public class SurfaceGenerator extends Object
Modifier and Type | Field and Description |
---|---|
private AtomDataServer |
atomDataServer |
(package private) BS |
bsVdw |
(package private) int |
colorPtr |
private String |
fileType |
private boolean |
isValid |
private JvxlData |
jvxlData |
private MarchingSquares |
marchingSquares |
private MeshData |
meshData |
private MeshDataServer |
meshDataServer |
private javajs.util.OC |
out |
private Parameters |
params |
(package private) javajs.util.P3 |
ptRef |
private Object |
readerData |
(package private) SurfaceReader |
surfaceReader |
(package private) javajs.util.V3 |
vAB |
(package private) javajs.util.V3 |
vAC |
private String |
version |
(package private) javajs.util.V3 |
vNorm |
private VolumeData |
volumeData |
Constructor and Description |
---|
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,
javajs.util.P3 pta,
javajs.util.P3 ptb,
javajs.util.P3 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() |
BS |
getBsIgnore() |
BS |
getBsSelected() |
int |
getColor(int which) |
ColorEncoder |
getColorEncoder() |
float |
getCutoff() |
String |
getFileName() |
String |
getFileType() |
private void |
getFunctionZfromXY() |
boolean |
getIAddGridPoints() |
private static Object |
getInterface(String name) |
boolean |
getIsPositiveOnly() |
JvxlData |
getJvxlData() |
(package private) MarchingSquares |
getMarchingSquares() |
(package private) MeshData |
getMeshData() |
(package private) MeshDataServer |
getMeshDataServer() |
Map<String,Object> |
getMoData() |
Parameters |
getParams() |
javajs.util.P4 |
getPlane() |
Object |
getProperty(String property,
int index) |
(package private) Object |
getReaderData() |
String |
getScript() |
javajs.util.List<Object[]> |
getSlabInfo() |
javajs.util.V3[] |
getSpanningVectors() |
private void |
getSurfaceSets() |
String[] |
getTitle() |
int[] |
getVertexSource() |
VolumeData |
getVolumeData() |
BS |
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 SurfaceReader |
newReader(String name) |
private SurfaceReader |
newReaderBr(String name,
BufferedReader br) |
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 |
setOutputChannel(JmolDocument binaryDoc,
javajs.util.OC out) |
boolean |
setParameter(String propertyName,
Object value)
setParameter is the main interface for surface generation.
|
boolean |
setProp(String propertyName,
Object value,
BS bs) |
private boolean |
setReader() |
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 javajs.util.OC out
SurfaceReader surfaceReader
int colorPtr
private Object readerData
final javajs.util.V3 vAC
final javajs.util.V3 vAB
final javajs.util.V3 vNorm
final javajs.util.P3 ptRef
BS bsVdw
public SurfaceGenerator(AtomDataServer atomDataServer, MeshDataServer meshDataServer, MeshData meshData, JvxlData jvxlData)
public boolean isValid()
public String getFileType()
public void setVersion(String version)
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 BS getBsSelected()
public BS getBsIgnore()
public VolumeData getVolumeData()
public javajs.util.P4 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 setProp(String propertyName, Object value, BS bs)
propertyName
- value
- bs
- private SurfaceReader newReader(String name)
private SurfaceReader newReaderBr(String name, BufferedReader br)
private void getSurfaceSets()
private void processState()
private boolean setReader()
private void generateSurface()
private void mapSurface()
public javajs.util.List<Object[]> getSlabInfo()
void colorIsosurface()
private SurfaceReader setFileData(Object value)
Object getReaderData()
void initializeIsosurface()
public void initState()
public String setLcao()
private void getFunctionZfromXY()
private float distanceVerticalToPlane(float x, float y, javajs.util.P3 pta, javajs.util.P3 ptb, javajs.util.P3 ptc)
private static float findNearestThreePoints(float x, float y, float[][] xyz, int[] result)
public void addRequiredFile(String fileName)
void log(String msg)
void setOutputChannel(JmolDocument binaryDoc, javajs.util.OC out)
public boolean isFullyLit()
public BS geVdwBitSet()
void fillAtomData(AtomData atomData, int mode)
public javajs.util.V3[] getSpanningVectors()