readSurfaceData(boolean isMapDataIgnored)
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Methods inherited from class org.jmol.jvxl.readers.JvxlXmlReader
getEncodedVertexData, getSurfacePointAndFraction, getVoxelBitSet, gotoAndReadVoxelData, init2JXR, jvxlDecodeContourData, jvxlDecodeTriangleData, jvxlDecodeVertexData, jvxlReadSurfaceInfo, jvxlSetColorRanges, postProcessVertices, readColorData, readSurfaceDataJXR, readSurfaceDataXML, readVector, readVolumeData
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Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getValue, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceDataVFR, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ
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Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
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, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, 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, BufferedReader br)
- Overrides:
init2
in classJvxlXmlReader
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readParameters
protected void readParameters() throws Exception
- Overrides:
readParameters
in classJvxlXmlReader
- Throws:
Exception
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jvxlReadFractionData
protected String jvxlReadFractionData(String type, int nPoints)
Description copied from class:JvxlXmlReader
"edge" data includes two parts -- a compressed bitset indicating exactly which edges, in order or processing by Jmol, are crossed by the surface, and a set of fractions indicating how far along that edge (good to 1 part in 8100) that surface crosses that edge. We are just reading he fractions here. "color" data comprises the corresponding sequence of data mapping values, again stored to a precision of 1 part in 8100, relative to a range of values.- Overrides:
jvxlReadFractionData
in classJvxlXmlReader
- Returns:
- data
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gotoData
protected void gotoData(int n, int nPoints) throws Exception
- Overrides:
gotoData
in classJvxlXmlReader
- Throws:
Exception
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jvxlReadDefinitionLine
private void jvxlReadDefinitionLine(boolean showMsg) throws Exception
- Throws:
Exception
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readSurfaceData
protected void readSurfaceData(boolean isMapDataIgnored) throws Exception
- Overrides:
readSurfaceData
in classJvxlXmlReader
- Throws:
Exception
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jvxlSkipData
protected void jvxlSkipData(int nPoints, boolean doSkipColorData) throws Exception
- Overrides:
jvxlSkipData
in classJvxlXmlReader
- Throws:
Exception
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jvxlSkipDataBlock
private void jvxlSkipDataBlock(int nPoints, boolean isInt) throws Exception
- Throws:
Exception
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countData
private int countData(String str)
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