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:

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`	`na`
`protected int`	`nb`
`protected int`	`nc`
`protected int`	`nx`
`protected int[]`	`nxyzStart`
`protected int`	`ny`
`protected int`	`nz`
`protected javajs.util.P3`	`origin`
`protected javajs.util.P3[]`	`vectors`

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader
ac, boundingBox, canDownsample, downsampleFactor, downsampleRemainders, endOfData, isAngstroms, nData, negativeAtomCount, nSkipX, nSkipY, nSkipZ, nSurfaces

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`	`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
```

nx
```
protected int nx
```

ny
```
protected int ny
```

nz
```
protected int nz
```

mode
```
protected int mode
```

nxyzStart
```
protected int[] nxyzStart
```

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
```

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)

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

nx

ny

nz

mode

nxyzStart

na

nb

nc

a

b

c

alpha

beta

gamma

origin

vectors

Constructor Detail

MapFileReader

Method Detail

init2

init2MFR

getVectorsAndOrigin

setCutoffAutomatic