org.jmol.jvxl.readers
Class JvxlReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.VolumeFileReader
org.jmol.jvxl.readers.JvxlXmlReader
org.jmol.jvxl.readers.JvxlReader
- All Implemented Interfaces:
- VertexDataServer
public class JvxlReader
- extends JvxlXmlReader
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, 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 |
Methods inherited from class org.jmol.jvxl.readers.JvxlXmlReader |
getEncodedVertexData, getSurfacePointAndFraction, getVoxelBitSet, gotoAndReadVoxelData, jvxlDecodeContourData, jvxlDecodeTriangleData, jvxlDecodeVertexData, jvxlReadSurfaceInfo, jvxlSetColorRanges, postProcessVertices, readColorData, readSurfaceData, readVector, readVolumeData, readVolumeFileSurfaceData |
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader |
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getValue, nextVoxel, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData |
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader |
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo |
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader |
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
JvxlReader
JvxlReader(SurfaceGenerator sg,
BufferedReader br)
readParameters
protected void readParameters()
throws Exception
- Overrides:
readParameters
in class JvxlXmlReader
- Throws:
Exception
jvxlReadData
protected String jvxlReadData(String type,
int nPoints)
- Overrides:
jvxlReadData
in class JvxlXmlReader
gotoData
protected void gotoData(int n,
int nPoints)
throws Exception
- Overrides:
gotoData
in class JvxlXmlReader
- Throws:
Exception
jvxlReadDefinitionLine
private void jvxlReadDefinitionLine(boolean showMsg)
throws Exception
- Throws:
Exception
readSurfaceData
protected void readSurfaceData(boolean isMapDataIgnored)
throws Exception
- Overrides:
readSurfaceData
in class JvxlXmlReader
- Throws:
Exception
jvxlSkipData
protected void jvxlSkipData(int nPoints,
boolean doSkipColorData)
throws Exception
- Overrides:
jvxlSkipData
in class JvxlXmlReader
- Throws:
Exception
jvxlSkipDataBlock
private void jvxlSkipDataBlock(int nPoints,
boolean isInt)
throws Exception
- Throws:
Exception
countData
private int countData(String str)