etomica.atom
Class AtomLeafAgentManager

java.lang.Object
  etomica.box.BoxListenerAdapter
      etomica.atom.AtomLeafAgentManager

All Implemented Interfaces:

IBoxListener, Serializable

public class AtomLeafAgentManager
extends BoxListenerAdapter
implements Serializable

AtomAgentManager acts on behalf of client classes (an AgentSource) to manage agents for every leaf Atom in a box. When leaf atoms are added or removed from the box, the agents array (indexed by the atom's global index) is updated. The client can access and modify the agents via getAgent and setAgent.

See Also:

Serialized Form

Nested Class Summary

static class	AtomLeafAgentManager.AgentIterator Iterator that loops over the agents, skipping null elements
static interface	AtomLeafAgentManager.AgentSource Interface for an object that wants an agent associated with each Atom in a Box.

Field Summary

protected Object[]	agents
protected AtomLeafAgentManager.AgentSource	agentSource
protected IBox	box
protected int	reservoirSize

Constructor Summary

AtomLeafAgentManager(AtomLeafAgentManager.AgentSource source, IBox box)

Method Summary

protected void	addAgent(IAtom a) Adds an agent for the given leaf atom to the agents array.
protected void	addAgent(IAtom a, int index) Adds an agent for the given leaf atom to the agents array at the given index.
void	boxAtomLeafIndexChanged(IBoxAtomIndexEvent e)
void	boxGlobalAtomLeafIndexChanged(IBoxIndexEvent e)
void	boxMoleculeAdded(IBoxMoleculeEvent e)
void	boxMoleculeRemoved(IBoxMoleculeEvent e)
void	dispose() Notifies the AtomAgentManager it should disconnect itself as a listener.
Object	getAgent(IAtom a) Returns the agent associated with the given IAtom.
IBox	getBox() Convenience method to return the box the Manager is tracking.
int	getReservoirSize()
AtomLeafAgentManager.AgentIterator	makeIterator() Returns an iterator that returns each non-null agent
void	setAgent(IAtom a, Object newAgent) Sets the agent associated with the given atom to be the given agent.
void	setReservoirSize(int newReservoirSize) Sets the size of the manager's "reservoir".
protected void	setupBox() Sets the Box in which this AtomAgentManager will manage Atom agents.

Methods inherited from class etomica.box.BoxListenerAdapter

boxAtomAdded, boxAtomRemoved, boxGlobalAtomIndexChanged, boxMoleculeIndexChanged, boxNeighborsUpdated, boxNumberMolecules

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

agentSource

protected final AtomLeafAgentManager.AgentSource agentSource

agents

protected Object[] agents

box

protected final IBox box

reservoirSize

protected int reservoirSize

Constructor Detail

AtomLeafAgentManager

public AtomLeafAgentManager(AtomLeafAgentManager.AgentSource source,
                            IBox box)

Method Detail

setReservoirSize

public void setReservoirSize(int newReservoirSize)

Sets the size of the manager's "reservoir". When an atom is removed, the agents array will only be trimmed if the number of holes in the array exceeds the reservoir size. Also, when the array has no holes and another atom is added, the array will resized to be numAtoms+reservoirSize to avoid reallocating a new array every time an atom is added. reservoirSize=0 means the array will always be the same size as the number of atoms (no holes). The default reservoir size is 30.

getReservoirSize

public int getReservoirSize()

makeIterator

public AtomLeafAgentManager.AgentIterator makeIterator()

Returns an iterator that returns each non-null agent

getAgent

public Object getAgent(IAtom a)

Returns the agent associated with the given IAtom. The IAtom must be from the Box associated with this instance.

setAgent

public void setAgent(IAtom a,
                     Object newAgent)

Sets the agent associated with the given atom to be the given agent. The IAtom must be from the Box associated with this instance. The IAtom's old agent is not released. This should be done manually if needed.

getBox

public IBox getBox()

Convenience method to return the box the Manager is tracking.

dispose

public void dispose()

Notifies the AtomAgentManager it should disconnect itself as a listener.

setupBox

protected void setupBox()

Sets the Box in which this AtomAgentManager will manage Atom agents.

boxMoleculeAdded

public void boxMoleculeAdded(IBoxMoleculeEvent e)

Specified by:

boxMoleculeAdded in interface IBoxListener

Overrides:

boxMoleculeAdded in class BoxListenerAdapter

boxMoleculeRemoved

public void boxMoleculeRemoved(IBoxMoleculeEvent e)

Specified by:

boxMoleculeRemoved in interface IBoxListener

Overrides:

boxMoleculeRemoved in class BoxListenerAdapter

boxAtomLeafIndexChanged

public void boxAtomLeafIndexChanged(IBoxAtomIndexEvent e)

Specified by:

boxAtomLeafIndexChanged in interface IBoxListener

Overrides:

boxAtomLeafIndexChanged in class BoxListenerAdapter

boxGlobalAtomLeafIndexChanged

public void boxGlobalAtomLeafIndexChanged(IBoxIndexEvent e)

Specified by:

boxGlobalAtomLeafIndexChanged in interface IBoxListener

Overrides:

boxGlobalAtomLeafIndexChanged in class BoxListenerAdapter

addAgent

protected void addAgent(IAtom a)

Adds an agent for the given leaf atom to the agents array.

addAgent

protected void addAgent(IAtom a,
                        int index)

Adds an agent for the given leaf atom to the agents array at the given index.