org.jmol.jvxl.readers.MsmsReader

All Implemented Interfaces:: VertexDataServer

class MsmsReader extends PmeshReader

Field Summary

Fields

Modifier and Type

Field

Description

private String

fileName

Fields inherited from class org.jmol.jvxl.readers.PmeshReader
fixedCount, isClosedFace, iToken, nPolygons, onePerLine, pmeshError, tokens, type, vertexBase, 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

MsmsReader()
Method Summary

Modifier and Type

Method

Description

(package private) void

init2(SurfaceGenerator sg, BufferedReader br)

protected boolean

readPolygons()

protected boolean

readVertices()

private void

skipHeader()

Methods inherited from class org.jmol.jvxl.readers.PmeshReader
checkBinary, getSurfaceData, init2PR, readBinaryHeader, readPolygonsPM, readVerticesAndPolygons, readVerticesPM, 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
- fileName
  
  private String fileName
Constructor Details
- MsmsReader
  
  MsmsReader()
Method Details
- init2
  
  void init2(SurfaceGenerator sg, BufferedReader br)
  
  Overrides:
  
  init2 in class PmeshReader
- readVertices
  
  protected boolean readVertices() throws Exception
  
  Overrides:
  
  readVertices in class PmeshReader
  
  Throws:
  
  Exception
- readPolygons
  
  protected boolean readPolygons() throws Exception
  
  Overrides:
  
  readPolygons in class PmeshReader
  
  Throws:
  
  Exception
- skipHeader
  
  private void skipHeader() throws Exception
  
  Throws:
  
  Exception

Class MsmsReader

Field Summary

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

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.PmeshReader

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

fileName

Constructor Details

MsmsReader

Method Details

init2

readVertices

readPolygons

skipHeader