org.jmol.jvxl.readers
Class KinemageReader
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.KinemageReader
- All Implemented Interfaces:
- VertexDataServer
class KinemageReader
- extends PmeshReader
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.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 |
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 |
POINTS_ALL
private static final int POINTS_ALL
- See Also:
- Constant Field Values
POINTS_MCMC
private static final int POINTS_MCMC
- See Also:
- Constant Field Values
POINTS_SCSC
private static final int POINTS_SCSC
- See Also:
- Constant Field Values
POINTS_MCSC
private static final int POINTS_MCSC
- See Also:
- Constant Field Values
POINTS_HETS
private static final int POINTS_HETS
- See Also:
- Constant Field Values
nDots
private int nDots
vMin
private float vMin
vMax
private float vMax
pointType
private int pointType
findString
private java.lang.String findString
lastAtom
private java.lang.String lastAtom
KinemageReader
KinemageReader(SurfaceGenerator sg,
java.io.BufferedReader br)
- Parameters:
sg
- br
-
readVolumeParameters
protected boolean readVolumeParameters(boolean isMapData)
- Overrides:
readVolumeParameters
in class PolygonFileReader
setup
private void setup(boolean isMapData)
- Parameters:
isMapData
-
readVertices
protected boolean readVertices()
throws java.lang.Exception
- Overrides:
readVertices
in class PmeshReader
- Throws:
java.lang.Exception
readDots
private void readDots()
throws java.lang.Exception
- Throws:
java.lang.Exception
readVectors
private void readVectors()
throws java.lang.Exception
- Throws:
java.lang.Exception
getPoint
private int getPoint(java.lang.String line,
int i,
int[] retColor,
boolean checkType)
getColor
private int getColor(java.lang.String color)
assignValueFromGapColorForKin
private float assignValueFromGapColorForKin(java.lang.String color)
- C++ code gives these as " value > x.x ? "xxxxx", etc.
so technically we are off by a smidgeon. But they are the
reference numbers, so we will use them inclusively instead.
- Parameters:
color
-
- Returns:
- value or NaN if outsided desired range
readPolygons
protected boolean readPolygons()
- Overrides:
readPolygons
in class PmeshReader