Package org.jmol.jvxl.readers
Class SurfaceGenerator
- java.lang.Object
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- org.jmol.jvxl.readers.SurfaceGenerator
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public class SurfaceGenerator extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description AtomDataServer
atomDataServer
javajs.util.BS
bsVdw
private int
colorPtr
java.lang.String
fileType
boolean
isValid
JvxlData
jvxlData
MarchingSquares
marchingSquares
MeshData
meshData
MeshDataServer
meshDataServer
private javajs.util.OC
out
Parameters
params
private javajs.util.P3
ptRef
private java.lang.Object
readerData
private SurfaceReader
surfaceReader
private javajs.util.V3
vAB
java.lang.String
version
private javajs.util.V3
vNorm
VolumeData
volumeDataTemp
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Constructor Summary
Constructors Constructor Description SurfaceGenerator(AtomDataServer atomDataServer, MeshDataServer meshDataServer, MeshData meshData, JvxlData jvxlData)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addRequiredFile(java.lang.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()
private void
getFunctionZfromXY()
private static java.lang.Object
getInterface(java.lang.String name)
javajs.util.V3[]
getOriginVaVbVc()
java.lang.Object
getProperty(java.lang.String property, int index)
only called from org.openscience.jvxl.Jvxl.main(package private) java.lang.Object
getReaderData()
private void
getSurfaceSets()
(package private) void
initializeIsosurface()
void
initState()
(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(Viewer vwr, java.lang.Object value)
void
setJvxlData(JvxlData jvxlData)
java.lang.String
setLcao()
(package private) void
setOutputChannel(javajs.api.GenericBinaryDocument binaryDoc, javajs.util.OC out)
boolean
setProp(java.lang.String propertyName, java.lang.Object value, javajs.util.BS bs)
private boolean
setReader()
void
setRequiredFile(java.lang.String oldName, java.lang.String fileName)
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Field Detail
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params
public Parameters params
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jvxlData
public JvxlData jvxlData
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meshData
public MeshData meshData
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volumeDataTemp
public VolumeData volumeDataTemp
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meshDataServer
public MeshDataServer meshDataServer
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atomDataServer
public AtomDataServer atomDataServer
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marchingSquares
public MarchingSquares marchingSquares
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version
public java.lang.String version
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isValid
public boolean isValid
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fileType
public java.lang.String fileType
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bsVdw
public javajs.util.BS bsVdw
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colorPtr
private int colorPtr
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surfaceReader
private SurfaceReader surfaceReader
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out
private javajs.util.OC out
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readerData
private java.lang.Object readerData
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vAB
private final javajs.util.V3 vAB
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vNorm
private final javajs.util.V3 vNorm
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ptRef
private final javajs.util.P3 ptRef
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Constructor Detail
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SurfaceGenerator
public SurfaceGenerator(AtomDataServer atomDataServer, MeshDataServer meshDataServer, MeshData meshData, JvxlData jvxlData)
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Method Detail
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setJvxlData
public void setJvxlData(JvxlData jvxlData)
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setProp
public boolean setProp(java.lang.String propertyName, java.lang.Object value, javajs.util.BS bs)
- Parameters:
propertyName
-value
-bs
-- Returns:
- TRUE if handled
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newReader
private SurfaceReader newReader(java.lang.String name)
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newReaderBr
private SurfaceReader newReaderBr(java.lang.String name, java.io.BufferedReader br)
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getInterface
private static java.lang.Object getInterface(java.lang.String name)
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getSurfaceSets
private void getSurfaceSets()
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processState
private void processState()
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setReader
private boolean setReader()
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generateSurface
private void generateSurface()
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mapSurface
private void mapSurface()
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colorIsosurface
void colorIsosurface()
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getProperty
public java.lang.Object getProperty(java.lang.String property, int index)
only called from org.openscience.jvxl.Jvxl.main- Parameters:
property
-index
-- Returns:
- Object
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setFileData
private SurfaceReader setFileData(Viewer vwr, java.lang.Object value)
- Parameters:
vwr
-value
-- Returns:
- SurfaceReader
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getReaderData
java.lang.Object getReaderData()
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initializeIsosurface
void initializeIsosurface()
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initState
public void initState()
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setLcao
public java.lang.String setLcao()
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getFunctionZfromXY
private void getFunctionZfromXY()
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distanceVerticalToPlane
private float distanceVerticalToPlane(float x, float y, javajs.util.P3 pta, javajs.util.P3 ptb, javajs.util.P3 ptc)
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findNearestThreePoints
private static float findNearestThreePoints(float x, float y, float[][] xyz, int[] result)
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addRequiredFile
public void addRequiredFile(java.lang.String fileName)
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setRequiredFile
public void setRequiredFile(java.lang.String oldName, java.lang.String fileName)
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log
void log(java.lang.String msg)
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setOutputChannel
void setOutputChannel(javajs.api.GenericBinaryDocument binaryDoc, javajs.util.OC out)
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fillAtomData
void fillAtomData(AtomData atomData, int mode)
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getOriginVaVbVc
public javajs.util.V3[] getOriginVaVbVc()
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