org.jmol.jvxl.readers.PmeshReader

All Implemented Interfaces:: VertexDataServer

Direct Known Subclasses:: KinemageReader, MsmsReader, ObjReader

class PmeshReader extends PolygonFileReader

PMESH format created for Jmol. This is not the "pmesh" format from Edinburgh: see http://i-sight.sourceforge.net/docs/GridView/MeshFileReader.html#ReadPMeshFile(java.lang.String,%20GridView.OutputPanel,%20javax.swing.JProgressBar) That format is read by the ObjReader.

Author:: Bob Hanson hansonr@stolaf.edu

Field Summary

Fields

Modifier and Type

Field

Description

protected int

fixedCount

private boolean

isBinary

protected boolean

isClosedFace

protected int

iToken

protected int

nPolygons

protected boolean

onePerLine

protected String

pmeshError

protected String[]

tokens

protected String

type

protected int

vertexBase

protected int[]

vertexMap

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

PmeshReader()
Method Summary

Modifier and Type

Method

Description

protected boolean

checkBinary(String fileName)

private float

getFloat()

private int

getInt()

(package private) void

getSurfaceData()

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

protected void

init2PR(SurfaceGenerator sg, BufferedReader br)

private String

nextToken()

(package private) boolean

readBinaryHeader()

protected boolean

readPolygons()

protected boolean

readPolygonsPM()

protected boolean

readVertices()

protected boolean

readVerticesAndPolygons()

protected boolean

readVerticesPM()

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
- isBinary
  
  private boolean isBinary
- nPolygons
  
  protected int nPolygons
- pmeshError
  
  protected String pmeshError
- type
  
  protected String type
- isClosedFace
  
  protected boolean isClosedFace
- fixedCount
  
  protected int fixedCount
- onePerLine
  
  protected boolean onePerLine
- vertexBase
  
  protected int vertexBase
- vertexMap
  
  protected int[] vertexMap
- tokens
  
  protected String[] tokens
- iToken
  
  protected int iToken
Constructor Details
- PmeshReader
  
  PmeshReader()
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()
- checkBinary
  
  protected boolean checkBinary(String fileName)
- getSurfaceData
  
  void getSurfaceData() throws Exception
  
  Specified by:
  
  getSurfaceData in class PolygonFileReader
  
  Throws:
  
  Exception
- readVerticesAndPolygons
  
  protected boolean readVerticesAndPolygons()
- readBinaryHeader
  
  boolean readBinaryHeader()
- readVertices
  
  protected boolean readVertices() throws Exception
  
  Throws:
  
  Exception
- readVerticesPM
  
  protected boolean readVerticesPM() throws Exception
  
  Throws:
  
  Exception
- readPolygons
  
  protected boolean readPolygons() throws Exception
  
  Throws:
  
  Exception
- readPolygonsPM
  
  protected boolean readPolygonsPM() throws Exception
  
  Throws:
  
  Exception
- 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 PmeshReader

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

isBinary

nPolygons

pmeshError

type

isClosedFace

fixedCount

onePerLine

vertexBase

vertexMap

tokens

iToken

Constructor Details

PmeshReader

Method Details

init2

init2PR

setHeader

checkBinary

getSurfaceData

readVerticesAndPolygons

readBinaryHeader

readVertices

readVerticesPM

readPolygons

readPolygonsPM

nextToken

getInt

getFloat