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
```
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, 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

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()`

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

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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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 Detail
- MapFileReader
```
MapFileReader()
```

Method Detail

init2

void init2(SurfaceGenerator sg,
           java.io.BufferedReader br)

Overrides:: init2 in class VolumeFileReader

init2MFR

protected void init2MFR(SurfaceGenerator sg,
                        java.io.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 Detail

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 Detail

MapFileReader

Method Detail

init2

init2MFR

checkInsideOut

getVectorsAndOrigin

setCutoffAutomatic