org.jmol.jvxl.readers
Class SurfaceGenerator

java.lang.Object
  extended by org.jmol.jvxl.readers.SurfaceGenerator

public class SurfaceGenerator
extends java.lang.Object


Field Summary
private  AtomDataServer atomDataServer
           
(package private)  java.util.BitSet bsVdw
           
(package private)  int colorPtr
           
private  java.lang.String fileType
           
private  boolean isValid
           
private  JvxlData jvxlData
           
private  MarchingSquares marchingSquares
           
private  MeshData meshData
           
private  MeshDataServer meshDataServer
           
private  java.io.OutputStream os
           
private  Parameters params
           
(package private)  javax.vecmath.Point3f ptRef
           
(package private)  SurfaceReader surfaceReader
           
(package private)  javax.vecmath.Vector3f vAB
           
(package private)  javax.vecmath.Vector3f vAC
           
private  java.lang.String version
           
(package private)  javax.vecmath.Vector3f vNorm
           
private  VolumeData volumeData
           
 
Constructor Summary
SurfaceGenerator()
           
SurfaceGenerator(AtomDataServer atomDataServer, MeshDataServer meshDataServer, MeshData meshData, JvxlData jvxlData)
           
 
Method Summary
 void addRequiredFile(java.lang.String fileName)
           
(package private)  void colorIsosurface()
           
private  float distanceVerticalToPlane(float x, float y, javax.vecmath.Point3f pta, javax.vecmath.Point3f ptb, javax.vecmath.Point3f ptc)
           
(package private)  void fillAtomData(AtomData atomData, int mode)
           
private static float findNearestThreePoints(float x, float y, float[][] xyz, int[] result)
           
private  void generateSurface()
           
(package private)  AtomDataServer getAtomDataServer()
           
 java.util.BitSet getBsIgnore()
           
 java.util.BitSet getBsSelected()
           
 int getColor(int which)
           
 ColorEncoder getColorEncoder()
           
 float getCutoff()
           
 java.lang.String getFileName()
           
 java.lang.String getFileType()
           
private  void getFunctionZfromXY()
           
 boolean getIAddGridPoints()
           
 boolean getIsPositiveOnly()
           
 JvxlData getJvxlData()
           
(package private)  MarchingSquares getMarchingSquares()
           
(package private)  MeshData getMeshData()
           
(package private)  MeshDataServer getMeshDataServer()
           
 java.util.Map<java.lang.String,java.lang.Object> getMoData()
           
 Parameters getParams()
           
 javax.vecmath.Point4f getPlane()
           
 java.lang.Object getProperty(java.lang.String property, int index)
           
 java.lang.String getScript()
           
 java.util.List<java.lang.Object[]> getSlabInfo()
           
private  void getSurfaceSets()
           
 java.lang.String[] getTitle()
           
 int[] getVertexSource()
           
 VolumeData getVolumeData()
           
 java.util.BitSet geVdwBitSet()
           
(package private)  void initializeIsosurface()
           
 void initState()
           
 boolean isCubeData()
           
 boolean isFullyLit()
           
 boolean isInsideOut()
           
 boolean isStateDataRead()
           
 boolean isValid()
           
(package private)  void log(java.lang.String msg)
           
private  void mapSurface()
           
private  void processState()
           
private  SurfaceReader setFileData(java.lang.Object value)
           
 void setJvxlData(JvxlData jvxlData)
           
 java.lang.String setLcao()
           
(package private)  void setMarchingSquares(MarchingSquares marchingSquares)
           
 void setModelIndex(int modelIndex)
           
(package private)  void setOutputStream(BinaryDocument binaryDoc, java.io.OutputStream os)
           
 boolean setParameter(java.lang.String propertyName, java.lang.Object value)
          setParameter is the main interface for surface generation.
 boolean setParameter(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs)
           
private  boolean setReader()
           
private  void setup(AtomDataServer atomDataServer, MeshDataServer meshDataServer, MeshData meshData, JvxlData jvxlData)
           
 void setVersion(java.lang.String version)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

jvxlData

private JvxlData jvxlData

meshData

private MeshData meshData

params

private Parameters params

volumeData

private VolumeData volumeData

meshDataServer

private MeshDataServer meshDataServer

atomDataServer

private AtomDataServer atomDataServer

marchingSquares

private MarchingSquares marchingSquares

version

private java.lang.String version

isValid

private boolean isValid

fileType

private java.lang.String fileType

os

private java.io.OutputStream os

surfaceReader

SurfaceReader surfaceReader

colorPtr

int colorPtr

vAC

final javax.vecmath.Vector3f vAC

vAB

final javax.vecmath.Vector3f vAB

vNorm

final javax.vecmath.Vector3f vNorm

ptRef

final javax.vecmath.Point3f ptRef

bsVdw

java.util.BitSet bsVdw
Constructor Detail

SurfaceGenerator

public SurfaceGenerator()

SurfaceGenerator

public SurfaceGenerator(AtomDataServer atomDataServer,
                        MeshDataServer meshDataServer,
                        MeshData meshData,
                        JvxlData jvxlData)
Method Detail

isValid

public boolean isValid()

getFileType

public java.lang.String getFileType()

setVersion

public void setVersion(java.lang.String version)

setup

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

isStateDataRead

public boolean isStateDataRead()

getFileName

public java.lang.String getFileName()

getMeshDataServer

MeshDataServer getMeshDataServer()

getAtomDataServer

AtomDataServer getAtomDataServer()

getColorEncoder

public ColorEncoder getColorEncoder()

getVertexSource

public int[] getVertexSource()

setJvxlData

public void setJvxlData(JvxlData jvxlData)

getJvxlData

public JvxlData getJvxlData()

getMeshData

MeshData getMeshData()

setMarchingSquares

void setMarchingSquares(MarchingSquares marchingSquares)

getMarchingSquares

MarchingSquares getMarchingSquares()

getParams

public Parameters getParams()

getScript

public java.lang.String getScript()

getTitle

public java.lang.String[] getTitle()

getBsSelected

public java.util.BitSet getBsSelected()

getBsIgnore

public java.util.BitSet getBsIgnore()

getVolumeData

public VolumeData getVolumeData()

getPlane

public javax.vecmath.Point4f getPlane()

getColor

public int getColor(int which)

setModelIndex

public void setModelIndex(int modelIndex)

getIAddGridPoints

public boolean getIAddGridPoints()

getIsPositiveOnly

public boolean getIsPositiveOnly()

isInsideOut

public boolean isInsideOut()

getCutoff

public float getCutoff()

getMoData

public java.util.Map<java.lang.String,java.lang.Object> getMoData()

isCubeData

public boolean isCubeData()

setParameter

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

Parameters:
propertyName -
value -
Returns:
True if handled; False if not

setParameter

public boolean setParameter(java.lang.String propertyName,
                            java.lang.Object value,
                            java.util.BitSet bs)
Parameters:
propertyName -
value -
bs -
Returns:
TRUE if done processing

getSurfaceSets

private void getSurfaceSets()

processState

private void processState()

setReader

private boolean setReader()

generateSurface

private void generateSurface()

mapSurface

private void mapSurface()

getSlabInfo

public java.util.List<java.lang.Object[]> getSlabInfo()

colorIsosurface

void colorIsosurface()

getProperty

public java.lang.Object getProperty(java.lang.String property,
                                    int index)

setFileData

private SurfaceReader setFileData(java.lang.Object value)

initializeIsosurface

void initializeIsosurface()

initState

public void initState()

setLcao

public java.lang.String setLcao()

getFunctionZfromXY

private void getFunctionZfromXY()

distanceVerticalToPlane

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

findNearestThreePoints

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

addRequiredFile

public void addRequiredFile(java.lang.String fileName)

log

void log(java.lang.String msg)

setOutputStream

void setOutputStream(BinaryDocument binaryDoc,
                     java.io.OutputStream os)

isFullyLit

public boolean isFullyLit()

geVdwBitSet

public java.util.BitSet geVdwBitSet()

fillAtomData

void fillAtomData(AtomData atomData,
                  int mode)