org.jmol.jvxl.readers.MapFileReader

All Implemented Interfaces:: VertexDataServer

Direct Known Subclasses:: BCifDensityReader, Dsn6BinaryReader, MrcBinaryReader, PyMOLMeshReader, XplorReader

abstract class MapFileReader extends VolumeFileReader

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

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.SurfaceFileReader
binarydoc, br, line, next, out

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
Constructor Summary

Constructors

Constructor

Description

MapFileReader()
Method Summary

Modifier and Type

Method

Description

protected void

checkInsideOut(int mapc, int mapr, int maps)

protected void

getVectorsAndOrigin()

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

protected void

init2MFR(SurfaceGenerator sg, BufferedReader br)

protected void

setCutoffAutomatic()

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

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- 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
Constructor Details
- MapFileReader
  
  MapFileReader()
Method Details
- init2
  
  void init2(SurfaceGenerator sg, BufferedReader br)
  
  Overrides:
  
  init2 in class VolumeFileReader
- init2MFR
  
  protected void init2MFR(SurfaceGenerator sg, BufferedReader br)
- checkInsideOut
  
  protected void checkInsideOut(int mapc, int mapr, int maps)
- getVectorsAndOrigin
  
  protected void getVectorsAndOrigin()
- setCutoffAutomatic
  
  protected void setCutoffAutomatic()

Class MapFileReader

Field Summary

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

Constructor Summary

Method Summary

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

Methods inherited from class java.lang.Object

Field Details

dmin

dmax

dmean

drange

mapc

mapr

maps

n0

n1

n2

mode

xyzStart

na

nb

nc

a

b

c

alpha

beta

gamma

origin

vectors

xIndex

yIndex

zIndex

p3

Constructor Details

MapFileReader

Method Details

init2

init2MFR

checkInsideOut

getVectorsAndOrigin

setCutoffAutomatic