org.jmol.jvxl.readers.Ras3DReader

All Implemented Interfaces:: VertexDataServer

class Ras3DReader extends PolygonFileReader

Field Summary

Fields

Modifier and Type

Field

Description

private boolean

asQuads

(package private) Map<String,Integer>

htVertices

private int

nPolygons

private String

pmeshError

private String

type

Fields inherited from class org.jmol.jvxl.readers.PolygonFileReader
nTriangles, nVertices

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

Ras3DReader()
Method Summary

Modifier and Type

Method

Description

private int

getPoint(String[] tokens, int i)

(package private) void

getSurfaceData()

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

protected void

init2PR(SurfaceGenerator sg, BufferedReader br)

private boolean

readVertices()

protected boolean

readVerticesAndPolygons()

protected void

setHeader()

Methods inherited from class org.jmol.jvxl.readers.PolygonFileReader
init2PFR, readSurfaceData, readVolumeData, readVolumeParameters

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader
closeReader, 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, getPlane, getPlaneSR, getSPF, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValue2, getValueAtPoint, gotoAndReadVoxelData, gotoData, 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
- pmeshError
  
  private String pmeshError
- type
  
  private String type
- asQuads
  
  private boolean asQuads
- nPolygons
  
  private int nPolygons
- htVertices
  
  Map<String,Integer> htVertices
Constructor Details
- Ras3DReader
  
  Ras3DReader()
Method Details
- init2
  
  void init2(SurfaceGenerator sg, BufferedReader br)
  
  Overrides:
  
  init2 in class SurfaceFileReader
- init2PR
  
  protected void init2PR(SurfaceGenerator sg, BufferedReader br)
- setHeader
  
  protected void setHeader()
- getSurfaceData
  
  void getSurfaceData() throws Exception
  
  Specified by:
  
  getSurfaceData in class PolygonFileReader
  
  Throws:
  
  Exception
- readVerticesAndPolygons
  
  protected boolean readVerticesAndPolygons()
- readVertices
  
  private boolean readVertices() throws Exception
  
  Throws:
  
  Exception
- getPoint
  
  private int getPoint(String[] tokens, int i)

Class Ras3DReader

Field Summary

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

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.PolygonFileReader

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

pmeshError

type

asQuads

nPolygons

htVertices

Constructor Details

Ras3DReader

Method Details

init2

init2PR

setHeader

getSurfaceData

readVerticesAndPolygons

readVertices

getPoint