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