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

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, 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

All Methods Instance Methods Concrete Methods
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 java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- fileName
```
private String fileName
```

Constructor Detail
- MsmsReader
```
MsmsReader()
```

Method Detail

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