Package org.jmol.jvxl.readers
Class MapFileReader
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceReader
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- org.jmol.jvxl.readers.SurfaceFileReader
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- org.jmol.jvxl.readers.VolumeFileReader
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- org.jmol.jvxl.readers.MapFileReader
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- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
BCifDensityReader
,Dsn6BinaryReader
,MrcBinaryReader
,PyMOLMeshReader
,XplorReader
abstract class MapFileReader extends VolumeFileReader
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Field Summary
Fields Modifier and Type Field 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
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Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces, readerClosed
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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, 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 Constructor Description MapFileReader()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader
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
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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
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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 Detail
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dmin
protected float dmin
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dmax
protected float dmax
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dmean
protected float dmean
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drange
protected float drange
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mapc
protected int mapc
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mapr
protected int mapr
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maps
protected int maps
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n0
protected int n0
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n1
protected int n1
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n2
protected int n2
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mode
protected int mode
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xyzStart
protected float[] xyzStart
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na
protected int na
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nb
protected int nb
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nc
protected int nc
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a
protected float a
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b
protected float b
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c
protected float c
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alpha
protected float alpha
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beta
protected float beta
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gamma
protected float gamma
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origin
protected javajs.util.P3 origin
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vectors
protected javajs.util.P3[] vectors
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xIndex
protected int xIndex
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yIndex
protected int yIndex
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zIndex
protected int zIndex
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p3
protected javajs.util.P3 p3
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Method Detail
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init2
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
- Overrides:
init2
in classVolumeFileReader
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init2MFR
protected void init2MFR(SurfaceGenerator sg, java.io.BufferedReader br)
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checkInsideOut
protected void checkInsideOut(int mapc, int mapr, int maps)
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getVectorsAndOrigin
protected void getVectorsAndOrigin()
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setCutoffAutomatic
protected void setCutoffAutomatic()
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