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

G

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

g_K - Variable in class org.simBio.bio.hodgkin_huxley_1952.I_K

conductance (milliS_per_cm2)

g_L - Variable in class org.simBio.bio.hodgkin_huxley_1952.I_L

conductances (milliS_per_cm2)

g_Na - Variable in class org.simBio.bio.hodgkin_huxley_1952.I_Na

conductances (milliS_per_cm2)

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

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

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

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

gamma - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.carrier.INaCa

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

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

GapJunction - Class in org.simBio.bio.henriquez_et_al_2001

Voltage-dependent gap junction model developed by Vogel and Weingart.

GapJunction() - Constructor for class org.simBio.bio.henriquez_et_al_2001.GapJunction

GapJunction - Class in org.simBio.bio.oka_et_al_2006.structure

Gap junction model.

GapJunction() - Constructor for class org.simBio.bio.oka_et_al_2006.structure.GapJunction

GapJunction - Class in org.simBio.bio.sarai_noma_2004.structure

GapJunction() - Constructor for class org.simBio.bio.sarai_noma_2004.structure.GapJunction

GapJunctionK - Class in org.simBio.bio.oka_et_al_2006.structure

Gap junction model.

GapJunctionK() - Constructor for class org.simBio.bio.oka_et_al_2006.structure.GapJunctionK

gate - Variable in class org.simBio.bio.faber_rudy_2000.current.IKr

gate - Variable in class org.simBio.bio.himeno_et_al_2008.ICaL

ultra-slow gate probability

gate - Variable in class org.simBio.bio.himeno_et_al_2008.IKACh

gate - Variable in class org.simBio.bio.kuratomi_et_al_2003.current.carrier.Carrier

reduced 2-state gate

gate - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.ICaL

ultra-slow gate probability

gate - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.carrier.Carrier

reduced 2-state gate

gate - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.ICaL

ultra-slow gate probability

gate - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.INa

ultra-slow gate

gate - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IK1

gate, blocked by polyamine (time dependent compornent)

gate - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKACh

gate - Variable in class org.simBio.bio.sarai_et_al_2006.current.cf.ICaL

ultra-slow gate probability

gate - Variable in class org.simBio.bio.takeuchi_et_al_2006.current.ICaL

ultra-slow gate probability

gate - Variable in class org.simBio.bio.tenTusscher_et_al_2004.current.IK1

gate - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.ICaL

ultra-slow gate probability

gate - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.INa

ultra-slow gate

gate - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IK1

gate, blocked by polyamine (time dependent compornent)

gate1 - Variable in class org.simBio.bio.himeno_et_al_2008.IKs

the open probability of voltage-dependent gate

gate1 - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.IKs

the open probability of voltage-dependent gate

gate1 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.Ito

activation gating variable

gate1 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKr

activation gating variable (the rapid component)

gate1 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKs

the open probability of voltage-dependent gate

gate1 - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Ito

activation gating variable

gate1 - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IKr

activation gating variable (the rapid component)

gate1 - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IKs

the open probability of voltage-dependent gate

gate2 - Variable in class org.simBio.bio.himeno_et_al_2008.IKs

the open probability of [Ca²⁺]_i-dependent gate

gate2 - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.IKs

the open probability of [Ca²⁺]_i-dependent gate

gate2 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.Ito

inactivation gating variable

gate2 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKr

activation gating variable (the slow component)

gate2 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKs

the open probability of [Ca2+]i-dependent gate

gate2 - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.Ito

inactivation gating variable

gate2 - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IKr

activation gating variable (the slow component)

gate2 - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IKs

the open probability of [Ca2+]i-dependent gate

gate3 - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.potassium.IKr

inactivation gating variable

gate3 - Variable in class org.simBio.bio.terashima_et_al_2006.current.potassium.IKr

inactivation gating variable

gate_b - Variable in class org.simBio.bio.faber_rudy_2000.current.ICaT

gate_g - Variable in class org.simBio.bio.faber_rudy_2000.current.ICaT

gate_xs1 - Variable in class org.simBio.bio.faber_rudy_2000.current.IKs

gate_xs2 - Variable in class org.simBio.bio.faber_rudy_2000.current.IKs

gateC2 - Variable in class org.simBio.bio.himeno_et_al_2008.IKs

the C2 state probability of [Ca²⁺]_i-dependent gate

gateC2 - Variable in class org.simBio.bio.kuzumoto_et_al_2007.current.cf.IKs

the C2 state probability of [Ca²⁺]_i-dependent gate

gCab - Variable in class org.simBio.bio.kurata_et_al_2005.current.ICab

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

getAction() - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDJList

Dragされた時に、選択された項目のActionを取得する

getAction() - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDTransferBean

getAddress() - Static method in class org.simBio.tools.remote.ParseNodeXML

getAfterScript(String) - Static method in class org.simBio.tools.remote.CommandServerUtil

getAllIndexString() - Method in class org.simBio.sim.dm.exchange.Exchanger

getAllIndexString() - Method in class org.simBio.sim.dm.exchange.ListExchanger

getAllIndexString() - Method in class org.simBio.sim.dm.exchange.NullExchanger

getAllIterationNumber() - Method in class org.simBio.sim.dm.exchange.Exchanger

getAllIterationNumber() - Method in class org.simBio.sim.dm.exchange.NullExchanger

getAllIterationNumber() - Method in class org.simBio.sim.dm.exchange.OneTimeListExchanger

getAllStateString() - Method in class org.simBio.sim.dm.exchange.Exchanger

getAllStateString() - Method in class org.simBio.sim.dm.exchange.FileNameExchanger

getAllStateString() - Method in class org.simBio.sim.dm.exchange.ListExchanger

getAllStateString() - Method in class org.simBio.sim.dm.exchange.NullExchanger

getAllStateString() - Method in class org.simBio.sim.dm.exchange.NumericalExchanger

getAttributeValue(Node, String) - Static method in class org.simBio.sim.dm.util.NodeHandler

getBackup() - Static method in class org.simBio.util.FileHandler

getBaseModel() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag attribute "path" from file protocol.

getBaseModel() - Method in interface org.simBio.sim.ps.ICollection

getBaseModel() - Method in class org.simBio.sim.ps.ParameterSpace

基本モデルXMLの名前を返す。

getBooleanProperty(Class, String) - Method in class org.simBio.util.PropertyManager

Return the property as boolean

getCapsuledDocument(Node) - Static method in class org.simBio.sim.dm.util.DOMHandler

Adding a Node to a new instance of DOM Document.

getCapsuledInputStream(Node) - Static method in class org.simBio.sim.dm.util.DOMHandler

Adding a Node to a new instance of DOM Document and return document as input stream.

getCBbound() - Method in class org.simBio.bio.matsuoka_et_al_2003.molecule.buffer.Ca.TroponinNL

getCBfactor() - Method in class org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme.CrossBridgeNL

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

getChildTextNode(Node) - Static method in class org.simBio.sim.dm.util.NodeHandler

getClassLoader() - Method in class org.simBio.sim.js.entry.Request

TODO protective copy is needed.

getClassName() - Method in class org.simBio.core.Initializer

Returns the className.

getCodebases() - Method in interface org.simBio.serialize.Serializer

getCodebases() - Method in class org.simBio.serialize.xml.XMLSerializer

This returns the search path of URLs for loading classes

getCodeBases() - Method in class org.simBio.sim.js.JSProtocolParser

Read tag attribute "URL" from file protocol.

getCollected() - Method in class org.simBio.sim.js.Taker

getColor(int) - Method in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

系列番号毎の描画色を取得する.

getColor() - Method in class org.simBio.sim.analyzer.graph.plot.AttributeString

色を取得する.

getColorParameter(String, Color) - Method in class org.simBio.sim.analyzer.VisualizeAnalyzer

Node名を指定して、Colorを取得します.

getCompiler() - Static method in class org.simBio.tools.remote.ParseNodeXML

getComponent(String) - Method in class org.simBio.serialize.xml.XMLSerializer

Return Class instance designated by the complete class name.

getContainer() - Method in class org.simBio.sim.analyzer.graph.Viewer

Gets the container.

getCount() - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

書き込みバッファの使用容量を取得する.

getCsvRootFile() - Method in class org.simBio.sim.dm.ProtocolParser

Get CSV-file.

getCurrentIndex() - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesValues

現在のデータ件数を取得する.

getDataMax(int) - Method in class org.simBio.sim.analyzer.graph.GraphReplotBuffer

Returns the maximum value in the calculation results of the specified index, from the redrawing buffer.

getDataMin(int) - Method in class org.simBio.sim.analyzer.graph.GraphReplotBuffer

Returns the minimum value in the calculation results of the specified index, from the redrawing buffer.

getDataXMLAsStream() - Method in class org.simBio.sim.dm.ParameterChanger

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

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

getDocument() - Method in class org.simBio.sim.dm.ParameterChanger

getDocumentAsInputStream(Node) - Static method in class org.simBio.sim.dm.util.DOMHandler

Get document as input stream.

getDocumentAsReader(Node) - Static method in class org.simBio.sim.dm.util.DOMHandler

Get document as buffered reader.

getDouble(long, int) - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

インデックスと系列番号を指定して、double値を読み込む

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

get value from node.

getDydt() - Method in class org.simBio.core.integrator.Concentration

getDydt() - Method in class org.simBio.core.integrator.Euler

getDydt() - Method in class org.simBio.core.integrator.RungeKutta

getDydt() - Method in interface org.simBio.core.Variable

return dy/dt
dy/dtの値を返す。

getDydtOverY() - Method in class org.simBio.core.integrator.Euler

getDydtOverY() - Method in class org.simBio.core.integrator.RungeKutta

dy/dtを現在値(y)で割った値を返す。

getDydtOverY() - Method in interface org.simBio.core.Variable

dy/dtを現在値(y)で割った値を返す。

getEffectiveFraction() - Method in class org.simBio.bio.matsuoka_et_al_2003.molecule.enzyme.CrossBridgeNL

getEraser() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag from file protocol.

getEval(int, int) - Method in interface org.simBio.sim.ps.ICollection

getEval(int, int) - Method in class org.simBio.sim.ps.ParameterSpace

getEval(int) - Method in class org.simBio.sim.ps.Result

getEvalLabel(int) - Method in class org.simBio.sim.ps.Result

getEvalLabels() - Method in class org.simBio.sim.analyzer.csv.keep.ParamEvalKeeper

getEvalLabels() - Method in interface org.simBio.sim.ps.IEvals

getEvalLabvel(int) - Method in interface org.simBio.sim.ps.ICollection

getEvalLabvel(int) - Method in class org.simBio.sim.ps.ParameterSpace

getEvals() - Method in class org.simBio.sim.analyzer.csv.keep.ParamEvalKeeper

getEvals() - Method in interface org.simBio.sim.ps.IEvals

getEvalSize() - Method in interface org.simBio.sim.ps.ICollection

getEvalSize() - Method in class org.simBio.sim.ps.ParameterSpace

getEvalSize() - Method in class org.simBio.sim.ps.Result

getExchanger() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag from file protocol.

getExternalSubset(String, String) - Method in class org.simBio.serialize.xml.LogSax2

Returns and logs a new external subset.

getFile(String) - Static method in class org.simBio.util.FileHandler

getFileName() - Method in class org.simBio.sim.analyzer.graph.Viewer

Gets an XML file name.

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

現在処理中のファイル名を取得する。

getFont() - Method in class org.simBio.sim.analyzer.graph.plot.AttributeString

フォントを取得する.

getFontParameter(String, String, String) - Method in class org.simBio.sim.analyzer.VisualizeAnalyzer

nodeNamePrefixを指定して、Fontを取得します.

getFormatString(double, double) - Method in class org.simBio.sim.analyzer.graph.Axis

Get default format string.

getFormatString(double, double) - Method in class org.simBio.sim.analyzer.graph.AxisX

getFormatString(double, double) - Method in class org.simBio.sim.analyzer.graph.AxisY

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

Gets the space at the bottom of the screen for displaying the scale. Please override as necessary with a subclass.

getFreeSpaceBottom(Graphics) - Method in class org.simBio.sim.analyzer.graph.AxisX

Get the space for the axis label

getFreeSpaceBottom(Graphics) - Method in class org.simBio.sim.analyzer.graph.AxisY

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

Gets the space on the left of the screen for displaying the scale. Please override as necessary with a concrete class.

getFreeSpaceLeft(Graphics) - Method in class org.simBio.sim.analyzer.graph.AxisX

getFreeSpaceLeft(Graphics) - Method in class org.simBio.sim.analyzer.graph.AxisY

Get the space for the axis label

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

Gets the space on the right of the screen for displaying the scale. Please override as necessary with a concrete class.

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

Gets the space at the top of the screen for displaying the scale. Please override as necessary with a subclass.

getFreeSpaceTop(Graphics) - Method in class org.simBio.sim.analyzer.graph.AxisY

getGenerateModel() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag attribute "path" from file protocol.

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

描画に必要な高さを取得する.

getIdentification() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag attribute "identification" from file protocol.

getIndent() - Method in class org.simBio.core.Component

make hierarchical indent using level
階層を元に字下げを作る。

getIndentedShortName() - Method in class org.simBio.core.Component

return indented short name
字下げをした名前を返す。

getIndexByTime(double) - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesSingle

指定した時刻に対応するインデックスを取得する.

getIndexByTime(double) - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesValues

指定した時刻に対応するインデックスを取得する.

getIndexString() - Method in class org.simBio.sim.dm.exchange.Exchanger

getIndexString() - Method in class org.simBio.sim.dm.exchange.NullExchanger

getInitialValue() - Method in class org.simBio.core.Initializer

Returns the initialValue.

getInserter() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag from file protocol.

getInserterBefore() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag from file protocol.

getInstance(Composite, Attributes) - Static method in class org.simBio.core.Initializer

return the only initializer in which parent and attributes are set.

getInstance(String) - Static method in class org.simBio.core.Initializer

getInstance() - Static method in class org.simBio.tools.remote.PropertyManager

return instance of PropertyManager

getInstance() - Static method in class org.simBio.util.PropertyManager

return instance of PropertyManager

getIterationNumber() - Method in class org.simBio.sim.dm.ParameterChanger

getJButton() - Method in class org.simBio.sim.analyzer.graph.simple.RateGraph

This method initializes jButton

getJButton() - Method in class org.simBio.sim.analyzer.graph.simple.RateGraph_KA

This method initializes jButton

getJComponent() - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDTransferBean

getJPanel() - Method in class org.simBio.sim.gui.GUI

This method initializes jPanel

getKey(int, int) - Method in interface org.simBio.sim.ps.ICollection

getKey(int, int) - Method in class org.simBio.sim.ps.ParameterSpace

getKeyLabel(int) - Method in interface org.simBio.sim.ps.ICollection

getKeyLabel(int) - Method in class org.simBio.sim.ps.ParameterSpace

getKeyLabels() - Method in class org.simBio.sim.analyzer.csv.keep.ParamEvalKeeper

getKeyLabels() - Method in interface org.simBio.sim.ps.IKeys

getKeys() - Method in class org.simBio.sim.analyzer.csv.keep.ParamEvalKeeper

getKeys() - Method in interface org.simBio.sim.ps.IKeys

getKeySize() - Method in interface org.simBio.sim.ps.ICollection

getKeySize() - Method in class org.simBio.sim.ps.ParameterSpace

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

Gets the length of the axis direction, when the numerical value is displayed. This result is used to control the display space of the label.

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

Display of the axis label

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

Axis label display

getLastXYSeriesCollection() - Method in interface org.simBio.sim.ps.ICollection

getLastXYSeriesCollection() - Method in class org.simBio.sim.ps.ParameterSpace

getLauncher() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag attribute "launch" from file protocol.

getLegend() - Method in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

getLegend() - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot

凡例描画用のItemオブジェクトを取得する.

getLink(String) - Method in class org.simBio.core.Composite

引数のnameで指定されたxmlのlinkが指し示す対象への参照を返す。

getListValues(String) - Method in class org.simBio.sim.dm.exchange.ListExchanger

getLong(long, int) - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

インデックスと系列番号を指定して、long値を読み込む

getMaxThreads() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag attribute "threads" from file protocol.

getMultiplier() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag from file protocol.

getName() - Method in class org.simBio.core.Component

complete name from root.

getName(int) - Method in class org.simBio.core.Component

complete name from prefix level.

getName() - Method in class org.simBio.core.Initializer

Returns the name.

getName() - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesSingle

名前(target X)を取得する.

getName() - Static method in class org.simBio.sim.js.Worker

getName() - Method in class org.simBio.util.taglets.EnOff

Return the name of this custom tag.

getName() - Method in class org.simBio.util.taglets.EnOn

Return the name of this custom tag.

getName() - Method in class org.simBio.util.taglets.JaOff

Return the name of this custom tag.

getName() - Method in class org.simBio.util.taglets.JaOn

Return the name of this custom tag.

getName() - Method in class org.simBio.util.taglets.Languages

Return the name of the custom tag.

getNewFile(String) - Static method in class org.simBio.util.FileHandler

get new File, the file, if already exist, will be renamed to the backup.

getNode(String) - Method in class org.simBio.core.Composite

serch the Node of the same name,
受け取った文字列と同じ名前の最初に見つかったNodeを返す。

getNode() - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesSingle

対応するNodeを取得する.

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

serch the Node of the same name(or upper level node).

getNodeIterator(Node, String) - Static method in class org.simBio.sim.dm.util.NodeHandler

getNodeIterator(Document, String) - Static method in class org.simBio.sim.dm.util.NodeHandler

getNodeList(Node, String) - Static method in class org.simBio.sim.dm.util.NodeHandler

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

serch the Node of the same name.

getNodesIterator() - Method in class org.simBio.core.Composite

ComponentListのIteratorを返す。

getNodesSize() - Method in class org.simBio.core.Composite

ComponentListの要素の数を返す。

getNormalizeTo() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag attribute "xpath" from file protocol.

getObserver(Conductor, XMLSerializer, Reader) - Method in interface org.simBio.sim.ps.ICollector

getObserver(Conductor, XMLSerializer, Reader) - Method in class org.simBio.sim.ps.ParameterSpace

getOSName() - Static method in class org.simBio.tools.remote.CommandServerUtil

OS取得

getOSProperty(String) - Method in class org.simBio.tools.remote.PropertyManager

OS名で取得するプロパティーキーを変える。

getParam(int) - Method in class org.simBio.sim.ps.Result

getParamLabel(int) - Method in class org.simBio.sim.ps.Result

getParamRatio(int, int) - Method in interface org.simBio.sim.ps.ICollection

getParamRatio(int, int) - Method in class org.simBio.sim.ps.ParameterSpace

getParamRetio(int) - Method in class org.simBio.sim.ps.Result

getParamSize() - Method in class org.simBio.sim.ps.Result

getParent() - Method in class org.simBio.core.Component

自分が属するCompositeへの参照を返す。

getParent() - Method in class org.simBio.core.Initializer

Returns the parent.

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

Gets the coordinate axis from Plot.

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

getPos(double, IPlot) - Method in class org.simBio.sim.analyzer.graph.AxisXLog

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

getPos(double, IPlot) - Method in class org.simBio.sim.analyzer.graph.AxisYLog

getPosition() - Method in class org.simBio.sim.js.entry.Index

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

getPrepareDouble(long, long) - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

先読みキャッシュにdouble値を読み込む.

getPrepareLong(long, long) - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

先読みキャッシュにlong値を読み込む.

getProcessor() - Method in class org.simBio.sim.js.entry.Request

getProperties(Class) - Method in class org.simBio.util.PropertyManager

Returns the list of properties

getProperty(String) - Method in class org.simBio.tools.remote.PropertyManager

プロパティーを取得する

getProperty(Class, String) - Method in class org.simBio.util.PropertyManager

Return property

getProperty(String) - Method in class org.simBio.util.PropertyManager

getProtocol() - Method in interface org.simBio.sim.ps.ICollection

getProtocol() - Method in class org.simBio.sim.ps.ParameterSpace

プロトコルXMLの名前を返す。

getProtocolAsStream() - Method in class org.simBio.sim.dm.ProtocolParser

Get protocol as stream.

getProtocolParser() - Method in class org.simBio.sim.dm.ParameterChanger

getProtocolParser() - Method in class org.simBio.sim.ps.serialize.ParseXMLs

Get ProtocolParser

getRangeMax() - Method in class org.simBio.sim.analyzer.graph.GraphReplotBuffer

Returns the maximum index of the redrawing buffer.

getRangeMin() - Method in class org.simBio.sim.analyzer.graph.GraphReplotBuffer

Returns the minimum index of the redrawing buffer.

getReadCache(long, long) - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

指定した位置のデータが読まれたキャッシュを取得する。

getReciever() - Method in interface org.simBio.sim.ps.ICollector

getReciever() - Method in class org.simBio.sim.ps.ParameterSpace

getRectangleBounds() - Method in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

getRectangleBounds() - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot

グラフ・タイトル・凡例の描画領域を取得する.

getRectanglePage() - Method in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

getRectanglePage() - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot

ページ全体の領域を取得する.

getRectangleView() - Method in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

getRectangleView() - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot

グラフ本体の描画領域を取得する.

getRequestNumber(JavaSpace, String, long) - Static method in class org.simBio.sim.js.Channel

getResultModel(Document) - Static method in class org.simBio.JSEntry

getRoot() - Method in class org.simBio.core.Component

自分が属するinstance treeのrootへの参照を返す。

getRoot() - Method in class org.simBio.sim.gui.DataListTable

getRootExchanger() - Method in class org.simBio.sim.dm.exchange.ExchangerFactory

getScaleHeight() - Method in interface org.simBio.sim.analyzer.graph.simple.ICanvas

scaling factor = reference height (0.01 mm) / physical height (pixel)

getScaleHeight() - Method in class org.simBio.sim.analyzer.graph.simple.Viewer

scaling factor = reference height (0.01 mm) / physical height (pixel)

getScaleWidth() - Method in interface org.simBio.sim.analyzer.graph.simple.ICanvas

scaling factor = reference width (0.01 mm) / physical width (pixel)

getScaleWidth() - Method in class org.simBio.sim.analyzer.graph.simple.Viewer

scaling factor = reference width (0.01 mm) / physical width (pixel)

getSerializer(File) - Static method in class org.simBio.serialize.SerializerFactory

Takes an XML file as input and returns an XMLSerializer which can parse it.

getSerializer(InputSource) - Static method in class org.simBio.serialize.SerializerFactory

Takes an XML input source as a parameter and returns an XMLSerializer to parse the XML.

getSerializer(InputSource, ClassLoader) - Static method in class org.simBio.serialize.SerializerFactory

Takes an XML input source and a class loader as parameters and returns an XMLSerializer to parse the XML.

getSeries() - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

系列数を取得する.

getSeriesName(int) - Method in interface org.simBio.sim.ps.ICollection

getSeriesName(int) - Method in class org.simBio.sim.ps.ParameterSpace

getSeriesName() - Method in class org.simBio.sim.ps.Result

getServer() - Static method in class org.simBio.tools.remote.ParseNodeXML

getService(Class) - Static method in class org.simBio.sim.js.jini.ServiceLocator

getService(Class, String, String) - Static method in class org.simBio.sim.js.jini.ServiceLocator

getService(Class, String) - Static method in class org.simBio.sim.js.jini.ServiceLocator

getServiceURL() - Method in class org.simBio.sim.js.JSProtocolParser

Read tag attribute "URL" from file protocol.

getSettings() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag attribute "settings" from file protocol.

getShortName() - Method in class org.simBio.core.Component

short name
短い名前を返す。

getSingleNode(Node, String) - Static method in class org.simBio.sim.dm.util.NodeHandler

getSingleNode(Node, String, Node) - Static method in class org.simBio.sim.dm.util.NodeHandler

getSize() - Method in class org.simBio.sim.analyzer.graph.GraphReplotBuffer

Returns the width (number of pixels displayed in the time axis) of the redrawing buffer

getSize() - Method in interface org.simBio.sim.ps.ICollection

getSize() - Method in class org.simBio.sim.ps.ParameterSpace

getSourceActions(JComponent) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDTransferHandler

ドラッグ用：ソースがサポートする転送アクションの種類を返します。

getSpace() - Static method in class org.simBio.sim.js.jini.SpaceLocator

getSpace(String) - Static method in class org.simBio.sim.js.jini.SpaceLocator

getStateString() - Method in class org.simBio.sim.dm.exchange.Exchanger

getStateString() - Method in class org.simBio.sim.dm.exchange.FileNameExchanger

getStateString() - Method in class org.simBio.sim.dm.exchange.ListExchanger

getStateString() - Method in class org.simBio.sim.dm.exchange.NullExchanger

getStateString() - Method in class org.simBio.sim.dm.exchange.NumericalExchanger

getStateString() - Method in class org.simBio.sim.dm.ParameterChanger

getTargets(Composite) - Static method in class org.simBio.util.NodeHandler

getTargetScript(String) - Static method in class org.simBio.tools.remote.CommandServerUtil

処理対象スクリプト取得 取得できなかった場合はnullを返す。

getText() - Method in class org.simBio.sim.analyzer.graph.plot.AttributeString

テキスト文字列を取得する.

getText() - Method in class org.simBio.sim.analyzer.graph.plot.PlotPrinter.TitleItem

(内部用)文字列を取得する.

getTexts() - Method in class org.simBio.sim.analyzer.graph.plot.PlotPrinter.LegendItem

(内部用)文字列配列を取得する.

getTime(long) - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesSingle

指定したインデックスの時刻を取得する.

getTime(long) - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesValues

インデックスを指定して時刻を取得する.

getTimeMax() - Method in class org.simBio.sim.analyzer.graph.BasicGraph

Get maximum time

getTimeMax() - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesSingle

最大時刻を取得する.

getTimeMax() - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesValues

最大時刻を取得する.

getTimeMin() - Method in class org.simBio.sim.analyzer.graph.BasicGraph

Get minimum time

getTimeMin() - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesSingle

最小時刻を取得する.

getTimeMin() - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesValues

最小時刻を取得する.

getTimeSeries(Object) - Method in class org.simBio.sim.analyzer.graph.BasicGraph

Gets a time series class for the specified Node.

getTitle() - Method in class org.simBio.sim.analyzer.graph.plot.AbstractPlot

getTitle() - Method in interface org.simBio.sim.analyzer.graph.plot.IPlot

タイトル描画用のItemオブジェクトを取得する.

getTocXML() - Method in class org.simBio.sim.dm.ProtocolParser

Get Toc XML-file path.

getTransferData(DataFlavor) - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDTransferBean

getTransferDataFlavors() - Method in class org.simBio.sim.gui.toolKit.dndmenu.DnDTransferBean

自クラスの転送可能な DataFlavor 配列を返す。

getTreeCellEditorComponent(JTree, Object, boolean, boolean, boolean, int) - Method in class org.simBio.sim.gui.CheckedJTree.CheckedJTreeCellRenderer

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class org.simBio.sim.gui.CheckedJTree.CheckedJTreeCellRenderer

getUnits() - Method in class org.simBio.core.Component

Returns the units.

getUnits() - Method in class org.simBio.core.Initializer

Returns the units.

getValue() - Method in class org.simBio.core.Component

always throws UnsupportedOperationException, need to implement 'Node'

getValue() - Method in class org.simBio.core.integrator.Concentration

getValue() - Method in interface org.simBio.core.Node

return current value
現在値を返す。

getValue() - Method in class org.simBio.core.Parameter

getValue(long) - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesSingle

指定したインデックスのデータを取得する.

getValue(long, int) - Method in class org.simBio.sim.analyzer.graph.results.TimeSeriesValues

インデックスを指定して計算値を取得する.

getValues(String) - Static method in class org.simBio.util.CsvHandler

getValueString() - Method in class org.simBio.core.Component

文字列として現在値を返す。

getValueString() - Method in class org.simBio.core.integrator.Concentration

getValueString() - Method in class org.simBio.core.Parameter

getWHratio() - Method in interface org.simBio.sim.analyzer.graph.IViewer

getWHratio() - Method in class org.simBio.sim.analyzer.graph.simple.Viewer

getWHratio() - Method in class org.simBio.sim.analyzer.graph.Viewer

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

描画に必要な横幅を取得する.

getWriteBufferCapacity() - Method in class org.simBio.sim.analyzer.graph.results.CachedBuffer

書き込みバッファの容量を取得する.

getWriter() - Method in class org.simBio.sim.dm.ProtocolParser

Read tag from file protocol.

getXmlName(int) - Method in interface org.simBio.sim.ps.ICollection

getXmlName(int) - Method in class org.simBio.sim.ps.ParameterSpace

getXmlName() - Method in class org.simBio.sim.ps.Result

getXmlRootDir() - Method in class org.simBio.sim.dm.ProtocolParser

Get XML root dir.

getXMLs() - Method in class org.simBio.sim.ps.serialize.ParseXMLs

Query XML-files.

getXpath(String) - Method in class org.simBio.sim.dm.ProtocolParser

Read input parameter xpath from file protocol.

getXYSeriesCollection() - Method in class org.simBio.sim.analyzer.csv.keep.TimeSeriesKeeper

getXYSeriesCollection() - Method in interface org.simBio.sim.ps.ITimeSeries

getXYSeriesCollection() - Method in class org.simBio.sim.ps.Result

getXYSerieses(BufferedReader) - Static method in class org.simBio.util.CsvHandler

convert csv file to XYSeriesCollection.

getXYSeriesLabel() - Method in class org.simBio.sim.analyzer.csv.keep.TimeSeriesKeeper

getXYSeriesLabel() - Method in interface org.simBio.sim.ps.ITimeSeries

GH - Variable in class org.simBio.bio.henriquez_et_al_2001.GapJunction

conductance at high state (pS)

gHH - Variable in class org.simBio.bio.henriquez_et_al_2001.GapJunction

conductance of HH state

gHL - Variable in class org.simBio.bio.henriquez_et_al_2001.GapJunction

conductance of HL state

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

gj - Variable in class org.simBio.bio.oka_et_al_2006.function.JunctionalConductance

the unitary conductance of gap junction channels (pS)

GK - Variable in class org.simBio.bio.matsuoka_et_al_2003.current.cf.IKpl

channel conductance

GK - Variable in class org.simBio.bio.terashima_et_al_2006.current.cf.IKpl

channel conductance

gK1 - Variable in class org.simBio.bio.kurata_et_al_2005.current.IK1

gKr - Variable in class org.simBio.bio.kurata_et_al_2005.current.IKr

gKs - Variable in class org.simBio.bio.kurata_et_al_2005.current.IKs

GL - Variable in class org.simBio.bio.henriquez_et_al_2001.GapJunction

conductance at low state (pS)

gLH - Variable in class org.simBio.bio.henriquez_et_al_2001.GapJunction

conductance of LH state

gLL - Variable in class org.simBio.bio.henriquez_et_al_2001.GapJunction

conductance of LL state

globalPropertyFile - Static variable in class org.simBio.sim.gui.Constant

グローバルプロパティファイル名（ホームディレクトリ上）

gmaxrel - Variable in class org.simBio.bio.faber_rudy_2000.current.RyR

gNa - Variable in class org.simBio.bio.kurata_et_al_2005.current.INa

gNab - Variable in class org.simBio.bio.kurata_et_al_2005.current.INab

GradientP - Class in org.simBio.bio.matsuoka_et_al_2004.function

proton driving force

GradientP() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.function.GradientP

GradientpH - Class in org.simBio.bio.matsuoka_et_al_2004.function

proton gradient on mitochondrial inner membrane.

GradientpH() - Constructor for class org.simBio.bio.matsuoka_et_al_2004.function.GradientpH

Graph - Class in org.simBio.sim.analyzer.graph

Graph (optimised) which displays 2D graph data in chronological order.

Graph() - Constructor for class org.simBio.sim.analyzer.graph.Graph

Graph - Class in org.simBio.sim.analyzer.graph.simple

2D graph.

Graph() - Constructor for class org.simBio.sim.analyzer.graph.simple.Graph

Graph4State - Class in org.simBio.sim.analyzer.graph

Draws the target as a surface. Overrides the line/point drawing methods in order to draw the surface.

Graph4State() - Constructor for class org.simBio.sim.analyzer.graph.Graph4State

Graph4State - Class in org.simBio.sim.analyzer.graph.simple

Graph4State() - Constructor for class org.simBio.sim.analyzer.graph.simple.Graph4State

graphics2d - Variable in class org.simBio.sim.analyzer.graph.BasicGraph

Graphics2D for redrawing during analyze()

GraphReplotBuffer - Class in org.simBio.sim.analyzer.graph

High speed graph redrawing buffer In order to redraw a time series graph at high speed, without plotting multiple calculation results in 1 pixel of the X axis (= time axis) direction, by storing the maximum/minimum values in advance, with 1 pixel unit of the X axis (= time axis) direction, high speed line drawing can be carried out at drawing time.

GraphReplotBuffer(Graph, IPlot, TimeSeriesValues, int) - Constructor for class org.simBio.sim.analyzer.graph.GraphReplotBuffer

graphs - Variable in class org.simBio.sim.analyzer.graph.simple.RateGraph_KA

gridStep - Variable in class org.simBio.sim.analyzer.graph.Axis

gridStep - Variable in class org.simBio.sim.analyzer.graph.simple.Axis

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

free gs_protein concentration

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

Multi newton raphson function

Gs_alpha_GTP - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.CAMP

Gs_alpha GTP-form concentration (mM)

Gs_alpha_GTP_AC - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.CAMP

Gs_alpha_GTP and AC complex concentration (mM)

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

Multi newton raphson function

Gs_alpha_GTPtot - Variable in class org.simBio.bio.kuzumoto_et_al_2007.molecule.CAMP

Gs_alpha_GTP total concentration (mM)

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

gs_beta_gamma_protein concentration

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

total gs_protein concentration

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

gto - Variable in class org.simBio.bio.kurata_et_al_2005.current.Ito

GUI - Class in org.simBio.sim.gui

Graphical User Interface, which has a tree-table and panel.

GUI(String) - Constructor for class org.simBio.sim.gui.GUI

Constructor for Controller.

GUI.JPrintablePanel - Class in org.simBio.sim.gui

GUI.JPrintablePanel() - Constructor for class org.simBio.sim.gui.GUI.JPrintablePanel