class JaguarReader extends VolumeFileReader
Modifier and Type | Field and Description |
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private float[] |
extents |
atomCount, boundingBox, canDownsample, endOfData, isAngstroms, negativeAtomCount, nSurfaces, readerClosed, thePlane
allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, isAnisotropic, isEccentric, isJvxl, isProgressive, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, mappingPlane, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin
Constructor and Description |
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JaguarReader(SurfaceGenerator sg,
java.io.BufferedReader br) |
Modifier and Type | Method and Description |
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private void |
readExtents(int voxelVectorIndex)
read the extentx=, extenty=, extentz= lines and cache them
then read the npts= line and construct the necessary data
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protected void |
readParameters()
nothing much here
|
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getValue, getVoxelBitSet, gotoData, nextVoxel, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readColorData, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
JaguarReader(SurfaceGenerator sg, java.io.BufferedReader br)
protected void readParameters() throws java.lang.Exception
readParameters
in class VolumeFileReader
java.lang.Exception
- -- generally a reader issueprivate void readExtents(int voxelVectorIndex) throws java.lang.Exception
voxelVectorIndex
- 0, 1, or 2java.lang.Exception
- -- generally a reader issue