org.jmol.jvxl.readers
Class KinemageReader

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.KinemageReader
All Implemented Interfaces:
VertexDataServer

 class KinemageReader
extends PmeshReader


Field Summary
private  java.lang.String findString
           
private  java.lang.String lastAtom
           
private  int nDots
           
private static int POINTS_ALL
           
private static int POINTS_HETS
           
private static int POINTS_MCMC
           
private static int POINTS_MCSC
           
private static int POINTS_SCSC
           
private  int pointType
           
private  float vMax
           
private  float vMin
           
 
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
KinemageReader(SurfaceGenerator sg, java.io.BufferedReader br)
           
 
Method Summary
private  float assignValueFromGapColorForKin(java.lang.String color)
          C++ code gives these as " value > x.x ? "xxxxx", etc.
private  int getColor(java.lang.String color)
           
private  int getPoint(java.lang.String line, int i, int[] retColor, boolean checkType)
           
private  void readDots()
           
protected  boolean readPolygons()
           
private  void readVectors()
           
protected  boolean readVertices()
           
protected  boolean readVolumeParameters(boolean isMapData)
           
private  void setup(boolean isMapData)
           
 
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
 
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

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
Constructor Detail

KinemageReader

KinemageReader(SurfaceGenerator sg,
               java.io.BufferedReader br)
Parameters:
sg -
br -
Method Detail

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