org.jmol.jvxl.readers
Class MsmsReader

java.lang.Object
  org.jmol.jvxl.readers.SurfaceReader
      org.jmol.jvxl.readers.SurfaceFileReader
          org.jmol.jvxl.readers.PolygonFileReader
              org.jmol.jvxl.readers.PmeshReader
                  org.jmol.jvxl.readers.MsmsReader

All Implemented Interfaces:

VertexDataServer

 class MsmsReader
extends PmeshReader

Field Summary

private String

fileName

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

fixedCount, isClosedFace, iToken, nPolygons, onePerLine, PMESH_BINARY_MAGIC_NUMBER, 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, os

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, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, 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

MsmsReader(SurfaceGenerator sg, String fileName, BufferedReader br)

Method Summary

protected boolean	readPolygons()
protected boolean	readVertices()
private void	skipHeader()

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

addTriangleCheck, checkBinary, getSurfaceData, readBinaryHeader, readVerticesAndPolygons, setHeader

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

readSurfaceData, readVolumeData, readVolumeParameters

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

closeReader, discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getSurfaceAtomIndex, getSurfacePointAndFraction, getSurfacePointIndexAndFraction, getValue, getValueAtPoint, gotoAndReadVoxelData, gotoData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

fileName

private String fileName

Constructor Detail

MsmsReader

MsmsReader(SurfaceGenerator sg,
           String fileName,
           BufferedReader br)

Method Detail

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