abstract class MapFileReader extends VolumeFileReader
Modifier and Type | Field and Description |
---|---|
protected float |
a |
protected float |
alpha |
protected float |
b |
protected float |
beta |
protected float |
c |
protected float |
dmax |
protected float |
dmean |
protected float |
dmin |
protected float |
drange |
protected float |
gamma |
protected int |
mapc |
protected int |
mapr |
protected int |
maps |
protected int |
mode |
protected int |
n0 |
protected int |
n1 |
protected int |
n2 |
protected int |
na |
protected int |
nb |
protected int |
nc |
protected javajs.util.P3 |
origin |
protected javajs.util.P3 |
p3 |
protected javajs.util.P3[] |
vectors |
protected int |
xIndex |
protected float[] |
xyzStart |
protected int |
yIndex |
protected int |
zIndex |
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
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 |
---|
MapFileReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
checkInsideOut(int mapc,
int mapr,
int maps) |
protected void |
getVectorsAndOrigin() |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
protected void |
init2MFR(SurfaceGenerator sg,
java.io.BufferedReader br) |
protected void |
setCutoffAutomatic() |
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, nextVoxel, readParameters, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
addTriangleCheck, 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, updateTriangles
protected float dmin
protected float dmax
protected float dmean
protected float drange
protected int mapc
protected int mapr
protected int maps
protected int n0
protected int n1
protected int n2
protected int mode
protected float[] xyzStart
protected int na
protected int nb
protected int nc
protected float a
protected float b
protected float c
protected float alpha
protected float beta
protected float gamma
protected javajs.util.P3 origin
protected javajs.util.P3[] vectors
protected int xIndex
protected int yIndex
protected int zIndex
protected javajs.util.P3 p3
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2
in class VolumeFileReader
protected void init2MFR(SurfaceGenerator sg, java.io.BufferedReader br)
protected void checkInsideOut(int mapc, int mapr, int maps)
protected void getVectorsAndOrigin()
protected void setCutoffAutomatic()