java.lang.Object
- org.jmol.jvxl.readers.SurfaceReader
- - org.jmol.jvxl.readers.SurfaceFileReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

PolygonFileReader, VolumeFileReader
```
abstract class SurfaceFileReader
extends SurfaceReader
```
PolygonFileReader or VolumeFileReader

Field Summary

Fields
Modifier and Type	Field	Description
`protected javajs.api.GenericBinaryDocument`	`binarydoc`
`protected java.io.BufferedReader`	`br`
`protected java.lang.String`	`line`
`protected int[]`	`next`
`protected javajs.util.OC`	`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

SurfaceFileReader()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`closeReader()`
`protected void`	`closeReaderSFR()`
`(package private) void`	`discardTempData(boolean discardAll)`
`protected java.lang.String`	`getQuotedStringNext()`
`protected java.lang.String[]`	`getTokens()`
`(package private) void`	`init(SurfaceGenerator sg)`	implemented in SurfaceFileReader and
`(package private) void`	`init2(SurfaceGenerator sg, java.io.BufferedReader br)`
`(package private) void`	`init2SFR(SurfaceGenerator sg, java.io.BufferedReader br)`
`(package private) javajs.api.GenericBinaryDocument`	`newBinaryDocument()`
`protected float`	`parseFloat()`
`protected float[]`	`parseFloatArray(float[] a, java.lang.String strStart, java.lang.String strEnd)`
`protected float[]`	`parseFloatArrayStr(java.lang.String s)`
`protected float`	`parseFloatRange(java.lang.String s, int iStart, int iEnd)`
`protected float`	`parseFloatStr(java.lang.String s)`
`protected int`	`parseInt()`
`protected int`	`parseIntNext(java.lang.String s)`
`protected int`	`parseIntStr(java.lang.String s)`
`protected java.lang.String`	`rd()`
`protected void`	`setOutputChannel(javajs.util.OC out)`
`protected void`	`setStream(java.lang.String fileName, boolean isBigEndian)`
`protected void`	`skipTo(java.lang.String info, java.lang.String what)`

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, initSR, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, readSurfaceData, readVolumeData, readVolumeParameters, 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 Detail

br
```
protected java.io.BufferedReader br
```

binarydoc

protected javajs.api.GenericBinaryDocument binarydoc

out
```
protected javajs.util.OC out
```

line
```
protected java.lang.String line
```

next
```
protected int[] next
```

Constructor Detail
- SurfaceFileReader
```
SurfaceFileReader()
```

Method Detail

setStream

protected void setStream(java.lang.String fileName,
                         boolean isBigEndian)

init
```
void init(SurfaceGenerator sg)
```
Description copied from class: SurfaceReader

implemented in SurfaceFileReader and

Specified by:

init in class SurfaceReader

init2

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

init2SFR

void init2SFR(SurfaceGenerator sg,
              java.io.BufferedReader br)

newBinaryDocument

javajs.api.GenericBinaryDocument newBinaryDocument()

setOutputChannel
```
protected void setOutputChannel(javajs.util.OC out)
```
Overrides:

setOutputChannel in class SurfaceReader

closeReader
```
protected void closeReader()
```
Specified by:

closeReader in class SurfaceReader

closeReaderSFR
```
protected void closeReaderSFR()
```

discardTempData
```
void discardTempData(boolean discardAll)
```
Overrides:

discardTempData in class SurfaceReader

getTokens

protected java.lang.String[] getTokens()

parseFloat
```
protected float parseFloat()
```

parseFloatStr

protected float parseFloatStr(java.lang.String s)

parseFloatRange

protected float parseFloatRange(java.lang.String s,
                                int iStart,
                                int iEnd)

parseInt
```
protected int parseInt()
```

parseIntStr

protected int parseIntStr(java.lang.String s)

parseIntNext

protected int parseIntNext(java.lang.String s)

parseFloatArrayStr

protected float[] parseFloatArrayStr(java.lang.String s)

parseFloatArray

protected float[] parseFloatArray(float[] a,
                                  java.lang.String strStart,
                                  java.lang.String strEnd)

getQuotedStringNext

protected java.lang.String getQuotedStringNext()

rd

protected java.lang.String rd()
                       throws java.lang.Exception

Throws:: java.lang.Exception

Class SurfaceFileReader

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

br

binarydoc

out

line

next

Constructor Detail

SurfaceFileReader

Method Detail

setStream

init

init2

init2SFR

newBinaryDocument

setOutputChannel

closeReader

closeReaderSFR

discardTempData

getTokens

parseFloat

parseFloatStr

parseFloatRange

parseInt

parseIntStr

parseIntNext

parseFloatArrayStr

parseFloatArray

getQuotedStringNext

skipTo

rd