Package mgui.neuro.components.compartments

Class AbstractCompartment

java.lang.Object

mgui.interfaces.AbstractInterfaceObject

mgui.models.networks.components.AbstractNetworkComponent

mgui.neuro.components.AbstractNeuroComponent

mgui.neuro.components.AbstractNeuronalComponent

mgui.neuro.components.compartments.AbstractCompartment

All Implemented Interfaces:

java.lang.Cloneable, java.lang.Comparable<DynamicModelComponent>, AttributeListener, AttributeObject, InterfaceObject, NamedObject, TreeObject, CleanableObject, DynamicModelComponent, DynamicModelODEComponent, TimeStepListener, Updateable, NeuronalComponent, org.opensourcephysics.numerics.ODE

Direct Known Subclasses:

SimpleCompartment

public abstract class AbstractCompartment
extends AbstractNeuronalComponent
implements DynamicModelODEComponent

Basic compartment for compartmental model components.

Version:

1.0

Author:

Andrew Reid

Field Summary

Fields

Modifier and Type	Field	Description
double	potential
org.opensourcephysics.numerics.ODESolver	solver
double[]	state

Fields inherited from class mgui.neuro.components.AbstractNeuronalComponent

parent

Fields inherited from class mgui.neuro.components.AbstractNeuroComponent

attributes, clock, connections, events, hasSubComponents, id, listeners, updated

Fields inherited from class mgui.interfaces.AbstractInterfaceObject

isDestroyed, tree_nodes

Constructor Summary

Constructors

Constructor	Description
AbstractCompartment()

Method Summary

Modifier and Type	Method	Description
java.lang.Object	clone()
protected boolean	executeEvent(DynamicModelEvent e)
org.opensourcephysics.numerics.ODESolver	getODESolver()
abstract void	getRate(double[] state, double[] rate)
double[]	getState()
protected void	init()
abstract void	reset()	Reset the compartment's temporary variables
void	resetSolver()
void	timeElapsed(double time)
boolean	updateFromClock()

Methods inherited from class mgui.neuro.components.AbstractNeuronalComponent

getParent, setParent

Methods inherited from class mgui.neuro.components.AbstractNeuroComponent

addConnection, addEvent, addListener, addToEngine, attributeUpdated, compareTo, executeEvents, fireListeners, fireListeners, getAttribute, getAttributes, getConnections, getDelay, getID, getName, getSolver, getSubComponents, hasSubComponents, removeConnection, removeListener, resetClock, setAttribute, setAttributes, setDelay, setID, setID, setName, setODESolver, setSolver, setSolver, updateComponent

Methods inherited from class mgui.models.networks.components.AbstractNetworkComponent

getAttributeValue

Methods inherited from class mgui.interfaces.AbstractInterfaceObject

clean, destroy, getTreeLabel, isDestroyed, issueTreeNode, setTreeNode, updateTreeNodes

Methods inherited from class java.lang.Object

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

Methods inherited from interface mgui.interfaces.util.CleanableObject

clean

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface mgui.models.dynamic.DynamicModelComponent

addConnection, addEvent, addToEngine, executeEvents, getID, getSubComponents, hasSubComponents, removeConnection, setID, setID

Methods inherited from interface mgui.interfaces.InterfaceObject

destroy, isDestroyed

Methods inherited from interface mgui.interfaces.NamedObject

getName, setName

Methods inherited from interface mgui.interfaces.trees.TreeObject

getTreeLabel, issueTreeNode, setTreeNode

Field Details

potential

public double potential

state

public double[] state

solver

public org.opensourcephysics.numerics.ODESolver solver

Constructor Details

AbstractCompartment

public AbstractCompartment()

Method Details

init

protected void init()

Overrides:

init in class AbstractNeuroComponent

executeEvent

protected boolean executeEvent(DynamicModelEvent e)
                        throws NeuroException

Overrides:

executeEvent in class AbstractNeuroComponent

Throws:

NeuroException

timeElapsed

public void timeElapsed(double time)

Specified by:

timeElapsed in interface TimeStepListener

Overrides:

timeElapsed in class AbstractNeuroComponent

updateFromClock

public boolean updateFromClock()

Overrides:

updateFromClock in class AbstractNeuroComponent

clone

public java.lang.Object clone()

Specified by:

clone in interface DynamicModelComponent

Specified by:

clone in class AbstractNeuronalComponent

resetSolver

public void resetSolver()
                 throws ODEException

Throws:

ODEException

reset

public abstract void reset()

Reset the compartment's temporary variables

Specified by:

reset in interface DynamicModelComponent

Overrides:

reset in class AbstractNeuroComponent

getODESolver

public org.opensourcephysics.numerics.ODESolver getODESolver()

Overrides:

getODESolver in class AbstractNeuroComponent

getRate

public abstract void getRate(double[] state,
double[] rate)

Specified by:

getRate in interface org.opensourcephysics.numerics.ODE

Overrides:

getRate in class AbstractNeuroComponent

getState

public double[] getState()

Specified by:

getState in interface org.opensourcephysics.numerics.ODE