org.jmol.jvxl.readers.Pmesh4Reader

All Implemented Interfaces:: VertexDataServer

class Pmesh4Reader extends PolygonFileReader

Field Summary

Fields

Modifier and Type

Field

Description

private int

color

private int

iToken

private int

nPolygons

private int

nX

private int

nY

private String

pmeshError

private String[]

tokens

(package private) float

transparency

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

Pmesh4Reader()
Method Summary

Modifier and Type

Method

Description

private void

createMesh()

private float

getFloat()

private int

getInt()

(package private) void

getSurfaceData()

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

private String

nextToken()

private void

readColor()

private boolean

readVertices()

private boolean

readVerticesAndPolygons()

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
- nPolygons
  
  private int nPolygons
- pmeshError
  
  private String pmeshError
- type
  
  private String type
- color
  
  private int color
- transparency
  
  float transparency
- nX
  
  private int nX
- nY
  
  private int nY
- tokens
  
  private String[] tokens
- iToken
  
  private int iToken
Constructor Details
- Pmesh4Reader
  
  Pmesh4Reader()
Method Details
- init2
  
  void init2(SurfaceGenerator sg, BufferedReader br)
  
  Overrides:
  
  init2 in class SurfaceFileReader
- getSurfaceData
  
  void getSurfaceData() throws Exception
  
  Specified by:
  
  getSurfaceData in class PolygonFileReader
  
  Throws:
  
  Exception
- readVerticesAndPolygons
  
  private boolean readVerticesAndPolygons()
- readColor
  
  private void readColor() throws Exception
  
  Throws:
  
  Exception
- readVertices
  
  private boolean readVertices() throws Exception
  
  Throws:
  
  Exception
- createMesh
  
  private void createMesh()
- nextToken
  
  private String nextToken() throws Exception
  
  Throws:
  
  Exception
- getInt
  
  private int getInt() throws Exception
  
  Throws:
  
  Exception
- getFloat
  
  private float getFloat() throws Exception
  
  Throws:
  
  Exception

Class Pmesh4Reader

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

nPolygons

pmeshError

type

color

transparency

nX

nY

tokens

iToken

Constructor Details

Pmesh4Reader

Method Details

init2

getSurfaceData

readVerticesAndPolygons

readColor

readVertices

createMesh

nextToken

getInt

getFloat