org.jmol.shapesurface

Class Isosurface

public class Isosurface extends MeshFileCollection implements MeshDataServer

Field Summary
booleanassociateNormals
intatomIndex
Point3fcenter
ColorEncodercolorEncoder
shortdefaultColix
booleaniHaveBitSets
intindexColorNegative
intindexColorPositive
IsosurfaceMesh[]isomeshes
booleanisPhaseColored
JvxlDatajvxlData
Point4flcaoDir
intlighting
intmoNumber
intnLCAO
protected SurfaceGeneratorsg
IsosurfaceMeshthisMesh
Method Summary
voidaddTriangleCheck(int iA, int iB, int iC, int check, boolean isAbsolute)
intaddVertexCopy(Point3f vertexXYZ, float value, int assocVertex)
voidallocMesh(String thisID)
Point3f[]calculateGeodesicSurface(BitSet bsSelected, float envelopeRadius)
protected voidclearSg()
voidcreateLcaoLobe(Vector3f lobeAxis, float factor)
voiddiscardTempData(boolean discardAll)
voiddrawLcaoCartoon(Vector3f z, Vector3f x, Vector3f rotAxis)
voidfillMeshData(MeshData meshData, int mode)
shortgetDefaultColix()
ObjectgetProperty(String property, int index)
booleangetScriptBitSets(String script, BitSet[] bsCmd)
VectorgetShapeDetail()
intgetSurfacePointIndex(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, Point3i offset, int vA, int vB, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, boolean isContourType)
StringgetUserColorScheme(String schemeName)
voidinitializeIsosurface()
voidinitShape()
voidinitState()
voidinvalidateTriangles()
voidnotifySurfaceGenerationCompleted()
voidnotifySurfaceMappingCompleted()
protected voidremapColors()
voidsetJvxlInfo()
voidsetModelIndex()
voidsetProperty(String propertyName, Object value, BitSet bs)
voidsetPropertySuper(String propertyName, Object value, BitSet bs)
protected voidsetScriptInfo()

Field Detail

associateNormals

private boolean associateNormals

atomIndex

private int atomIndex

center

private Point3f center

colorEncoder

private ColorEncoder colorEncoder

defaultColix

private short defaultColix

iHaveBitSets

private boolean iHaveBitSets

indexColorNegative

private int indexColorNegative

indexColorPositive

private int indexColorPositive

isomeshes

private IsosurfaceMesh[] isomeshes

isPhaseColored

private boolean isPhaseColored

jvxlData

private JvxlData jvxlData

lcaoDir

private Point4f lcaoDir

lighting

private int lighting

moNumber

private int moNumber

nLCAO

private int nLCAO

sg

protected SurfaceGenerator sg

thisMesh

private IsosurfaceMesh thisMesh

Method Detail

addTriangleCheck

public void addTriangleCheck(int iA, int iB, int iC, int check, boolean isAbsolute)

addVertexCopy

public int addVertexCopy(Point3f vertexXYZ, float value, int assocVertex)

allocMesh

public void allocMesh(String thisID)

calculateGeodesicSurface

public Point3f[] calculateGeodesicSurface(BitSet bsSelected, float envelopeRadius)

clearSg

protected void clearSg()

createLcaoLobe

private void createLcaoLobe(Vector3f lobeAxis, float factor)

discardTempData

private void discardTempData(boolean discardAll)

drawLcaoCartoon

private void drawLcaoCartoon(Vector3f z, Vector3f x, Vector3f rotAxis)

fillMeshData

public void fillMeshData(MeshData meshData, int mode)

getDefaultColix

private short getDefaultColix()

getProperty

public Object getProperty(String property, int index)

getScriptBitSets

private boolean getScriptBitSets(String script, BitSet[] bsCmd)

getShapeDetail

public Vector getShapeDetail()

getSurfacePointIndex

public int getSurfacePointIndex(float cutoff, boolean isCutoffAbsolute, int x, int y, int z, Point3i offset, int vA, int vB, float valueA, float valueB, Point3f pointA, Vector3f edgeVector, boolean isContourType)

getUserColorScheme

private String getUserColorScheme(String schemeName)

initializeIsosurface

private void initializeIsosurface()

initShape

public void initShape()

initState

private void initState()

invalidateTriangles

public void invalidateTriangles()

notifySurfaceGenerationCompleted

public void notifySurfaceGenerationCompleted()

notifySurfaceMappingCompleted

public void notifySurfaceMappingCompleted()

remapColors

protected void remapColors()

setJvxlInfo

private void setJvxlInfo()

setModelIndex

private void setModelIndex()

setProperty

public void setProperty(String propertyName, Object value, BitSet bs)

setPropertySuper

private void setPropertySuper(String propertyName, Object value, BitSet bs)

setScriptInfo

protected void setScriptInfo()