A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

D

d - Variable in class org.simBio.bio.faber_rudy_2000.current.ICaL

d - Variable in class org.simBio.bio.noble_et_al_1998.Model

d - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.ICa

d - Variable in class org.simBio.bio.tenTusscher_et_al_2004.flux.Release

d_Gs_alpha_GTPtot - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.BetaAR_Gs

Multi newton raphson function

data - Variable in class org.simBio.sim.js.entry.Request

content of the file

data - Variable in class org.simBio.sim.js.entry.Result

DataListTable - Class in org.simBio.sim.gui

Composite を元に、データ編集用の構造体を作成する.

DataListTable() - Constructor for class org.simBio.sim.gui.DataListTable

空のDataItemBean を作成する。

DataListTable(Composite) - Constructor for class org.simBio.sim.gui.DataListTable

dATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.Troponin

dATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.ICaPump

variation of ATP concentration (mM/ms)

dATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.INaK

differential ATP [mM/msec]

dATP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.carrier.IPMCA

instantaneous rate of the ATP consumption (M/s)

dATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.ICaPump

variation of ATP concentration (mM/ms)

dATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaK

differential ATP [mM/msec]

dATP - Variable in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL

dATP - Variable in class org.simBio.bio.sarai_et_al_2006.current.carrier.IPMCA

rate of the ATP consumption (mM/ms)

dATP_ - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.INaK

dCa - Variable in class org.simBio.bio.negroni_lascano_1996.Troponin

decomposite(int, double[], int[]) - Static method in class org.simBio.util.numerical.methods.LUdecomposition

Decomposite the specified array to LU array.

DEFAULT_CHANNEL - Static variable in class org.simBio.sim.js.Channel

DEFAULT_ENCODING - Static variable in class org.simBio.util.FileHandler

default encoding

DEFAULT_EPSILON - Static variable in class org.simBio.util.numerical.methods.BroydenMethod

A tiny value as tolerance.

DEFAULT_EPSILON - Static variable in class org.simBio.util.numerical.methods.SecantMethod

A tiny value as tolerance.

DefaultAfterProcess - Class in org.simBio.tools.remote.process

DefaultAfterProcess() - Constructor for class org.simBio.tools.remote.process.DefaultAfterProcess

defaultTreeCellRenderer - Variable in class org.simBio.sim.gui.CheckedJTree.CheckedJTreeCellRenderer

DELIM - Static variable in class org.simBio.tools.remote.RemoteConstant

delimiter

delta - Variable in class org.simBio.bio.sarai_et_al_2003.VoltageClamp

time, which is needed to make Vm holding potential (ms)

demo(InputStream, InputStream) - Static method in class org.simBio.ResultGenerator

Make protocols of parameter exchanging by running thrue all iterations.

denominator - Variable in class org.simBio.bio.sarai_et_al_2006.function.Ratio

denominator

DevelopmentMode - Class in org.simBio.util

dGp0 - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase

standard free-energy change of ATP synthase

diadicFactor - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.IRyR

Ca diadicFactor

diadicFactor - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.channel.IRyR

Ca diadicFactor

diadicFactor - Variable in class org.simBio.bio.takeuchi_et_al_2006.current.IRyR

Ca diadicFactor

Diffusion - Class in org.simBio.bio.faber_rudy_2000.function

diffusion.

Diffusion() - Constructor for class org.simBio.bio.faber_rudy_2000.function.Diffusion

Diffusion - Class in org.simBio.bio.matsuoka_et_al_2003.current

Calculate current component of K, Na & Ca ion according to the diffusion.

Diffusion() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.current.Diffusion

Diffusion - Class in org.simBio.bio.matsuoka_et_al_2003.function

using dy/dt to calculate first order ordinary differential equation.

Diffusion() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.function.Diffusion

Diffusion - Class in org.simBio.bio.matsuoka_et_al_2004.molecule

calculation of diffusion equation.

Diffusion() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.molecule.Diffusion

Diffusion - Class in org.simBio.bio.terashima_et_al_2006.current

Calculate current component of K, Na & Ca ion according to the diffusion.

Diffusion() - Constructor for class org.simBio.bio.terashima_et_al_2006.current.Diffusion

Diffusion_a - Class in org.simBio.bio.matsuoka_et_al_2003.function

The first order ordinary differential equation is solved using analytic equation.

Diffusion_a() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.function.Diffusion_a

Diffusion_t - Class in org.simBio.bio.matsuoka_et_al_2003.function

The first order ordinary differential equation is solved using analytic equation.

Diffusion_t() - Constructor for class org.simBio.bio.matsuoka_et_al_2003.function.Diffusion_t

dinfi - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.ICa

discardProc(String) - Method in class org.simBio.sim.gui.toolKit.SimpleGUIFrameWork

メモリ上の編集内容の破棄を行う このメソッドでは、実体のファイルを削除する意図は**ありません**

dL - Variable in class org.simBio.bio.kurata_et_al_2005.current.ICaL

dL - Variable in class org.simBio.bio.negroni_lascano_1996.exp.LChange

length step

DnDAction - Class in org.simBio.sim.gui.toolKit.dndmenu

Drag&Dropサポートのある Action.

DnDAction() - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDAction

DnDAction(String) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDAction

DnDAction(String, Icon) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDAction

DnDActionDroppable - Interface in org.simBio.sim.gui.toolKit.dndmenu

Drag and Drop を受け付けるコンポーネントに定義して、受け入れられるDataFlavorと、アクションを設定する.

DnDJButton - Class in org.simBio.sim.gui.toolKit.dndmenu

SymBio用、ツールバーボタン Class.

DnDJButton() - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJButton

Drag and Drop ボタンを生成する。

DnDJButton(String) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJButton

Drag and Drop ボタンを生成する。

DnDJButton(Icon) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJButton

Drag and Drop ボタンを生成する。

DnDJButton(String, Icon) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJButton

Drag and Drop ボタンを生成する。

DnDJButton(Action) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJButton

Drag and Drop ボタンを生成する。

DnDJList - Class in org.simBio.sim.gui.toolKit.dndmenu

Drag & Dropのドラッグ元として使用できるJList.

DnDJList() - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJList

DnDJList(Object[]) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJList

DnDJList(Vector) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJList

DnDJList(ListModel) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJList

DnDJToolBar - Class in org.simBio.sim.gui.toolKit.dndmenu

Drag & Dropでメニュー項目を設定できる JToolBar.

DnDJToolBar() - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

DnDJToolBar(int) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

DnDJToolBar(String) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

DnDJToolBar(String, int) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

DnDMouseMotionListener - Class in org.simBio.sim.gui.toolKit.dndmenu

MouseListener / MouseMoveListener の双方に登録することで、ドラッグ操作の判定を行う.

DnDMouseMotionListener() - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDMouseMotionListener

dndStart(MouseEvent) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDMouseMotionListener

ドラッグ＆ドロップを開始する際に呼ばれるメソッド

DnDTransferBean - Class in org.simBio.sim.gui.toolKit.dndmenu

Drag&Dropで転送されるオブジェクトを入れるBean.

DnDTransferBean(JComponent, Action, String) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDTransferBean

DnDTransferHandler - Class in org.simBio.sim.gui.toolKit.dndmenu

Drag&Dropツールバーのための、TransferHandler Class.

DnDTransferHandler(JComponent) - Constructor for class org.simBio.sim.gui.toolKit.dndmenu.DnDTransferHandler

doDropAction(DnDAction, JComponent) - Method in interface org.simBio.sim.gui.toolKit.dndmenu.DnDActionDroppable

ドロップでデータを受け入れる。

doDropAction(DnDAction, JComponent) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDJToolBar

menu.TransferableActionのドロップ処理を実施する。

doLaunch(String[]) - Method in class org.simBio.sim.dm.ParameterChanger

if protocol has launcher, than launch model.

doLayout() - Method in class org.simBio.sim.gui.CheckedJTree.CheckedJTreeCellRenderer

DOMHandler - Class in org.simBio.sim.dm.util

This class handle the DOM tree.

DOMHandler() - Constructor for class org.simBio.sim.dm.util.DOMHandler

doRepaint() - Method in class org.simBio.sim.analyzer.graph.AbstractGraph

doRepaint() - Method in class org.simBio.sim.analyzer.graph.Axis

Performs a repaint.

doRepaint() - Method in class org.simBio.sim.analyzer.VisualizeAnalyzer

再描画を行う.

dP - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.MembranePotential

proton driving force

dP - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.RedoxPotentialCyta

proton gradient

dP - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ATPsynthase

proton driving force on mitochondrial inner membrane

dP - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexI

proton driving force on mitochondrial inner membrane

dP - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.RespiratoryChain.ComplexIII

proton driving force of mitochondrial inner membrane

dP - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ProtonLeak

proton gradient of mitohocndrial inner membrane

dpH - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.GradientP

proton gradient between cytosol and matrix

dpH - Variable in class org.simBio.bio.matsuoka_et_al_2004.function.MembranePotential

proton gradient of mitochondrial matrix to cytosol

dPsicell - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT

membrane potential at matrix side of mitochondrial inner membrane (mV)

dPsimito - Variable in class org.simBio.bio.matsuoka_et_al_2004.molecule.Transporter.ANT

membrane potential at matrix side of mitochondrial inner membrane (mV)

dR - Variable in class org.simBio.bio.kurata_et_al_2005.flux.Release

draw(Graphics2D, int, int) - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot.Item

描画を行う 画面の場合：prepareXXX() にて事前生成したタイトル／凡例を表示する。 印刷の場合：prepareXXX() にて保存した値にて、タイトル／凡例を描画する。

draw(Graphics2D, int, int) - Method in class org.simBio.sim.analyzer.graph.plot.PlotDisplay.LegendItem

draw(Graphics2D, int, int) - Method in class org.simBio.sim.analyzer.graph.plot.PlotDisplay.TitleItem

draw(Graphics2D, int, int) - Method in class org.simBio.sim.analyzer.graph.plot.PlotPrinter.LegendItem

draw(Graphics2D, int, int) - Method in class org.simBio.sim.analyzer.graph.plot.PlotPrinter.TitleItem

drawBar(int, int, int, int, int) - Method in interface org.simBio.sim.analyzer.graph.simple.ICanvas

drawBar(int, int, int, int, int) - Method in class org.simBio.sim.analyzer.graph.simple.Viewer

drawLine(IPlot, Graphics2D, double, double, double, double, int) - Method in class org.simBio.sim.analyzer.graph.AbstractGraph

Strikes a point on a graph. When a line is drawn instead of a point in Graph4State, it separates so that it is easy to inherit.

drawLine(IPlot, Graphics2D, double, double, double, double, int) - Method in class org.simBio.sim.analyzer.graph.Graph4State

drawLine(Graphics2D, double, double, double, double, int) - Method in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

drawLine(Graphics2D, double, double, double, double, int) - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot

線を描画する.

drawLine(IPlot, Graphics2D, double, double, double, double, int) - Method in class org.simBio.sim.analyzer.graph.StepChart

drawPoint(IPlot, Graphics2D, double, double, int) - Method in class org.simBio.sim.analyzer.graph.AbstractGraph

Draws a line on a graph. When a line is drawn instead of a point in Graph4State, it separates so that it is easy to inherit.

drawPoint(IPlot, Graphics2D, double, double, int) - Method in class org.simBio.sim.analyzer.graph.Graph4State

drawPoint(Graphics2D, double, double, int) - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot

点を描画する.

drawPoint(Graphics2D, double, double, int) - Method in class org.simBio.sim.analyzer.graph.plot.PlotDisplay

drawPoint(Graphics2D, double, double, int) - Method in class org.simBio.sim.analyzer.graph.plot.PlotPrinter

drawPoint(int, int, int, int) - Method in interface org.simBio.sim.analyzer.graph.simple.ICanvas

drawPoint(int, int, int, int) - Method in class org.simBio.sim.analyzer.graph.simple.Viewer

drawPoint(IPlot, Graphics2D, double, double, int) - Method in class org.simBio.sim.analyzer.graph.StepChart

drowDesc(Graphics, IPlot, String) - Method in class org.simBio.sim.analyzer.graph.Axis

Draws the axis label in graphics.

drowDesc(Graphics, IPlot, String) - Method in class org.simBio.sim.analyzer.graph.AxisX

drowDesc(Graphics, IPlot, String) - Method in class org.simBio.sim.analyzer.graph.AxisY

drowGrid(Graphics, IPlot, double) - Method in class org.simBio.sim.analyzer.graph.Axis

Draws a grid in graphics with a value at the specified position.

drowGrid(Graphics, IPlot, double) - Method in class org.simBio.sim.analyzer.graph.AxisX

drowGrid(Graphics, IPlot, double) - Method in class org.simBio.sim.analyzer.graph.AxisY

drowLabel(Graphics, IPlot, double, String) - Method in class org.simBio.sim.analyzer.graph.Axis

Draws the numerical value of the value parameter in graphics at the specified position.

drowLabel(Graphics, IPlot, double, String) - Method in class org.simBio.sim.analyzer.graph.AxisX

drowLabel(Graphics, IPlot, double, String) - Method in class org.simBio.sim.analyzer.graph.AxisY

dt - Variable in class org.simBio.bio.function.Analytic2state

dt - Variable in class org.simBio.bio.matsuoka_et_al_2003.function.Diffusion_a

dt - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.ICa

dt - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.IKr

dt - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.IKs

dt - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.INa

dt - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito

dt - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.Ito_endo

dt - Variable in class org.simBio.bio.tenTusscher_et_al_2004.flux.Release

dtau - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.ICa

dtMax - Variable in class org.simBio.core.Conductor

maximum time step of integration

dtMin - Variable in class org.simBio.core.Conductor

minimum time step of integration

DualCaBuffer - Class in org.simBio.bio.faber_rudy_2000.molecule

Faber GM, Rudy Y.
Action potential and contractility changes in [Na⁺]_i overloaded cardiac myocytes: a simulation study.
Biophy J 2000;78:2392-2404

DualCaBuffer() - Constructor for class org.simBio.bio.faber_rudy_2000.molecule.DualCaBuffer

duration - Variable in class org.simBio.bio.negroni_lascano_1996.exp.LChange

step duration

duration - Variable in class org.simBio.core.Conductor

duration of integration

dXdt - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.CrossBridgeLength

derivative value of inextensibleLength

dXdt - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.Troponin

dXdt - Variable in class org.simBio.bio.negroni_lascano_1996.CrossBridge

dXdt - Variable in class org.simBio.bio.negroni_lascano_1996.Troponin

dXdtFactor - Variable in class org.simBio.bio.kuzumoto_et_al_2007.contraction.Troponin

dydt - Variable in class org.simBio.core.integrator.Euler

dy/dt