org.jmol.jvxl.readers
Class MsmsReader

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceReader
      extended by org.jmol.jvxl.readers.SurfaceFileReader
          extended by org.jmol.jvxl.readers.PolygonFileReader
              extended by org.jmol.jvxl.readers.PmeshReader
                  extended by org.jmol.jvxl.readers.MsmsReader
All Implemented Interfaces:
VertexDataServer

 class MsmsReader
extends PmeshReader


Field Summary
private  java.lang.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, 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, java.lang.String fileName, java.io.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 java.lang.String fileName
Constructor Detail

MsmsReader

MsmsReader(SurfaceGenerator sg,
           java.lang.String fileName,
           java.io.BufferedReader br)
Method Detail

readVertices

protected boolean readVertices()
                        throws java.lang.Exception
Overrides:
readVertices in class PmeshReader
Throws:
java.lang.Exception

readPolygons

protected boolean readPolygons()
                        throws java.lang.Exception
Overrides:
readPolygons in class PmeshReader
Throws:
java.lang.Exception

skipHeader

private void skipHeader()
                 throws java.lang.Exception
Throws:
java.lang.Exception