org.jmol.shape

Class AtomShape

java.lang.Object

org.jmol.shape.Shape

org.jmol.shape.AtomShape

Direct Known Subclasses:

Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors

public abstract class AtomShape
extends Shape

Field Summary

Fields

Modifier and Type	Field and Description
int	atomCount
Atom[]	atoms
protected java.util.BitSet	bsColixSet
protected java.util.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

Constructors

Constructor and Description
AtomShape()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getShapeState()
int	getSize(int atomIndex)
protected void	initModelSet()
protected void	setColixAndPalette(short colix, byte paletteID, int atomIndex)
void	setModelClickability()
void	setProperty(java.lang.String propertyName, java.lang.Object value, java.util.BitSet bs) may come from any source -- executed AFTER a shape's own setProperty method
protected void	setSize(int size, java.util.BitSet bsSelected)
protected void	setSize(RadiusData rd, java.util.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, getTranslucentLabel, 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 java.util.BitSet bsSizeSet

bsColixSet

protected java.util.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

Returns:

size

setSize

protected void setSize(int size,
           java.util.BitSet bsSelected)

Overrides:

setSize in class Shape

setSize

protected void setSize(RadiusData rd,
           java.util.BitSet bsSelected)

Overrides:

setSize in class Shape

setProperty

public void setProperty(java.lang.String propertyName,
               java.lang.Object value,
               java.util.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 java.lang.String getShapeState()

Overrides:

getShapeState in class Shape