public class JvxlReader extends JvxlXmlReader
bsVoxelBitSet, colorDataCount, edgeDataCount, haveContourData, haveReadColorData, isXmlFile, JVXL_VERSION, surfaceDataCount, tempDataXml, thisInside
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces
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
Constructor and Description |
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JvxlReader() |
Modifier and Type | Method and Description |
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private int |
countData(java.lang.String str) |
protected void |
gotoData(int n,
int nPoints) |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
private void |
jvxlReadDefinitionLine(boolean showMsg) |
protected java.lang.String |
jvxlReadFractionData(java.lang.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.
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protected void |
jvxlSkipData(int nPoints,
boolean doSkipColorData) |
private void |
jvxlSkipDataBlock(int nPoints,
boolean isInt) |
protected void |
readParameters() |
protected void |
readSurfaceData(boolean isMapDataIgnored) |
getEncodedVertexData, getSurfacePointAndFraction, getVoxelBitSet, gotoAndReadVoxelData, init2JXR, jvxlDecodeContourData, jvxlDecodeTriangleData, jvxlDecodeVertexData, jvxlReadSurfaceInfo, jvxlSetColorRanges, postProcessVertices, readColorData, readSurfaceDataJXR, readSurfaceDataXML, readVector, readVolumeData
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSPFv, getValue, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceDataVFR, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane2, getSPF, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValue2, getValueAtPoint, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, readAndSetVolumeParameters, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2
in class JvxlXmlReader
protected void readParameters() throws java.lang.Exception
readParameters
in class JvxlXmlReader
java.lang.Exception
protected java.lang.String jvxlReadFractionData(java.lang.String type, int nPoints)
JvxlXmlReader
jvxlReadFractionData
in class JvxlXmlReader
protected void gotoData(int n, int nPoints) throws java.lang.Exception
gotoData
in class JvxlXmlReader
java.lang.Exception
private void jvxlReadDefinitionLine(boolean showMsg) throws java.lang.Exception
java.lang.Exception
protected void readSurfaceData(boolean isMapDataIgnored) throws java.lang.Exception
readSurfaceData
in class JvxlXmlReader
java.lang.Exception
protected void jvxlSkipData(int nPoints, boolean doSkipColorData) throws java.lang.Exception
jvxlSkipData
in class JvxlXmlReader
java.lang.Exception
private void jvxlSkipDataBlock(int nPoints, boolean isInt) throws java.lang.Exception
java.lang.Exception
private int countData(java.lang.String str)