public class JvxlReader extends JvxlXmlReader
bsVoxelBitSet, colorDataCount, edgeDataCount, haveContourData, haveReadColorData, isXmlFile, JVXL_VERSION, surfaceDataCount, tempDataXml, thisInsideac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfacesallowSigma, 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 |
|---|
JvxlReader() |
| Modifier and Type | Method and 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) |
getEncodedVertexData, getSurfacePointAndFraction, getVoxelBitSet, gotoAndReadVoxelData, init2JXR, jvxlDecodeContourData, jvxlDecodeTriangleData, jvxlDecodeVertexData, jvxlReadSurfaceInfo, jvxlSetColorRanges, postProcessVertices, readColorData, readSurfaceDataJXR, readSurfaceDataXML, readVector, readVolumeDatacheckAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getValue, init2VFR, initializeSurfaceData, nextVoxel, readSurfaceDataVFR, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZcloseReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipToaddTriangleCheck, 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, updateTrianglesvoid init2(SurfaceGenerator sg, BufferedReader br)
init2 in class JvxlXmlReaderprotected void readParameters()
throws Exception
readParameters in class JvxlXmlReaderExceptionprotected String jvxlReadFractionData(String type, int nPoints)
JvxlXmlReaderjvxlReadFractionData in class JvxlXmlReaderprotected void gotoData(int n,
int nPoints)
throws Exception
gotoData in class JvxlXmlReaderExceptionprivate void jvxlReadDefinitionLine(boolean showMsg)
throws Exception
Exceptionprotected void readSurfaceData(boolean isMapDataIgnored)
throws Exception
readSurfaceData in class JvxlXmlReaderExceptionprotected void jvxlSkipData(int nPoints,
boolean doSkipColorData)
throws Exception
jvxlSkipData in class JvxlXmlReaderExceptionprivate void jvxlSkipDataBlock(int nPoints,
boolean isInt)
throws Exception
Exceptionprivate int countData(String str)