org.jmol.shape
Class AtomShape

java.lang.Object
  extended by org.jmol.shape.Shape
      extended by org.jmol.shape.AtomShape
Direct Known Subclasses:
Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors

public abstract class AtomShape
extends Shape


Field Summary
 int atomCount
           
 Atom[] atoms
           
protected  BitSet bsColixSet
           
protected  BitSet bsSizeSet
           
 short[] colixes
           
 boolean isActive
           
 short[] mads
           
 byte[] paletteIDs
           
 
Fields inherited from class org.jmol.shape.Shape
g3d, isBioShape, modelSet, myVisibilityFlag, RADIUS_MAX, shapeID, translucentAllowed, translucentLevel, viewer, xmlProperties
 
Constructor Summary
AtomShape()
           
 
Method Summary
 String getShapeState()
           
 int getSize(int atomIndex)
           
protected  void initModelSet()
           
protected  void setColixAndPalette(short colix, byte paletteID, int atomIndex)
           
 void setModelClickability()
           
 void setProperty(String propertyName, Object value, BitSet bs)
          may come from any source -- executed AFTER a shape's own setProperty method
protected  void setSize(int size, BitSet bsSelected)
           
protected  void setSize(RadiusData rd, BitSet bsSelected)
           
 
Methods inherited from class org.jmol.shape.Shape
appendCmd, checkBoundsMinMax, checkObjectClicked, checkObjectDragged, checkObjectHovered, coordinateInRange, encodeColor, findNearestAtomIndex, getColix, getColorCommand, getColorCommand, getFontCommand, getIndexFromName, getProperty, getProperty, getShapeCommands, getShapeCommands, getShapeDetail, getSize, getViewer, initializeShape, initShape, merge, setColix, setColix, setColix, setModelSet, setShapeProperty, setShapeSize, setStateInfo, setStateInfo, setVisibilityFlags, wasClicked
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

mads

public short[] mads

colixes

public short[] colixes

paletteIDs

public byte[] paletteIDs

bsSizeSet

protected BitSet bsSizeSet

bsColixSet

protected BitSet bsColixSet

atomCount

public int atomCount

atoms

public Atom[] atoms

isActive

public boolean isActive
Constructor Detail

AtomShape

public AtomShape()
Method Detail

initModelSet

protected void initModelSet()
Overrides:
initModelSet in class Shape

getSize

public int getSize(int atomIndex)
Overrides:
getSize in class Shape

setSize

protected void setSize(int size,
                       BitSet bsSelected)
Overrides:
setSize in class Shape

setSize

protected void setSize(RadiusData rd,
                       BitSet bsSelected)
Overrides:
setSize in class Shape

setProperty

public void setProperty(String propertyName,
                        Object value,
                        BitSet bs)
Description copied from class: Shape
may come from any source -- executed AFTER a shape's own setProperty method

Overrides:
setProperty in class Shape

setColixAndPalette

protected void setColixAndPalette(short colix,
                                  byte paletteID,
                                  int atomIndex)

setModelClickability

public void setModelClickability()
Overrides:
setModelClickability in class Shape

getShapeState

public String getShapeState()
Overrides:
getShapeState in class Shape