public class JvxlReader extends JvxlXmlReader
bsVoxelBitSet, colorDataCount, edgeDataCount, haveContourData, haveReadColorData, isXmlFile, JVXL_VERSION, surfaceDataCount, tempDataXml, thisInside
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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JvxlReader(SurfaceGenerator sg,
java.io.BufferedReader br) |
Modifier and Type | Method and Description |
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private int |
countData(java.lang.String str) |
protected void |
gotoData(int n,
int nPoints) |
protected java.lang.String |
jvxlReadData(java.lang.String type,
int nPoints) |
private void |
jvxlReadDefinitionLine(boolean showMsg) |
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, jvxlDecodeContourData, jvxlDecodeTriangleData, jvxlDecodeVertexData, jvxlReadSurfaceInfo, jvxlSetColorRanges, postProcessVertices, readColorData, readSurfaceData, readVector, readVolumeData, readVolumeFileSurfaceData
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getValue, nextVoxel, 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, getSurfacePointIndexAndFraction, getValueAtPoint, initializeMapping, initializeVolumetricData, jvxlUpdateInfo, readAndSetVolumeParameters, readTheVolumeData, resetIsosurface, selectPocket, setBoundingBox, setMappingPlane, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
JvxlReader(SurfaceGenerator sg, java.io.BufferedReader br)
protected void readParameters() throws java.lang.Exception
readParameters
in class JvxlXmlReader
java.lang.Exception
protected java.lang.String jvxlReadData(java.lang.String type, int nPoints)
jvxlReadData
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)