class BCifDensityReader extends MapFileReader
| Modifier and Type | Field and Description |
|---|---|
(package private) float |
checkSum |
java.util.Map<java.lang.String,java.lang.Object> |
cifData |
private boolean |
isDiff |
private int |
pt |
java.util.Map<java.lang.String,java.lang.Object> |
thisData |
protected float[] |
values |
a, alpha, b, beta, c, dmax, dmean, dmin, drange, gamma, mapc, mapr, maps, mode, n0, n1, n2, na, nb, nc, origin, p3, vectors, xIndex, xyzStart, yIndex, zIndexac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosedallowSigma, 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 |
|---|
BCifDensityReader() |
| Modifier and Type | Method and Description |
|---|---|
protected void |
closeReader() |
protected void |
getCifData(java.lang.String fileName,
java.lang.Object data) |
protected float |
getCifFloat(java.lang.String key) |
protected java.util.Map<java.lang.String,java.lang.Object> |
getCifMap(java.lang.String type) |
protected java.lang.String |
getCifString(java.lang.String key) |
private float |
getXYZ(javajs.util.P3 a,
float x) |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
protected float |
nextVoxel() |
protected float[] |
readCifFloats(java.lang.String key,
float[] values) |
protected javajs.util.P3 |
readCifP3(java.lang.String key,
javajs.util.P3 p3) |
protected void |
readParameters() |
protected void |
skipData(int nPoints) |
checkInsideOut, getVectorsAndOrigin, init2MFR, setCutoffAutomaticcheckAtomLine, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, 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, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeDataV, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTrianglesprivate int pt
float checkSum
protected float[] values
public java.util.Map<java.lang.String,java.lang.Object> cifData
public java.util.Map<java.lang.String,java.lang.Object> thisData
private boolean isDiff
protected void getCifData(java.lang.String fileName,
java.lang.Object data)
protected javajs.util.P3 readCifP3(java.lang.String key,
javajs.util.P3 p3)
protected java.util.Map<java.lang.String,java.lang.Object> getCifMap(java.lang.String type)
protected java.lang.String getCifString(java.lang.String key)
protected float getCifFloat(java.lang.String key)
protected float[] readCifFloats(java.lang.String key,
float[] values)
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2 in class MapFileReaderprotected void readParameters()
throws java.lang.Exception
readParameters in class VolumeFileReaderjava.lang.Exceptionprivate float getXYZ(javajs.util.P3 a,
float x)
protected float nextVoxel()
throws java.lang.Exception
nextVoxel in class VolumeFileReaderjava.lang.Exceptionprotected void skipData(int nPoints)
throws java.lang.Exception
skipData in class VolumeFileReaderjava.lang.Exceptionprotected void closeReader()
closeReader in class VolumeFileReader