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Public Member Functions | Static Public Member Functions | Public Attributes | Static Public Attributes | Protected Member Functions | Protected Attributes | Static Package Functions | Private Member Functions | Private Attributes | Static Private Attributes

org::jmol::shapesurface::Isosurface Class Reference

Inheritance diagram for org::jmol::shapesurface::Isosurface:
Inheritance graph
Collaboration diagram for org::jmol::shapesurface::Isosurface:
Collaboration graph

List of all members.

Public Member Functions

int addTriangleCheck (int iA, int iB, int iC, int check, int check2, boolean isAbsolute, int color)
int addVertexCopy (Point3f vertexXYZ, float value, int assocVertex)
void allocMesh (String thisID, Mesh m)
Point3f[] calculateGeodesicSurface (BitSet bsSelected, float envelopeRadius)
void checkBoundsMinMax (Point3f pointMin, Point3f pointMax)
Point3fi checkObjectClicked (int x, int y, int action, BitSet bsVisible)
boolean checkObjectDragged (int prevX, int prevY, int x, int y, int modifiers, BitSet bsVisible)
boolean checkObjectHovered (int x, int y, BitSet bsVisible)
void deleteMesh (int i)
void fillMeshData (MeshData meshData, int mode, IsosurfaceMesh mesh)
void findNearestAtomIndex (int xMouse, int yMouse, Atom[] closest, BitSet bsNot)
String getColorCommand (String type, short colix)
String getColorCommand (String type, byte pid, short colix)
int getIndexFromName (String thisID)
Mesh getMesh (String thisID)
void getPlane (int x)
boolean getProperty (String property, Object[] data)
Object getProperty (String property, int index)
List getShapeDetail ()
String getShapeState ()
int getSize (Group group)
int getSize (int atomIndex)
int getSurfacePointIndexAndFraction (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, float[] fReturn)
float getValue (int x, int y, int z, int ptyz)
Viewer getViewer ()
final void initializeShape (Viewer viewer, Graphics3D g3d, ModelSet modelSet, int shapeID)
void initShape ()
void invalidateTriangles ()
void merge (Shape shape)
void notifySurfaceGenerationCompleted ()
void notifySurfaceMappingCompleted ()
short setColix (short colix, byte paletteID, int atomIndex)
void setModelClickability ()
void setModelIndex (int atomIndex, int modelIndex)
void setModelSet (ModelSet modelSet)
void setProperty (String propertyName, Object value, BitSet bs)
void setShapeProperty (String propertyName, Object value, BitSet bsSelected)
void setShapeSize (int size, RadiusData rd, BitSet bsSelected)
void setVisibilityFlags (BitSet bs)
boolean wasClicked (int x, int y)

Static Public Member Functions

static void appendCmd (StringBuffer s, String cmd)
static short getColix (short[] colixes, int i, Atom atom)
static String getFontCommand (String type, Font3D font)
static String getPolygonColorData (int ccount, short[] colixes)
static String getShapeCommands (Hashtable htDefine, Hashtable htMore, String selectCmd)
static String getShapeCommands (Hashtable htDefine, Hashtable htMore)
static void setStateInfo (Hashtable ht, int i1, int i2, String key)
static void setStateInfo (Hashtable ht, int i, String key)

Public Attributes

String actualID
short colix
Mesh currentMesh
boolean explicitID
Graphics3D g3d
boolean isBioShape
boolean isFixed
int meshCount
Mesh[] meshes = new Mesh[4]
int modelCount
ModelSet modelSet
String myType
int myVisibilityFlag
int nUnnamed
String script
int shapeID
String[] title
Viewer viewer

Static Public Attributes

static final float RADIUS_MAX = 4

Protected Member Functions

void checkExplicit (String id)
void clean ()
void clearSg ()
int coordinateInRange (int x, int y, Point3f vertex, int dmin2, Point3i ptXY)
void deleteMesh (String key)
void getCapSlabInfo (String script)
void getModelIndex (String script)
void initModelSet ()
short setColix (short colix, byte paletteID, Atom atom)
short setColix (short colix, byte paletteID, Bond bond)
void setScriptInfo (String strCommand)
void setSize (int size, BitSet bsSelected)
void setSize (RadiusData rd, BitSet bsSelected)
void setStatusPicked (int flag, Point3f v)

Protected Attributes

boolean allowContourLines
boolean allowMesh = true
boolean haveContours = false
Hashtable htObjects
boolean iHaveModelIndex
JvxlData jvxlData
Mesh linkedMesh
int modelIndex
Mesh pickedMesh = null
int pickedModel
int pickedVertex
String previousMeshID
SurfaceGenerator sg
IsosurfaceMesh thisMesh
boolean translucentAllowed = true
float translucentLevel
List xmlProperties

Static Package Functions

static String encodeColor (short colix)

Private Member Functions

boolean checkWithin (Point3f pti)
void createLcaoLobe (Vector3f lobeAxis, float factor, int nElectrons)
void discardTempData (boolean discardAll)
void drawLcaoCartoon (Vector3f z, Vector3f x, Vector3f rotAxis, int nElectrons)
String findValue (int x, int y, boolean isPicking, BitSet bsVisible)
Object getCapSlabObject (int i, String script)
boolean getClosestNormal (IsosurfaceMesh m, Point3f toPt, Point3f ptRet, Vector3f normalRet)
void getClosestPoint (IsosurfaceMesh m, int imin, Point3f toPt, Point3f ptRet, Vector3f normalRet)
void getColorState (StringBuffer sb, Mesh mesh)
short getDefaultColix ()
void getMeshCommand (StringBuffer sb, int i)
boolean getScriptBitSets (String script, BitSet[] bsCmd)
void initializeIsosurface ()
void initState ()
boolean isPickable (IsosurfaceMesh m, BitSet bsVisible)
void navigate (int dz)
void newSg ()
void remapColors (ColorEncoder ce)
void setColorCommand (ColorEncoder ce)
void setHeading (Point3f pt, Vector3f vNorm, int nSeconds)
void setJvxlInfo ()
void setModelIndex ()
void setPropertySuper (String propertyName, Object value, BitSet bs)

Private Attributes

boolean associateNormals
int atomIndex
Point3f center
short defaultColix
boolean explicitContours
boolean iHaveBitSets
int indexColorNegative
int indexColorPositive
boolean isColorExplicit
IsosurfaceMesh[] isomeshes = new IsosurfaceMesh[4]
boolean isPhaseColored
Point4f lcaoDir = new Point4f()
int lighting
short meshColix
int moNumber
int nLCAO = 0
Point3f offset
final Point3i ptXY = new Point3i()
float scale3d
float withinDistance
List withinPoints

Static Private Attributes

static final int MAX_OBJECT_CLICK_DISTANCE_SQUARED = 10 * 10

Detailed Description

Definition at line 138 of file Isosurface.java.

The documentation for this class was generated from the following file:

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