org.simBio.core
Class Conductor

java.lang.Object
  org.simBio.core.Component
      org.simBio.core.Parameter
          org.simBio.core.Composite
              org.simBio.core.Reactor
                  org.simBio.core.Conductor

All Implemented Interfaces:

java.lang.Runnable, Node, Visitor

public class Conductor
extends Reactor
implements java.lang.Runnable, Visitor

root instance to conduct integration. At this moment, ODE is calculated by Euler method.
モデルツリーのルートになり、積分計算を行います。 Runnableをimplementsしており、Threadを1つ使います。

Version:

$Id: Conductor.java,v 1.7 2007/09/18 07:27:34 nsarai Exp $

Author:

Nobuaki Sarai

Field Summary

double	adjustDyOverY for variable time step, empirical method
double	dtMax maximum time step of integration
double	dtMin minimum time step of integration
Node	duration duration of integration
Node	elapsedTime elapsed time
Node	timeStep time step of integration

Fields inherited from class org.simBio.core.Parameter

value

Constructor Summary

Conductor()

Method Summary

void	addCalculationObserver(CalculationObserver obs) 計算を開始・終了した時に、通知が行われる監視オブジェクトを追加します。
void	calculate(double t) call calculate(double t) of the every Reactor.
void	checkException() Check if this thread has thrown an exception.
protected void	end() end of integration
void	exit() exit run() of this Thread.
protected void	integrate() integrate ODEs.
void	prepare() initialization for calculation.
protected void	quit() call before exit thread.
void	removeCalculationObserver(CalculationObserver obs) 計算を開始・終了した時に、通知が行われる監視オブジェクトを削除します。
void	run() main entry of this thread.
protected void	setLinks() call after instance tree has constructed.
void	start() start calculation.
void	stop() stop calculation.
void	visit(Component component) Add Variables to the list.
void	visit(Composite composite) add Reactors to ReactorList, and Analyzers to AnalyzerList.

Methods inherited from class org.simBio.core.Composite

accept, getLink, getNode, getNodesIterator, getNodesSize

Methods inherited from class org.simBio.core.Parameter

addValue, getValue, getValueString, setInitializer, setValue, setValueString, setValueToField

Methods inherited from class org.simBio.core.Component

addDydt, getIndent, getIndentedShortName, getName, getName, getParent, getRoot, getShortName, getUnits, isNamed, isPrefixed, logIndented

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.simBio.core.Node

addDydt, addValue, getValue, setValue

Field Detail

elapsedTime

public Node elapsedTime

elapsed time

duration

public Node duration

duration of integration

timeStep

public Node timeStep

time step of integration

dtMin

public double dtMin

minimum time step of integration

dtMax

public double dtMax

maximum time step of integration

adjustDyOverY

public double adjustDyOverY

for variable time step, empirical method

Constructor Detail

Conductor

public Conductor()

Method Detail

visit

public void visit(Component component)

Add Variables to the list.
Variableをlistに登録します。

Specified by:

visit in interface Visitor

See Also:

Visitor.visit(org.simBio.core.Component)

visit

public void visit(Composite composite)

add Reactors to ReactorList, and Analyzers to AnalyzerList.
Reactor, Analyzerをlistに登録します。

Specified by:

visit in interface Visitor

See Also:

Visitor.visit(org.simBio.core.Composite)

run

public void run()

main entry of this thread.
setLinks()を呼び出した後、待機ループにはいります。 計算開始flagが立てられると、integrate()を呼び出し、積分計算をします。 終了flagが立てられると、NodeList.quit()を呼び出し、threadを終了します。

Specified by:

run in interface java.lang.Runnable

See Also:

Runnable.run()

setLinks

protected void setLinks()

call after instance tree has constructed.
次のようなinstance treeの場合、

        external
                cell
                        Vm
                        Na
                        K
                        NaChannel
                                4sGate
                                2sGate
                        /NaChannel
                        K1Channel
                /cell
        /external
        

次の順序で全てのNodeのsetLinks()を呼び出します。

                        Vm
                        Na
                        K
                                4sGate
                                2sGate
                        NaChannel
                        K1Channel
                cell
        external


Overrides:
setLinks in class Component


See Also:
Component.setLinks()

quit

protected void quit()

call before exit thread.

Overrides:

quit in class Component

See Also:

Component.quit()

prepare

public void prepare()

initialization for calculation.

Overrides:

prepare in class Parameter

See Also:

Component.prepare()

end

protected void end()

end of integration

Overrides:

end in class Component

See Also:

Component.end()

integrate

protected void integrate()

integrate ODEs.

First prepare() is called, then for every time step:

1. calculate(double t)
2. analyze(double t) of all Analyzer
3. update(double t) of all Variable
4. Elapsed time is renewed, and continue calculation during duration.

Last end() is called.

最初にprepare()を呼び出します。各time step毎に、

1. calculate(double t)
2. 全てのVariableのupdate(double t). (注： Variables.update()を、xmlで指定して作成するように変更すれば、計算方式を変更できます。)
3. 全てのAnalyzerのanalyze(double t)をtreeの末端から順に呼び出します。
4. elapsed timeを更新し、durationに設定された時間分だけ、計算をします。

最後に、end()を呼び出します。

See Also:

calculate(double)

calculate

public void calculate(double t)

call calculate(double t) of the every Reactor.
Reactor.calculate(double)を呼び出す順序は、以下のようになります。

                                4sGate
                                2sGate
                        NaChannel
                        K1Channel
                cell
        external
        

Specified by:

calculate in class Reactor

Parameters:

t - elapsed time (ms)

See Also:

Reactor.calculate(double)

checkException

public void checkException()
                    throws java.lang.Exception

Check if this thread has thrown an exception.

Throws:

java.lang.Exception

start

public void start()

start calculation. set calculate flag = true

stop

public void stop()

stop calculation. set calculate flag = false

exit

public void exit()

exit run() of this Thread. set active flag = false

addCalculationObserver

public void addCalculationObserver(CalculationObserver obs)

計算を開始・終了した時に、通知が行われる監視オブジェクトを追加します。

Parameters:

obs - 監視オブジェクト

removeCalculationObserver

public void removeCalculationObserver(CalculationObserver obs)

計算を開始・終了した時に、通知が行われる監視オブジェクトを削除します。

Parameters:

obs - 監視オブジェクト