org.jmol.jvxl.readers

Class SurfaceGenerator

public class SurfaceGenerator extends Object

Field Summary
AtomDataServeratomDataServer
ColorEncodercolorEncoder
intcolorPtr
JvxlDatajvxlData
MarchingSquaresmarchingSquares
MeshDatameshData
MeshDataServermeshDataServer
Parametersparams
Point3fptRef
booleanrangeDefined
Vector3fvAB
Vector3fvAC
Vector3fvNorm
VolumeDatavolumeData
VoxelReadervoxelReader
Constructor Summary
SurfaceGenerator()
SurfaceGenerator(AtomDataServer atomDataServer, MeshDataServer meshDataServer, ColorEncoder colorEncoder, MeshData meshData, JvxlData jvxlData)
Method Summary
floatdistanceVerticalToPlane(float x, float y, Point3f pta, Point3f ptb, Point3f ptc)
static floatfindNearestThreePoints(float x, float y, float[][] xyz, int[] result)
voidgenerateSurface()
AtomDataServergetAtomDataServer()
BitSetgetBsIgnore()
BitSetgetBsSelected()
intgetColor(int which)
ColorEncodergetColorEncoder()
floatgetCutoff()
voidgetFunctionZfromXY()
booleangetIAddGridPoints()
booleangetIsPositiveOnly()
booleangetIUseBitSets()
JvxlDatagetJvxlData()
MarchingSquaresgetMarchingSquares()
MeshDatagetMeshData()
MeshDataServergetMeshDataServer()
HashtablegetMoData()
ParametersgetParams()
Point4fgetPlane()
ObjectgetProperty(String property, int index)
StringgetScript()
String[]getTitle()
VolumeDatagetVolumeData()
voidinitializeIsosurface()
voidinitState()
booleanisCubeData()
booleanisInsideOut()
booleanisStateDataRead()
voidmapSurface(Object value)
voidprocessState()
VoxelReadersetFileData(Object value)
voidsetJvxlData(JvxlData jvxlData)
StringsetLcao()
voidsetMarchingSquares(MarchingSquares marchingSquares)
voidsetModelIndex(int modelIndex)
booleansetParameter(String propertyName, Object value)
setParameter is the main interface for surface generation.
booleansetParameter(String propertyName, Object value, BitSet bs)
voidsetReader()
voidsetup(AtomDataServer atomDataServer, MeshDataServer meshDataServer, ColorEncoder colorEncoder, MeshData meshData, JvxlData jvxlData)

Field Detail

atomDataServer

private AtomDataServer atomDataServer

colorEncoder

private ColorEncoder colorEncoder

colorPtr

int colorPtr

jvxlData

private JvxlData jvxlData

marchingSquares

private MarchingSquares marchingSquares

meshData

private MeshData meshData

meshDataServer

private MeshDataServer meshDataServer

params

private Parameters params

ptRef

final Point3f ptRef

rangeDefined

private boolean rangeDefined

vAB

final Vector3f vAB

vAC

final Vector3f vAC

vNorm

final Vector3f vNorm

volumeData

private VolumeData volumeData

voxelReader

VoxelReader voxelReader

Constructor Detail

SurfaceGenerator

public SurfaceGenerator()

SurfaceGenerator

public SurfaceGenerator(AtomDataServer atomDataServer, MeshDataServer meshDataServer, ColorEncoder colorEncoder, MeshData meshData, JvxlData jvxlData)

Method Detail

distanceVerticalToPlane

private float distanceVerticalToPlane(float x, float y, Point3f pta, Point3f ptb, Point3f ptc)

findNearestThreePoints

private static float findNearestThreePoints(float x, float y, float[][] xyz, int[] result)

generateSurface

private void generateSurface()

getAtomDataServer

AtomDataServer getAtomDataServer()

getBsIgnore

public BitSet getBsIgnore()

getBsSelected

public BitSet getBsSelected()

getColor

public int getColor(int which)

getColorEncoder

ColorEncoder getColorEncoder()

getCutoff

public float getCutoff()

getFunctionZfromXY

private void getFunctionZfromXY()

getIAddGridPoints

public boolean getIAddGridPoints()

getIsPositiveOnly

public boolean getIsPositiveOnly()

getIUseBitSets

public boolean getIUseBitSets()

getJvxlData

public JvxlData getJvxlData()

getMarchingSquares

MarchingSquares getMarchingSquares()

getMeshData

MeshData getMeshData()

getMeshDataServer

MeshDataServer getMeshDataServer()

getMoData

public Hashtable getMoData()

getParams

Parameters getParams()

getPlane

public Point4f getPlane()

getProperty

public Object getProperty(String property, int index)

getScript

public String getScript()

getTitle

public String[] getTitle()

getVolumeData

VolumeData getVolumeData()

initializeIsosurface

void initializeIsosurface()

initState

public void initState()

isCubeData

public boolean isCubeData()

isInsideOut

public boolean isInsideOut()

isStateDataRead

public boolean isStateDataRead()

mapSurface

private void mapSurface(Object value)

processState

private void processState()

setFileData

VoxelReader setFileData(Object value)

setJvxlData

public void setJvxlData(JvxlData jvxlData)

setLcao

public String setLcao()

setMarchingSquares

void setMarchingSquares(MarchingSquares marchingSquares)

setModelIndex

public void setModelIndex(int modelIndex)

setParameter

public boolean setParameter(String propertyName, Object value)
setParameter is the main interface for surface generation.

Parameters: propertyName value

Returns: True if handled; False if not

setParameter

public boolean setParameter(String propertyName, Object value, BitSet bs)

setReader

private void setReader()

setup

private void setup(AtomDataServer atomDataServer, MeshDataServer meshDataServer, ColorEncoder colorEncoder, MeshData meshData, JvxlData jvxlData)