class PmeshReader extends PolygonFileReader
Modifier and Type | Field and Description |
---|---|
protected int |
fixedCount |
private boolean |
isBinary |
protected boolean |
isClosedFace |
protected int |
iToken |
protected int |
nPolygons |
protected boolean |
onePerLine |
protected java.lang.String |
pmeshError |
protected java.lang.String[] |
tokens |
protected java.lang.String |
type |
protected int |
vertexBase |
protected int[] |
vertexMap |
nTriangles, nVertices
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 and Description |
---|
PmeshReader() |
Modifier and Type | Method and Description |
---|---|
protected boolean |
checkBinary(java.lang.String fileName) |
private float |
getFloat() |
private int |
getInt() |
(package private) void |
getSurfaceData() |
(package private) void |
init2(SurfaceGenerator sg,
java.io.BufferedReader br) |
protected void |
init2PR(SurfaceGenerator sg,
java.io.BufferedReader br) |
private java.lang.String |
nextToken() |
(package private) boolean |
readBinaryHeader() |
protected boolean |
readPolygons() |
protected boolean |
readPolygonsPM() |
protected boolean |
readVertices() |
protected boolean |
readVerticesAndPolygons() |
protected boolean |
readVerticesPM() |
protected void |
setHeader() |
init2PFR, readSurfaceData, readVolumeData, readVolumeParameters
closeReader, closeReaderSFR, discardTempData, getQuotedStringNext, getTokens, init, init2SFR, newBinaryDocument, parseFloat, parseFloatArray, parseFloatArrayStr, parseFloatRange, parseFloatStr, parseInt, parseIntNext, parseIntStr, rd, setOutputChannel, setStream, skipTo
addTriangleCheck, addVC, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, discardTempDataSR, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getPlane, getPlane2, 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
private boolean isBinary
protected int nPolygons
protected java.lang.String pmeshError
protected java.lang.String type
protected boolean isClosedFace
protected int fixedCount
protected boolean onePerLine
protected int vertexBase
protected int[] vertexMap
protected java.lang.String[] tokens
protected int iToken
void init2(SurfaceGenerator sg, java.io.BufferedReader br)
init2
in class SurfaceFileReader
protected void init2PR(SurfaceGenerator sg, java.io.BufferedReader br)
protected void setHeader()
protected boolean checkBinary(java.lang.String fileName)
void getSurfaceData() throws java.lang.Exception
getSurfaceData
in class PolygonFileReader
java.lang.Exception
protected boolean readVerticesAndPolygons()
boolean readBinaryHeader()
protected boolean readVertices() throws java.lang.Exception
java.lang.Exception
protected boolean readVerticesPM() throws java.lang.Exception
java.lang.Exception
protected boolean readPolygons() throws java.lang.Exception
java.lang.Exception
protected boolean readPolygonsPM() throws java.lang.Exception
java.lang.Exception
private java.lang.String nextToken() throws java.lang.Exception
java.lang.Exception
private int getInt() throws java.lang.Exception
java.lang.Exception
private float getFloat() throws java.lang.Exception
java.lang.Exception