abstract class MapFileReader extends VolumeFileReader
Modifier and Type | Field and Description |
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protected float |
a |
protected javax.vecmath.Point3f |
adjustment |
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 |
na |
protected int |
nb |
protected int |
nc |
protected int |
nx |
protected int[] |
nxyzStart |
protected int |
ny |
protected int |
nz |
protected javax.vecmath.Point3f |
origin |
protected javax.vecmath.Point3f[] |
vectors |
atomCount, boundingBox, canDownsample, downsampleFactor, endOfData, isAngstroms, negativeAtomCount, nSurfaces, readerClosed, thePlane
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 |
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MapFileReader(SurfaceGenerator sg,
java.io.BufferedReader br) |
Modifier and Type | Method and Description |
---|---|
protected void |
getVectorsAndOrigin() |
protected void |
setCutoffAutomatic() |
checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, initializeSurfaceData, nextVoxel, readParameters, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData
discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo
addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSpanningVectors, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, 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 nx
protected int ny
protected int nz
protected int mode
protected int[] nxyzStart
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 javax.vecmath.Point3f origin
protected javax.vecmath.Point3f adjustment
protected javax.vecmath.Point3f[] vectors
MapFileReader(SurfaceGenerator sg, java.io.BufferedReader br)