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 BufferedReader

br

protected 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, 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

SurfaceFileReader()
Method Summary

Modifier and Type

Method

Description

protected void

closeReader()

protected void

closeReaderSFR()

(package private) void

discardTempData(boolean discardAll)

protected String

getQuotedStringNext()

protected String[]

getTokens()

(package private) void

init(SurfaceGenerator sg)

implemented in SurfaceFileReader and

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

(package private) void

init2SFR(SurfaceGenerator sg, BufferedReader br)

(package private) javajs.api.GenericBinaryDocument

newBinaryDocument()

protected float

parseFloat()

protected float[]

parseFloatArray(float[] a, String strStart, String strEnd)

protected float[]

parseFloatArrayStr(String s)

protected float

parseFloatRange(String s, int iStart, int iEnd)

protected float

parseFloatStr(String s)

protected int

parseInt()

protected int

parseIntNext(String s)

protected int

parseIntStr(String s)

protected String

rd()

protected void

setOutputChannel(javajs.util.OC out)

protected void

setStream(String fileName, boolean isBigEndian)

protected void

skipTo(String info, 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 Details
- br
  
  protected BufferedReader br
- binarydoc
  
  protected javajs.api.GenericBinaryDocument binarydoc
- out
  
  protected javajs.util.OC out
- line
  
  protected String line
- next
  
  protected int[] next
Constructor Details
- SurfaceFileReader
  
  SurfaceFileReader()
Method Details
- setStream
  
  protected void setStream(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, BufferedReader br)
- init2SFR
  
  void init2SFR(SurfaceGenerator sg, 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 String[] getTokens()
- parseFloat
  
  protected float parseFloat()
- parseFloatStr
  
  protected float parseFloatStr(String s)
- parseFloatRange
  
  protected float parseFloatRange(String s, int iStart, int iEnd)
- parseInt
  
  protected int parseInt()
- parseIntStr
  
  protected int parseIntStr(String s)
- parseIntNext
  
  protected int parseIntNext(String s)
- parseFloatArrayStr
  
  protected float[] parseFloatArrayStr(String s)
- parseFloatArray
  
  protected float[] parseFloatArray(float[] a, String strStart, String strEnd)
- getQuotedStringNext
  
  protected String getQuotedStringNext()
- skipTo
  
  protected void skipTo(String info, String what) throws Exception
  
  Throws:
  
  Exception
- rd
  
  protected String rd() throws Exception
  
  Throws:
  
  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 Details

br

binarydoc

out

line

next

Constructor Details

SurfaceFileReader

Method Details

setStream

init

init2

init2SFR

newBinaryDocument

setOutputChannel

closeReader

closeReaderSFR

discardTempData

getTokens

parseFloat

parseFloatStr

parseFloatRange

parseInt

parseIntStr

parseIntNext

parseFloatArrayStr

parseFloatArray

getQuotedStringNext

skipTo

rd