abstract class SurfaceFileReader extends SurfaceReader
Modifier and Type | Field and Description |
---|---|
protected javajs.api.GenericBinaryDocument |
binarydoc |
protected java.io.BufferedReader |
br |
protected java.lang.String |
line |
protected int[] |
next |
protected javajs.util.OC |
out |
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 |
---|
SurfaceFileReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
closeReader() |
protected void |
closeReaderSFR() |
(package private) void |
discardTempData(boolean discardAll) |
protected java.lang.String |
getQuotedStringNext() |
protected java.lang.String[] |
getTokens() |
(package private) void |
init(SurfaceGenerator sg)
implemented in SurfaceFileReader and
|
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
(package private) void |
init2SFR(SurfaceGenerator sg,
java.io.BufferedReader br) |
(package private) javajs.api.GenericBinaryDocument |
newBinaryDocument() |
protected float |
parseFloat() |
protected float[] |
parseFloatArray(float[] a,
java.lang.String strStart,
java.lang.String strEnd) |
protected float[] |
parseFloatArrayStr(java.lang.String s) |
protected float |
parseFloatRange(java.lang.String s,
int iStart,
int iEnd) |
protected float |
parseFloatStr(java.lang.String s) |
protected int |
parseInt() |
protected int |
parseIntNext(java.lang.String s) |
protected int |
parseIntStr(java.lang.String s) |
protected java.lang.String |
rd() |
protected void |
setOutputChannel(javajs.util.OC out) |
protected void |
setStream(java.lang.String fileName,
boolean isBigEndian) |
protected void |
skipTo(java.lang.String info,
java.lang.String what) |
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlane2, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, readSurfaceData, readVolumeData, readVolumeParameters, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles
protected java.io.BufferedReader br
protected javajs.api.GenericBinaryDocument binarydoc
protected javajs.util.OC out
protected java.lang.String line
protected int[] next
protected void setStream(java.lang.String fileName, boolean isBigEndian)
void init(SurfaceGenerator sg)
SurfaceReader
init
in class SurfaceReader
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
void init2SFR(SurfaceGenerator sg, java.io.BufferedReader br)
javajs.api.GenericBinaryDocument newBinaryDocument()
protected void setOutputChannel(javajs.util.OC out)
setOutputChannel
in class SurfaceReader
protected void closeReader()
closeReader
in class SurfaceReader
protected void closeReaderSFR()
void discardTempData(boolean discardAll)
discardTempData
in class SurfaceReader
protected java.lang.String[] getTokens()
protected float parseFloat()
protected float parseFloatStr(java.lang.String s)
protected float parseFloatRange(java.lang.String s, int iStart, int iEnd)
protected int parseInt()
protected int parseIntStr(java.lang.String s)
protected int parseIntNext(java.lang.String s)
protected float[] parseFloatArrayStr(java.lang.String s)
protected float[] parseFloatArray(float[] a, java.lang.String strStart, java.lang.String strEnd)
protected java.lang.String getQuotedStringNext()
protected void skipTo(java.lang.String info, java.lang.String what) throws java.lang.Exception
java.lang.Exception
protected java.lang.String rd() throws java.lang.Exception
java.lang.Exception