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

Field Summary

Fields

Modifier and Type	Field and Description
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, 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 and Description
KinemageReader(SurfaceGenerator sg, java.io.BufferedReader br)

Method Summary

Methods

Modifier and Type	Method and Description
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