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