Package org.jmol.jvxl.readers
Class MapFileReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.VolumeFileReader
org.jmol.jvxl.readers.MapFileReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
BCifDensityReader
,Dsn6BinaryReader
,MrcBinaryReader
,PyMOLMeshReader
,XplorReader
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected float
protected float
protected float
protected float
protected float
protected float
protected float
protected float
protected float
protected float
protected int
protected int
protected int
protected int
protected int
protected int
protected int
protected int
protected int
protected int
protected javajs.util.P3
protected javajs.util.P3
protected javajs.util.P3[]
protected int
protected float[]
protected int
protected int
Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
Fields inherited from class org.jmol.jvxl.readers.SurfaceReader
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, jvxlCutoffRange, 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
checkInsideOut
(int mapc, int mapr, int maps) protected void
(package private) void
init2
(SurfaceGenerator sg, BufferedReader br) protected void
init2MFR
(SurfaceGenerator sg, BufferedReader br) protected void
Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
checkAtomLine, closeReader, getJVXLCutoff, getNextVoxelValue, getPlane, getPlaneNCI, getSPFv, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, init2VFR, initializeSurfaceData, nextVoxel, readParameters, readSurfaceData, readSurfaceDataVFR, readVolumeData, readVolumeDataVFR, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData, skipDataVFR, swapXZ
Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
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
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Field Details
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dmin
protected float dmin -
dmax
protected float dmax -
dmean
protected float dmean -
drange
protected float drange -
mapc
protected int mapc -
mapr
protected int mapr -
maps
protected int maps -
n0
protected int n0 -
n1
protected int n1 -
n2
protected int n2 -
mode
protected int mode -
xyzStart
protected float[] xyzStart -
na
protected int na -
nb
protected int nb -
nc
protected int nc -
a
protected float a -
b
protected float b -
c
protected float c -
alpha
protected float alpha -
beta
protected float beta -
gamma
protected float gamma -
origin
protected javajs.util.P3 origin -
vectors
protected javajs.util.P3[] vectors -
xIndex
protected int xIndex -
yIndex
protected int yIndex -
zIndex
protected int zIndex -
p3
protected javajs.util.P3 p3
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Constructor Details
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MapFileReader
MapFileReader()
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Method Details
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init2
- Overrides:
init2
in classVolumeFileReader
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init2MFR
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checkInsideOut
protected void checkInsideOut(int mapc, int mapr, int maps) -
getVectorsAndOrigin
protected void getVectorsAndOrigin() -
setCutoffAutomatic
protected void setCutoffAutomatic()
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