Package org.jmol.jvxl.readers
Class PmeshReader
java.lang.Object
org.jmol.jvxl.readers.SurfaceReader
org.jmol.jvxl.readers.SurfaceFileReader
org.jmol.jvxl.readers.PolygonFileReader
org.jmol.jvxl.readers.PmeshReader
- All Implemented Interfaces:
VertexDataServer
- Direct Known Subclasses:
KinemageReader
,MsmsReader
,ObjReader
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
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int
private boolean
protected boolean
protected int
protected int
protected boolean
protected String
protected String[]
protected String
protected int
protected int[]
Fields inherited from class org.jmol.jvxl.readers.PolygonFileReader
nTriangles, nVertices
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
checkBinary
(String fileName) private float
getFloat()
private int
getInt()
(package private) void
(package private) void
init2
(SurfaceGenerator sg, BufferedReader br) protected void
init2PR
(SurfaceGenerator sg, BufferedReader br) private String
(package private) boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected boolean
protected void
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
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Field Details
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isBinary
private boolean isBinary -
nPolygons
protected int nPolygons -
pmeshError
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type
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isClosedFace
protected boolean isClosedFace -
fixedCount
protected int fixedCount -
onePerLine
protected boolean onePerLine -
vertexBase
protected int vertexBase -
vertexMap
protected int[] vertexMap -
tokens
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iToken
protected int iToken
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Constructor Details
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PmeshReader
PmeshReader()
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Method Details
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init2
- Overrides:
init2
in classSurfaceFileReader
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init2PR
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setHeader
protected void setHeader() -
checkBinary
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getSurfaceData
- Specified by:
getSurfaceData
in classPolygonFileReader
- Throws:
Exception
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readVerticesAndPolygons
protected boolean readVerticesAndPolygons() -
readBinaryHeader
boolean readBinaryHeader() -
readVertices
- Throws:
Exception
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readVerticesPM
- Throws:
Exception
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readPolygons
- Throws:
Exception
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readPolygonsPM
- Throws:
Exception
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nextToken
- Throws:
Exception
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getInt
- Throws:
Exception
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getFloat
- Throws:
Exception
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