abstract class SurfaceFileReader extends SurfaceReader
Modifier and Type | Field and Description |
---|---|
protected BinaryDocument |
binarydoc |
protected java.io.BufferedReader |
br |
protected java.lang.String |
line |
protected int[] |
next |
protected java.io.OutputStream |
os |
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, 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 |
---|
SurfaceFileReader(SurfaceGenerator sg,
java.io.BufferedReader br) |
Modifier and Type | Method and Description |
---|---|
protected void |
closeReader() |
(package private) void |
discardTempData(boolean discardAll) |
protected java.lang.String |
getNextQuotedString() |
protected java.lang.String[] |
getTokens() |
protected float |
parseFloat() |
protected float |
parseFloat(java.lang.String s) |
protected float[] |
parseFloatArray() |
protected float[] |
parseFloatArray(java.lang.String s) |
protected int |
parseInt() |
protected int |
parseInt(java.lang.String s) |
protected int |
parseIntNext(java.lang.String s) |
protected java.lang.String |
readLine() |
protected void |
setOutputStream(java.io.OutputStream os) |
protected void |
skipTo(java.lang.String info,
java.lang.String what) |
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSpanningVectors, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, readSurfaceData, readVolumeData, readVolumeParameters, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected java.io.BufferedReader br
protected BinaryDocument binarydoc
protected java.io.OutputStream os
protected java.lang.String line
protected int[] next
SurfaceFileReader(SurfaceGenerator sg, java.io.BufferedReader br)
protected void setOutputStream(java.io.OutputStream os)
setOutputStream
in class SurfaceReader
protected void closeReader()
closeReader
in class SurfaceReader
void discardTempData(boolean discardAll)
discardTempData
in class SurfaceReader
protected java.lang.String[] getTokens()
protected float parseFloat()
protected float parseFloat(java.lang.String s)
protected int parseInt()
protected int parseInt(java.lang.String s)
protected int parseIntNext(java.lang.String s)
protected float[] parseFloatArray(java.lang.String s)
protected float[] parseFloatArray()
protected java.lang.String getNextQuotedString()
protected void skipTo(java.lang.String info, java.lang.String what) throws java.lang.Exception
java.lang.Exception
protected java.lang.String readLine() throws java.lang.Exception
java.lang.Exception