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