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

A

ACSCIterator - class iterators.ACSCIterator.

ACSCIterator() - Constructor for class iterators.ACSCIterator

ACSC_SwitchIterator - class iterators.ACSC_SwitchIterator.

ACSC_SwitchIterator() - Constructor for class iterators.ACSC_SwitchIterator

ADDED - Static variable in interface genegui.GuiInterface

Static values for affector/node template change

ADDING_PARAM_SET_STRING - Static variable in class parameters.ParameterSetArray

ADD_WINDOW - Static variable in class genegui.InspectorList

ADesc - Variable in class affectors.Affector

Descriptors for use by the GUI; set these to point to static final Strings that say in as few words as possible what the Affector does (ADesc), what nodes need to be specified (NDesc), and what parameters it uses (PDesc).

AdamsIntegrator - class integrators.AdamsIntegrator.

Fourth-order Adams-Bashforth-Moulton predictor-corrector method, using coefficients given in Melvin Maron, Numerical Analysis: A Practical Approach c.

AdamsIntegrator() - Constructor for class integrators.AdamsIntegrator

Affector - class affectors.Affector.

Stores the formula for how a node changes over time.

AffectorTemplate - class main.AffectorTemplate.

AffectorTemplate(String) - Constructor for class main.AffectorTemplate

AffectorViewPanel - class genegui.AffectorViewPanel.

AffectorViewPanel.java Displays information about an An Affector Template and allows some values to be modified.

AffectorViewPanel(AffectorTemplate, MainGui) - Constructor for class genegui.AffectorViewPanel

Affector_Template - class affectors.Affector_Template.

This should be a description of what this Affector does and where it might be used This description will show up in the online html documentation files.

Affector_Template() - Constructor for class affectors.Affector_Template

Constructor for this Affector.

actionPerformed(ActionEvent) - Method in class genegui.InspectorList

actionPerformed(ActionEvent) - Method in class genegui.ParInspector

actionPerformed(ActionEvent) - Method in class genegui.PhasePortraitDlog

actor - Variable in class main.GeneNet

add(ModelState, ParameterSet, float, String) - Method in class genegui.SuccessList

Add a new pair to the list.

addActionListener(ActionListener) - Method in class genegui.GeneNetInterface

addActionListener(ActionListener) - Method in class genegui.InspectorList

addActionListener(ActionListener) - Method in class main.NetworkFile

addActionListener(ActionListener) - Method in class parameters.ParameterSetArray

addAffector(Affector) - Method in class affectors.EnhancerRegionAff

This function is used to add regular affectors to be used by the meta-affector.

addAffector(AffectorTemplate) - Method in class main.NodeTemplate

addAffectorDisplay(NetworkPaintPanel.AffectorDisplay) - Method in class genegui.NetworkPaintPanel.NodeDisplay

Adds a new AffectorDisplay to the list of displays associated with this node (as inputs).

addAffectors(Network) - Method in class main.Cell

addCalculator(String) - Method in class main.Network

addDefaultParam(String, float, float, float, String) - Static method in class affectors.Affector

addExpAffector(Affector, Cell) - Method in class main.Node

addExperimentToNode(String, Affector) - Method in class main.Cell

addGUIListener(GuiInterface) - Method in class genegui.MainGui

addInternalFrame(JInternalFrame) - Method in class genegui.MainGui

Add an internal frame to the GUI.

addIterator(ModelIterator, String, String, String, String, String, boolean) - Method in class iterators.UberIteratorFunction

addModelStateChangeListener(ModelStateChangeListener) - Method in class genegui.ModelState

Called to add a new ModelStateChangeListener.

addModelStateView(ModelStateView) - Method in class genegui.ModelState

Called to add a new ModelStateView to the local list.

addModelStateView(ModelStateView) - Method in class genegui.ModelStateEditor

Called when a new ModelStateView is to be added to the ModelStateEditor.

addNeighbor(Cell) - Method in class main.Cell

addNetworkListener(NetworkEventListener) - Method in class main.GeneNet

addNetworkListener(NetworkEventListener) - Method in class main.Network

addNode(String) - Method in class main.Network

addNode(String, float) - Method in class stoppers.CellThresholdStop

addNode(String, float) - Method in class stoppers.MultiNodeThresholdStop

addNodes(Network) - Method in class main.Cell

addObject(Model, BetterTokenizer, String, String) - Method in class iterators.CooptimizerFunction

addObject(Model, BetterTokenizer, String, String) - Method in class iterators.Function

addObject(Network, Model, BetterTokenizer, String, String, String, String, String, boolean, String) - Method in class iterators.UberIteratorFunction

addParamSetArray(ParameterSetArray) - Static method in class main.Globals

addParameter(String, float, float, float, int) - Method in class parameters.ParameterSet

If any of the passed in values are < 0, then the defaults are used (which come from the currently loaded model, via the Parameter constructor.

addParameter(Parameter) - Method in class parameters.ParameterSet

If there is a prototype, this function tries to find the new parameter's name in the prototype.

addRule(ParameterRule) - Method in class parameterrules.ParameterRuleSet

addSet(ParameterSet) - Method in class parameters.ParameterSetArray

addStateChangeListener(NodeStateChangeListener, int) - Method in class genegui.ModelState

Adds a NodeStateChangeListener to the ModelState.

addValueField(String, String) - Method in class parameters.ParameterSet

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.AffectorViewPanel

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.CellSurfaceViewer

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in interface genegui.GuiInterface

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.MainGui

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.ModelStateEditor

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.ModelStateNodePalette

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.ModelStateView

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.NetworkViewer2

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.NodeStateViewer

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.NodeViewPanel

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.ParameterViewer

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class genegui.TimeGraph

Called when a change is made to the passed AffectorTemplate

affectorTemplateChanged(int, AffectorTemplate, GuiInterface) - Method in class main.GeneNet

Called when a change is made to the passed AffectorTemplate

affectorType - Variable in class affectors.Affector

affectorType - Variable in class main.AffectorTemplate

affectors - package affectors

affectors - Variable in class main.Node

affectorsToString(PrintWriter, String) - Method in class main.NodeTemplate

areParametersGood(float[], int, ParameterSet) - Method in class parameterrules.ParameterRuleSet

areParametersGood(float[], int) - Method in class parameters.ParameterSet

arrangeParametersByModel() - Method in class parameters.ParameterSet

Rearranges the parameters in this set so that the position in set corresponds to the position of the parameter in Affector.

arrayHeight - Static variable in class main.Cell

arrayHeight - Variable in class main.Model

arrayWidth - Static variable in class main.Cell

arrayWidth - Variable in class main.Model

atBeginning() - Method in class parameters.ParameterSetArray

atEnd() - Method in class parameters.ParameterSetArray

autoArrange() - Method in class genegui.NetworkPaintPanel

Automatically re-arranges all display elements to a certain "optimal" display pattern.

autoarrange() - Method in class genegui.MainGui

Places various Desktop comononents in nice starting places TheConsole - Lower left TheError Console Lower left The Help Window - Upper right

B

BROWN_NOISE - Static variable in class main.MoreMath

BackwardEulerIntegrator - class integrators.BackwardEulerIntegrator.

BackwardEulerIntegrator is a custom-modified backward Euler method with simple-minded adaptive stepsizing that exploits the same partially explicit corrector formula as the SemiExplicitAPCIntegrator.

BackwardEulerIntegrator() - Constructor for class integrators.BackwardEulerIntegrator

BetterTokenizer - class main.BetterTokenizer.

The BetterTokenizer class takes an input stream and * parses it into "tokens", allowing the tokens to be * read one at a time.

BetterTokenizer(InputStream) - Constructor for class main.BetterTokenizer

Creates a stream tokenizer that parses the specified input * stream.

BetterTokenizer(Reader) - Constructor for class main.BetterTokenizer

Create a tokenizer that parses the given character stream.

BoundaryRule - class parameterrules.BoundaryRule.

Implements the rule that the "leftSide" must be greater than or less than the ratio of two products of input parameters.

C

CC - Static variable in class affectors.Affector

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

CERTIFICATION - Static variable in class affectors.Affector

Position meanings for Type[].

CHANGED - Static variable in interface genegui.GuiInterface

CLOSE - Static variable in interface genegui.GuiInterface

Static values for newtworkIO operations

CLOSING_STRING - Static variable in class parameters.ParameterSetArray

COMPLEX - Static variable in class main.NodeTemplate

CONVERSION - Static variable in class affectors.Affector

Type.[TERMTYPE] values;

CalculatorNode - class main.CalculatorNode.

a CalculatorNode is a wrapper useful for doing arithmetic on a group of Nodes, like treating a group of similar Nodes as if it were a single pool.

CashKarpIntegrator - class integrators.CashKarpIntegrator.

Fifth-order adaptive step-size Runga-Kutta.

CashKarpIntegrator() - Constructor for class integrators.CashKarpIntegrator

Cell - class main.Cell.

This class represents a single cell in the model.

Cell(float, float) - Constructor for class main.Cell

Main constructor

Cell.Hexagon - class main.Cell.Hexagon.

An internal class used for generating hexagonal cell shape

Cell.Hexagon(int) - Constructor for class main.Cell.Hexagon

Cell.Square - class main.Cell.Square.

An internal class used for generating square cell shape

Cell.Square(int) - Constructor for class main.Cell.Square

CellIC - class initialconditions.CellIC.

CellIC() - Constructor for class initialconditions.CellIC

CellIC(String, float, int, int) - Constructor for class initialconditions.CellIC

CellState - class genegui.CellState.

CellState.java A class used in conjuction with ModelState.

CellState() - Constructor for class genegui.CellState

Simple constructor does little to be proud of.

CellState(int) - Constructor for class genegui.CellState

Main constructor assigns a 0 value to all nodes.

CellSurfaceViewer - class genegui.CellSurfaceViewer.

CellViewer.java This is a re-write of the CellViewer class to make it more efficient and possibly less silly.

CellSurfaceViewer(Model, MainGui, String, boolean) - Constructor for class genegui.CellSurfaceViewer

Simple constructor.

CellSurround2Stop - class stoppers.CellSurround2Stop.

A stopper that looks for a single cell with a high value of a Node, surrounded by cells with low values of that Node.

CellSurround2Stop() - Constructor for class stoppers.CellSurround2Stop

CellSurround2Stop(float) - Constructor for class stoppers.CellSurround2Stop

CellSurroundStop - class stoppers.CellSurroundStop.

A stopper that looks for a single cell with a high value of a Node, surrounded by cells with low values of that Node.

CellSurroundStop() - Constructor for class stoppers.CellSurroundStop

CellSurroundStop(float) - Constructor for class stoppers.CellSurroundStop

CellThresholdStop - class stoppers.CellThresholdStop.

CellThresholdStop() - Constructor for class stoppers.CellThresholdStop

CellThresholdStop(float) - Constructor for class stoppers.CellThresholdStop

CenterCenterDistanceStat - class stat.CenterCenterDistanceStat.

Calculates the distance between the centers of the current and compare parameter set arrays.

CenterCenterDistanceStat() - Constructor for class stat.CenterCenterDistanceStat

CenterIC - class initialconditions.CenterIC.

An initial condition class that sets a middle cell to one value and then the cells immediately surrounding that middle cell to a second value.

CenterIC() - Constructor for class initialconditions.CenterIC

CenterIC(String, int, int, float, float) - Constructor for class initialconditions.CenterIC

Chi(float, float, float) - Method in class affectors.Affector

Cleavage2A_ICAff - class affectors.Cleavage2A_ICAff.

This is one half of an affector that cleaves a single node into two other nodes.

Cleavage2A_ICAff() - Constructor for class affectors.Cleavage2A_ICAff

Cleavage2B_ICAff - class affectors.Cleavage2B_ICAff.

This is one half of an affector that cleaves a single node into two other nodes under the influence of an inhibitor.

Cleavage2B_ICAff() - Constructor for class affectors.Cleavage2B_ICAff

CleavageA_ECAff - class affectors.CleavageA_ECAff.

This is one half of an affector that cleaves a single node into two other nodes.

CleavageA_ECAff() - Constructor for class affectors.CleavageA_ECAff

CleavageA_ICAff - class affectors.CleavageA_ICAff.

This is one half of an affector that cleaves a single node into two other nodes.

CleavageA_ICAff() - Constructor for class affectors.CleavageA_ICAff

CleavageA_ICDipAff - class affectors.CleavageA_ICDipAff.

Diploid version of CleaveageA_ICAff.

CleavageA_ICDipAff() - Constructor for class affectors.CleavageA_ICDipAff

CleavageB_ECAff - class affectors.CleavageB_ECAff.

This is one half of an affector that cleaves a single node into two other nodes.

CleavageB_ECAff() - Constructor for class affectors.CleavageB_ECAff

CleavageB_ICAff - class affectors.CleavageB_ICAff.

This is one half of an affector that cleaves a single node into two other nodes.

CleavageB_ICAff() - Constructor for class affectors.CleavageB_ICAff

CleavageB_ICDipAff - class affectors.CleavageB_ICDipAff.

Diploid version of CleaveageB_ICAff.

CleavageB_ICDipAff() - Constructor for class affectors.CleavageB_ICDipAff

CleaveA_Aff - class affectors.CleaveA_Aff.

This is one half of an affector that cleaves a single cytoplasmic node into two other cytoplasmic nodes.

CleaveA_Aff() - Constructor for class affectors.CleaveA_Aff

CleaveB_Aff - class affectors.CleaveB_Aff.

This is one half of an affector that cleaves a single cytoplasmic node into two other cytoplasmic nodes.

CleaveB_Aff() - Constructor for class affectors.CleaveB_Aff

ColumnIC - class initialconditions.ColumnIC.

ColumnIC() - Constructor for class initialconditions.ColumnIC

ColumnIC(String, float, int) - Constructor for class initialconditions.ColumnIC

CompAct2Aff - class affectors.CompAct2Aff.

The simplest regulated transcription affector.

CompAct2Aff() - Constructor for class affectors.CompAct2Aff

Configuration - class genegui.Configuration.

Configuration() - Constructor for class genegui.Configuration

Console - class genegui.Console.

Console.java Implements an InternalJFrame "console" for displaying output from Ingeneue the standard and/or error output streams.

Console(String, PrintStream) - Constructor for class genegui.Console

ConstantInputAff - class affectors.ConstantInputAff.

This affector returns a constant value.

ConstantInputAff() - Constructor for class affectors.ConstantInputAff

ConstantLevelAff - class affectors.ConstantLevelAff.

This affector returns a constant value to cause the target node to go to the specified final value (Final) when coupled to constant linear decay.

ConstantLevelAff() - Constructor for class affectors.ConstantLevelAff

ConversionEAff - class affectors.ConversionEAff.

Generalized rate-based conversion of one Node to another.

ConversionEAff() - Constructor for class affectors.ConversionEAff

ConversionIAff - class affectors.ConversionIAff.

Generalized rate-based conversion of one Node to another.

ConversionIAff() - Constructor for class affectors.ConversionIAff

CooptimizerFunction - class iterators.CooptimizerFunction.

CooptimizerFunction(ModelRunner) - Constructor for class iterators.CooptimizerFunction

CrossCorrStat - class stat.CrossCorrStat.

Saves the cross-correlation coefficient between each two parameters in the wheel plot.

CrossCorrStat() - Constructor for class stat.CrossCorrStat

calcJacobian(float[], Cell, int, float) - Static method in class main.MoreMath

Calculates the jacobian matrix for the equations in a network around the Node values of the input cell.

calculateDefaultIntersect(Network) - Method in class main.AffectorTemplate

calculateDistancesToSet(ParameterSetArray) - Method in class parameters.ParameterSetArray

Calculated the minimum and maximum distances between parameter sets in this and the input parameter set array.

calculateStat() - Method in class stat.CenterCenterDistanceStat

calculateStat() - Method in class stat.DumpStat

calculateStat() - Method in class stat.DumpSuccessArrayStat

calculateStat() - Method in class stat.DumpValueFieldsStat

calculateStat() - Method in class stat.FilterParamsStat

calculateStat() - Method in class stat.ParamTendenciesStat

calculateStat() - Method in class stat.Stat

calculateStat() - Method in class stat.SummaryStat

calculateStat() - Method in class stat.ValueFieldHistogramStat

cellNumSides - Static variable in class main.Globals

The number of sides that each cell has

cells - Variable in class iterators.ModelIterator

cells - Variable in class main.Model

changeParameters(float[], int, ParameterSet) - Method in class parameterrules.DimerHalfMaxRule

changeParameters(float[], int, ParameterSet) - Method in class parameterrules.LessThanRule

changeParameters(float[], int, ParameterSet) - Method in class parameterrules.MultiplyParameterRule

changeParameters(float[], int, ParameterSet) - Method in class parameterrules.ParameterRule

This method should change parameters so that they conform to this rule.

changeParameters(float[], int, ParameterSet) - Method in class parameterrules.ProductBetweenRule

changeParameters(float[], int, ParameterSet) - Method in class parameterrules.RatioBetweenRule

changeValue(float) - Method in class initialconditions.InitialCondition

changeWarningInput(String) - Static method in class genegui.ErrorPopUp

characteristicTime - Static variable in class main.Globals

Some scaling adjustment, sort of like a partial non-dimensionalization for some affectors

checkBullseye(Cell[], float) - Method in class stoppers.CellSurround2Stop

Returns the maximum value of the target node in the surrounding cells.

checkDamping() - Method in class stoppers.OscillatorStop

checkDamping(float[], int, float[], int, float) - Method in class stoppers.OscillatorStopSpecial

checkForNaN() - Method in class main.ModelRunner

Checks through all nodes of all cells in the model to see whether any of them have out of range numbers (NaN).

ckGetErrorEstimate(int) - Method in class integrators.CashKarpIntegrator

ckGetErrorEstimate() - Method in class main.CalculatorNode

ckIntegrate() - Method in class main.CalculatorNode

ckUpdateToNewTimestep() - Method in class main.CalculatorNode

cleanUp() - Method in class main.Model

clear() - Method in class genegui.SuccessList

Clears the contents of the list.

clearAccumulatedParameterSets() - Method in class genegui.IteratorViewer

clearExperiment() - Method in class main.Cell

clearGUI() - Method in class genegui.MainGui

Clears all viewers, editors, etc.

clearNodes() - Method in class stoppers.CellThresholdStop

clearNodes() - Method in class stoppers.MultiNodeThresholdStop

clearSpawnedViewers() - Method in class genegui.IteratorViewer

clearStatic() - Static method in class affectors.Affector

cloneState() - Method in class genegui.CellState

Makes a clone of this CellState instance and returns it as a new CellState instance.

cloneState() - Method in class genegui.ModelState

Makes a duplicate of this model state.

close() - Method in class genegui.MainGui

Routine to cleanly shutdown the GUI.

close() - Method in class genegui.SingleCellSelector

Called to properly close the cell selection window

close() - Static method in class main.GeneNet

Do a tidy shutdown of the program

closeGlobalOutfile() - Static method in class main.GlobalIO

closeModelStateView(ModelStateView) - Method in class genegui.ModelStateEditor

To be called by the ModelState when a modelStateView is being closed down.

collapse() - Method in class integrators.Integrator.NVmatrix

I haven't yet had the heart to test this messy thing...

collapse() - Method in class integrators.Integrator.NVvector

collapse() returns an array of floats without the unused spaces associated with unsided Nodes; the purpose of this is to facilitate the use of canned matrix operation routines (should we need to), which won't know anything about sided-ness and so on.

commentChar(int) - Method in class main.BetterTokenizer

* Specified that the character argument starts a single-line * comment.

compare(Object, Object) - Method in interface main.MoreMath.Comparer

The interface implementation should compare the two * objects and return an int using these rules: * if (a > b) return > 0; * if (a == b) return 0; * if (a < b) return < 0;

compare(Object, Object) - Method in class stat.ParamTendenciesStat

computeStripeScore() - Method in class stoppers.FPStripeStop

computeStripeScore() - Method in class stoppers.SimpleStop

continueEvaluate(ParameterSet) - Method in class iterators.Function

//ELI 7/7/99 Use this method to continue evaluating a function without resetting anything.

continueF(float[]) - Method in class iterators.ModelIterator

//ELI 7/7/99 This method calls Function.continueEvaluate() to continue evaluating whatever function was running before.

convertToNVvector(NodeValues[]) - Method in class integrators.Integrator.NVvector

Use this to copy an array of NodeValues objects into a pre-made NVvector.

convertToNodeValues(Integrator.NVvector) - Method in class integrators.Integrator.NVvector

Use this if you want a copy of this vector in the form of an array of NodeValues objects.

copy() - Method in class affectors.Affector

copy() - Method in class affectors.EnhancerRegionAff

copy() - Method in class affectors.MultiEnhancerAff

copy() - Method in class affectors.Product

copy() - Method in class affectors.ProductAff

copy() - Method in class affectors.SaturationEnhancerAff

copy() - Method in class affectors.SumAff

copy() - Method in class iterators.ACSCIterator

copy() - Method in class iterators.ACSC_SwitchIterator

copy() - Method in class iterators.CooptimizerFunction

copy() - Method in class iterators.EllipIterator

copy() - Method in class iterators.FilterCamIterator

copy() - Method in class iterators.FindVolumeIterator

copy() - Method in class iterators.Function

copy() - Method in class iterators.ModelIterator

copy() - Method in class iterators.PhasePortraitIterator

copy() - Method in class iterators.PowellIterator

// ******* This version of F for diagnostic purposes only public float F(float [] thePoint) { numFunctionCalls++; return (10 + SQR(thePoint[0]) + SQR(thePoint[1])); } // ******* This version of F for diagnostic purposes only //

copy() - Method in class iterators.RandInitRunIterator

copy() - Method in class iterators.SteepestDescentIterator

copy() - Method in class iterators.SurfaceIterator

copy() - Method in class iterators.TransectIterator

copy() - Method in class iterators.VulvaClassifyIterator

copy() - Method in class main.CalculatorNode

copy() - Method in class main.Node

copy() - Method in class parameterrules.BoundaryRule

copy() - Method in class parameterrules.LessThanRule

copy() - Method in class parameterrules.MultiplyParameterRule

copy() - Method in class parameterrules.ParameterRule

copy() - Method in class parameterrules.ParameterRuleSet

copy() - Method in class parameterrules.RatioBetweenRule

copy() - Method in class parameters.Parameter

copy() - Method in class parameters.ParameterSet

copyCellValues(int, int) - Method in class genegui.ModelState

Copies all the values for one cell to another

copyInto(NodeValues) - Method in class integrators.NodeValues

Provide a pre-made NodeValues object as an argument.

copyNVarray(NodeValues[], NodeValues[]) - Method in class integrators.Integrator

copyNumber - Variable in class affectors.Affector

copyValueFieldNames(ParameterSet) - Method in class parameters.ParameterSet

copy_(Affector) - Method in class affectors.Affector

createModel() - Method in class main.NetworkFile

Make a new Model from the currently stored text.

D

DEGRADATION - Static variable in class affectors.Affector

Type.[TERMTYPE] values;

DecayAff - class affectors.DecayAff.

This is the standard affector for decay of a Node.

DecayAff() - Constructor for class affectors.DecayAff

DecayRegDownAff - class affectors.DecayRegDownAff.

Use this for decay of a Node when the decay rate can be lowered (half life raised) by the presence of another node.

DecayRegDownAff() - Constructor for class affectors.DecayRegDownAff

DecayRegUpAff - class affectors.DecayRegUpAff.

Use this for decay of a Node when the decay rate can be raised (half life lowered) by the presence of another node.

DecayRegUpAff() - Constructor for class affectors.DecayRegUpAff

DefinedValuesAff - class affectors.DefinedValuesAff.

An artificial Affector which brings a Node from its initial value to a second value starting at a specified time and taking a specified amount of time to do the change.

DefinedValuesAff() - Constructor for class affectors.DefinedValuesAff

DefinedValuesIndicatorAff - class affectors.DefinedValuesIndicatorAff.

An artificial Affector which sets nodes to specific values.

DefinedValuesIndicatorAff() - Constructor for class affectors.DefinedValuesIndicatorAff

Dephosphor1StepA_ICAff - class affectors.Dephosphor1StepA_ICAff.

This is one half of an affector that dephosphorylates a single node at a speed determined by a phosphatase enzyme according to a sigmoid curve.

Dephosphor1StepA_ICAff() - Constructor for class affectors.Dephosphor1StepA_ICAff

Dephosphor1StepB_ICAff - class affectors.Dephosphor1StepB_ICAff.

This is one half of an affector that dephosphorylates a single node.

Dephosphor1StepB_ICAff() - Constructor for class affectors.Dephosphor1StepB_ICAff

DephosphorylateA_Aff - class affectors.DephosphorylateA_Aff.

This is one half of an affector that dephosphorylates a single node assuming a constant background phosphotase activity.

DephosphorylateA_Aff() - Constructor for class affectors.DephosphorylateA_Aff

DephosphorylateB_Aff - class affectors.DephosphorylateB_Aff.

This is one half of an affector that dephosphorylates a single node assuming a constant background phosphotase activity.

DephosphorylateB_Aff() - Constructor for class affectors.DephosphorylateB_Aff

DephosphorylationA_ICAff - class affectors.DephosphorylationA_ICAff.

This is one half of an affector that dephosphorylates a single node at a speed determined by a phosphatase enzyme according to a sigmoid curve.

DephosphorylationA_ICAff() - Constructor for class affectors.DephosphorylationA_ICAff

DephosphorylationB_ICAff - class affectors.DephosphorylationB_ICAff.

This is one half of an affector that dephosphorylates a single node.

DephosphorylationB_ICAff() - Constructor for class affectors.DephosphorylationB_ICAff

DimerHalfMaxRule - class parameterrules.DimerHalfMaxRule.

Because of the way things are scaled, dimers can have concentrations more than 1.

DimerizeAllMembrane_AAff - class affectors.DimerizeAllMembrane_AAff.

This is one half of a dimerization where the ligand and receptor can bind within the same membrane as well as across different faces.

DimerizeAllMembrane_AAff() - Constructor for class affectors.DimerizeAllMembrane_AAff

DimerizeAllMembrane_BAff - class affectors.DimerizeAllMembrane_BAff.

This is the other half of a dimerization where the ligand and receptor can bind within the same membrane as well as across different faces.

DimerizeAllMembrane_BAff() - Constructor for class affectors.DimerizeAllMembrane_BAff

DimerizeCrossMembrane_AAff - class affectors.DimerizeCrossMembrane_AAff.

This is one half of a membrane-bound dimerization reaction where one single Node resides in one cell and the other single Node resides in a neighboring cell.

DimerizeCrossMembrane_AAff() - Constructor for class affectors.DimerizeCrossMembrane_AAff

DimerizeCrossMembrane_BAff - class affectors.DimerizeCrossMembrane_BAff.

This is the other half of a membrane-bound dimerization reaction where one single Node resides in one cell and the other single Node resides in a neighboring cell.

DimerizeCrossMembrane_BAff() - Constructor for class affectors.DimerizeCrossMembrane_BAff

DimerizeCytoMem_AAff - class affectors.DimerizeCytoMem_AAff.

This is one third of a dimerization between a membrane bound and a cytoplasmic protein, leading to a membrane bound complex.

DimerizeCytoMem_AAff() - Constructor for class affectors.DimerizeCytoMem_AAff

DimerizeCytoMem_BAff - class affectors.DimerizeCytoMem_BAff.

This is one third of a heterodimerization between a membrane bound and a cytoplasmic protein, leading to a membrane-bound complex.

DimerizeCytoMem_BAff() - Constructor for class affectors.DimerizeCytoMem_BAff

DimerizeCytoMem_CAff - class affectors.DimerizeCytoMem_CAff.

This is the third half of a heterodimerization between a membrane-bound and a cytoplasmic protein, leading to a membrane-bound complex.

DimerizeCytoMem_CAff() - Constructor for class affectors.DimerizeCytoMem_CAff

DimerizeMemCyto_AAff - class affectors.DimerizeMemCyto_AAff.

This is one third of a dimerization between a membrane bound and a cytoplasmic protein, leading to a cytoplasmic complex.

DimerizeMemCyto_AAff() - Constructor for class affectors.DimerizeMemCyto_AAff

DimerizeMemCyto_BAff - class affectors.DimerizeMemCyto_BAff.

This is one third of a heterodimerization between a membrane bound and a cytoplasmic protein, leading to a cytoplasmic complex.

DimerizeMemCyto_BAff() - Constructor for class affectors.DimerizeMemCyto_BAff

DimerizeMemCyto_CAff - class affectors.DimerizeMemCyto_CAff.

This is the third half of a heterodimerization between a membrane-bound and a cytoplasmic protein, leading to a cytoplasmic complex.

DimerizeMemCyto_CAff() - Constructor for class affectors.DimerizeMemCyto_CAff

Dimerize_AAff - class affectors.Dimerize_AAff.

This is the one half of a dimerization where both undimerized Nodes reside in the same cell.

Dimerize_AAff() - Constructor for class affectors.Dimerize_AAff

Dimerize_BAff - class affectors.Dimerize_BAff.

This is the one half of a dimerization where both undimerized Nodes reside in the same cell.

Dimerize_BAff() - Constructor for class affectors.Dimerize_BAff

DissociationA_Aff - class affectors.DissociationA_Aff.

One third of a triplet of affectors which mediates dissociation of protein complexes.

DissociationA_Aff() - Constructor for class affectors.DissociationA_Aff

DissociationB_Aff - class affectors.DissociationB_Aff.

One third of a triplet of affectors which mediates dissociation of protein complexes.

DissociationB_Aff() - Constructor for class affectors.DissociationB_Aff

DissociationC_Aff - class affectors.DissociationC_Aff.

One third of a triplet of affectors which mediates dissociation of protein complexes.

DissociationC_Aff() - Constructor for class affectors.DissociationC_Aff

DissociationCytoMemA_Aff - class affectors.DissociationCytoMemA_Aff.

One third of a triplet of affectors which mediates dissociation of protein complexes where one of the ligands is cytoplasmic and the other is membrane-bound.

DissociationCytoMemA_Aff() - Constructor for class affectors.DissociationCytoMemA_Aff

DissociationCytoMemB_Aff - class affectors.DissociationCytoMemB_Aff.

One third of a triplet of affectors which mediates dissociation of protein complexes where one of the ligands is cytoplasmic and the other is membrane-bound.

DissociationCytoMemB_Aff() - Constructor for class affectors.DissociationCytoMemB_Aff

DissociationCytoMemC_Aff - class affectors.DissociationCytoMemC_Aff.

One third of a triplet of affectors which mediates dissociation of protein complexes where one of the ligands is cytoplasmic and the other is membrane-bound.

DissociationCytoMemC_Aff() - Constructor for class affectors.DissociationCytoMemC_Aff

DissociationEC_Com_Aff - class affectors.DissociationEC_Com_Aff.

One third of a triplet of affectors which mediates dissociation of receptor-ligand complexes.

DissociationEC_Com_Aff() - Constructor for class affectors.DissociationEC_Com_Aff

DissociationEC_Lig_Aff - class affectors.DissociationEC_Lig_Aff.

One third of a triplet of affectors which mediates dissociation of receptor-ligand complexes.

DissociationEC_Lig_Aff() - Constructor for class affectors.DissociationEC_Lig_Aff

DissociationEC_Rec_Aff - class affectors.DissociationEC_Rec_Aff.

One third of a triplet of affectors which mediates dissociation of receptor-ligand complexes.

DissociationEC_Rec_Aff() - Constructor for class affectors.DissociationEC_Rec_Aff

DumpStat - class stat.DumpStat.

Saves the values of the parameters in each parameter set to a file.

DumpStat() - Constructor for class stat.DumpStat

DumpSuccessArrayStat - class stat.DumpSuccessArrayStat.

A way of getting a list of the parameter sets which did or didn't pass some test.

DumpSuccessArrayStat() - Constructor for class stat.DumpSuccessArrayStat

DumpValueFieldsStat - class stat.DumpValueFieldsStat.

Saves the values of the value fields stored with each parameter set to a file.

DumpValueFieldsStat() - Constructor for class stat.DumpValueFieldsStat

deleting() - Method in class parameters.ParameterSetArray

Call this before deleting the param set array.

deselectAllCells() - Method in class genegui.ModelStateView

Deselects all cells.

didBomb() - Method in class iterators.ModelIterator

didPass() - Method in class iterators.ACSCIterator

didPass() - Method in class iterators.ACSC_SwitchIterator

didPass() - Method in class iterators.ModelIterator

didPass() - Method in class iterators.VulvaClassifyIterator

didPass() - Method in class parameters.ParameterSet

didPass(float) - Method in class stoppers.CellSurround2Stop

didPass() - Method in class stoppers.CellSurround2Stop

didPass() - Method in class stoppers.CellThresholdStop

didPass(float) - Method in class stoppers.CellThresholdStop

didPass(float) - Method in class stoppers.FindMaxRatioStop

didPass() - Method in class stoppers.FindMaxRatioStop

didPass() - Method in class stoppers.MetaFPStripeStop

didPass() - Method in class stoppers.MetaStop

didPass(float) - Method in class stoppers.MetaStop

didPass() - Method in class stoppers.MetaStopTwo

didPass(float) - Method in class stoppers.MetaStopTwo

didPass(float) - Method in class stoppers.NeuroNoiseStop

didPass() - Method in class stoppers.NeuroNoiseStop

didPass(float) - Method in class stoppers.NeuroTest2Stop

didPass() - Method in class stoppers.NeuroTest2Stop

didPass(float) - Method in class stoppers.NeuroTest3Stop

didPass() - Method in class stoppers.NeuroTest3Stop

didPass(float) - Method in class stoppers.OscillatorStop

didPass() - Method in class stoppers.OscillatorStop

didPass(float) - Method in class stoppers.OscillatorStopSpecial

didPass() - Method in class stoppers.OscillatorStopSpecial

didPass() - Method in class stoppers.SimpleStop

didPass(float) - Method in class stoppers.SimpleStop

didPass(float) - Method in class stoppers.TwoCellDifferenceStop

didPass() - Method in class stoppers.TwoCellDifferenceStop

displaySelected(JPanel) - Method in class genegui.NetworkViewer2

Sets the content of the JPanel on the rightside of the JSplitPanel.

doReset() - Method in class main.ModelRunner

doRun() - Method in class iterators.ACSCIterator

doRun() - Method in class iterators.ACSC_SwitchIterator

doRun() - Method in class iterators.EllipIterator

// ******* This version of theFunction for diagnostic purposes only public float F(float [] thePoint) { double score,x3eight,sinx3eight,fac0,fac1,fac2,fac3; numFunctionCalls++; x3eight= 8.0 * thePoint[3]; sinx3eight = Math.sin(x3eight); sinx3eight = thePoint[3] * sinx3eight*sinx3eight; fac0 = 5.0 * (thePoint[0] - sinx3eight); score = fac0*fac0; fac1 = 5.0 * (thePoint[1] - sinx3eight); score += fac1*fac1; fac2 = Math.cos(x3eight); fac2 = 5.0 * (thePoint[2] - fac2*fac2); score += fac2*fac2; fac3 = 0.5 * Math.abs(thePoint[3]); score += fac3; return (float)score; } // ******* This version of theFunction for diagnostic purposes only //

doRun() - Method in class iterators.FilterCamIterator

doRun() - Method in class iterators.FindVolumeIterator

doRun() - Method in class iterators.MatingIterator

doRun() - Method in class iterators.ModelIterator

doRun() - Method in class iterators.PhasePortraitIterator

doRun() - Method in class iterators.PopEvolveExpanderIterator

doRun() - Method in class iterators.PowellIterator

doRun() - Method in class iterators.RandInitRunIterator

doRun() - Method in class iterators.SteepestDescentIterator

// ******* This version of theFunction for diagnostic purposes only public float F(float [] thePoint) { double score,x3eight,sinx3eight,fac0,fac1,fac2,fac3; numFunctionCalls++; x3eight= 8.0 * thePoint[3]; sinx3eight = Math.sin(x3eight); sinx3eight = thePoint[3] * sinx3eight*sinx3eight; fac0 = 5.0 * (thePoint[0] - sinx3eight); score = fac0*fac0; fac1 = 5.0 * (thePoint[1] - sinx3eight); score += fac1*fac1; fac2 = Math.cos(x3eight); fac2 = 5.0 * (thePoint[2] - fac2*fac2); score += fac2*fac2; fac3 = 0.5 * Math.abs(thePoint[3]); score += fac3; return (float)score; } // ******* This version of F for diagnostic purposes only //

doRun() - Method in class iterators.SurfaceIterator

doRun() - Method in class iterators.TransectIterator

doRun() - Method in class iterators.UberIterator

doRun() - Method in class iterators.VulvaClassifyIterator

doRun() - Method in class main.ModelRunner

This has the code which actually runs a model.

doStartRun() - Method in class iterators.ModelIterator

doStartRun() - Method in class main.ModelRunner

Call doStartRun() to initialize a model for running it.

doStep() - Method in class main.ModelRunner

doesContainTarget(Node) - Method in class affectors.Affector

draw(Graphics, int, int, int, double[], double[]) - Method in class parameters.ParameterSet

ParameterSet objects can draw themselves as cam's using this draw command.

E

END_OF_RUN - Static variable in class main.Model

EXIT - Static variable in interface genegui.GuiInterface

EllipIterator - class iterators.EllipIterator.

EllipIterator() - Constructor for class iterators.EllipIterator

EndoEAff - class affectors.EndoEAff.

For endocytosis from an extracellular node - sided; use this one in the node that is getting endocytosed.

EndoEAff() - Constructor for class affectors.EndoEAff

EndoIAff - class affectors.EndoIAff.

For endocytosis to an intracellular node - non-sided; use this one in the node representing the intracellular compartment.

EndoIAff() - Constructor for class affectors.EndoIAff

EnhancerRegionAff - class affectors.EnhancerRegionAff.

EnhancerRegion surrounds other enhancers and multiplies them by the scaling (characteristicTime / halfLife).

EnhancerRegionAff() - Constructor for class affectors.EnhancerRegionAff

EnzymeConversionEC_Pro_Aff - class affectors.EnzymeConversionEC_Pro_Aff.

This is one half of an affector that converts a single node into another based on some enzymatic activity.

EnzymeConversionEC_Pro_Aff() - Constructor for class affectors.EnzymeConversionEC_Pro_Aff

EnzymeConversionEC_Sub_Aff - class affectors.EnzymeConversionEC_Sub_Aff.

This is one half of an affector that converts a single node into another based on some enzymatic activity.

EnzymeConversionEC_Sub_Aff() - Constructor for class affectors.EnzymeConversionEC_Sub_Aff

ErrorPopUp - class genegui.ErrorPopUp.

ErrorPopUp.java

ErrorPopUp() - Constructor for class genegui.ErrorPopUp

ExoEAff - class affectors.ExoEAff.

For exocytosis from an intracellular to a membrane-bound Node.

ExoEAff() - Constructor for class affectors.ExoEAff

ExoIAff - class affectors.ExoIAff.

For exocytosis from an intracellular to a membrane-bound Node.

ExoIAff() - Constructor for class affectors.ExoIAff

Experiment - class main.Experiment.

This class is supposed to be able to conduct experiments on the currently loaded net.

Experiment() - Constructor for class main.Experiment

Experiment(Model, String) - Constructor for class main.Experiment

echoOff() - Static method in class main.GeneralInput

echoOn(PrintWriter) - Static method in class main.GeneralInput

eigenvalues(float[], int, float[], float[]) - Static method in class main.MoreMath

Numerical recipes in C code for finding eigenvalues of a general, real, non-symmetric matrix.

endExperiment() - Method in class main.Experiment

eolIsSignificant(boolean) - Method in class main.BetterTokenizer

Determines whether or not ends of line are treated as tokens.

evaluate(ParameterSet) - Method in class iterators.CooptimizerFunction

evaluate(ParameterSet) - Method in class iterators.Function

this is the default evaluate method that just runs this models runner with its native stopper and parameter values defined by pars.

evaluate(ParameterSet) - Method in class iterators.ICSamplingFunction

evaluate(ParameterSet) - Method in class iterators.ICVaryingFunction

evaluate(ParameterSet) - Method in class iterators.UberIteratorFunction

F

F(float[]) - Method in class iterators.ModelIterator

FF - Static variable in class affectors.Affector

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

FPStripeStop - class stoppers.FPStripeStop.

FPStripeStop() - Constructor for class stoppers.FPStripeStop

FileEditor - class genegui.FileEditor.

General purpose file editor used for editing model files.

FileEditor() - Constructor for class genegui.FileEditor

Simple constructor.

FileEditor(StyledDocument) - Constructor for class genegui.FileEditor

Less simple constructor.

FilterCamIterator - class iterators.FilterCamIterator.

This class is only an iterator for convenience.

FilterCamIterator() - Constructor for class iterators.FilterCamIterator

FilterParamsStat - class stat.FilterParamsStat.

FilterParamsStat() - Constructor for class stat.FilterParamsStat

FindMaxRatioStop - class stoppers.FindMaxRatioStop.

A stopper that measures the maximum ratio between a node's concentration in two different cells over some time.

FindMaxRatioStop() - Constructor for class stoppers.FindMaxRatioStop

FindMaxRatioStop(float) - Constructor for class stoppers.FindMaxRatioStop

FindVolumeIterator - class iterators.FindVolumeIterator.

FindVolumeIterator() - Constructor for class iterators.FindVolumeIterator

Formula1Aff - class affectors.Formula1Aff.

A relic Affector.

Formula1Aff() - Constructor for class affectors.Formula1Aff

Function - class iterators.Function.

Function() - Constructor for class iterators.Function

Function(ModelRunner) - Constructor for class iterators.Function

f1 - Variable in class iterators.MultiFloatReturn

f2 - Variable in class iterators.MultiFloatReturn

f3 - Variable in class iterators.MultiFloatReturn

f4 - Variable in class iterators.MultiFloatReturn

finalScore - Variable in class iterators.ModelIterator

finalize() - Method in class main.Globals

findIDTag(BetterTokenizer, String) - Static method in class main.GeneralInput

findNextIDToken(BetterTokenizer) - Static method in class main.GeneralInput

findOrCreateParam(String) - Static method in class affectors.Affector

for use of the CalculatorNode or other things that need to look up parameters if they already exist but make them if they do not...

findParam(String) - Static method in class affectors.Affector

firstFreeParam - Static variable in class affectors.Affector

fixAllAffectors(Cell) - Method in class main.CalculatorNode

fixNodes(Cell, String[]) - Method in class affectors.Affector

fixNodes(Cell, String[]) - Method in class affectors.DimerizeAllMembrane_AAff

Overridden because this affector uses the same node in two places.

fixNodes(Cell, String[]) - Method in class affectors.DimerizeAllMembrane_BAff

Overridden because this affector uses the same node in two places.

fixNodes(Cell, String[]) - Method in class affectors.HeatShockAff

fixNodes(Cell, String[]) - Method in class affectors.MxferInAff

Overridden because this affector uses the same node in two places.

fixNodes(Cell, String[]) - Method in class affectors.MxferOutAff

Overridden because this affector uses the same node in two places.

fixNodes(Cell, String[]) - Method in class affectors.Txn1ECAff

fixNodes(Cell, String[]) - Method in class affectors.Txn2bAff

fixNodes(Cell, String[]) - Method in class affectors.Txn2bDipAff

fixNodes(Cell, String[]) - Method in class affectors.XferInAff

Overridden because this affector uses the same node in seven places.

flag - Static variable in class main.Globals

G

GAUSSIAN - Static variable in class main.MoreMath

GG - Static variable in class affectors.Affector

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

GRAPH_BAR - Static variable in class genegui.CellSurfaceViewer

GRAPH_CELL - Static variable in class genegui.CellSurfaceViewer

GRAPH_FUNCTION_EXP - Static variable in class genegui.CellSurfaceViewer

GRAPH_FUNCTION_EXP - Static variable in class genegui.NetworkViewer2

GRAPH_FUNCTION_LINEAR - Static variable in class genegui.CellSurfaceViewer

GRAPH_FUNCTION_LINEAR - Static variable in class genegui.NetworkViewer2

GRAPH_FUNCTION_LOG - Static variable in class genegui.CellSurfaceViewer

GRAPH_FUNCTION_LOG - Static variable in class genegui.NetworkViewer2

GRAPH_FUNCTION_PSUEDO - Static variable in class genegui.CellSurfaceViewer

GRAPH_FUNCTION_PSUEDO - Static variable in class genegui.NetworkViewer2

GRAPH_FUNCTION_THRESH - Static variable in class genegui.CellSurfaceViewer

GRAPH_FUNCTION_THRESH - Static variable in class genegui.NetworkViewer2

GUI_CAPABLE - Static variable in class affectors.Affector

Position meanings for Type[].

GeneNet - class main.GeneNet.

GeneNet.java The MainClass.

GeneNet() - Constructor for class main.GeneNet

GeneNetInterface - class genegui.GeneNetInterface.

GeneNetInterface() - Constructor for class genegui.GeneNetInterface

GeneralInput - class main.GeneralInput.

GeneralInput() - Constructor for class main.GeneralInput

GlobalIO - class main.GlobalIO.

GlobalIO() - Constructor for class main.GlobalIO

Globals - class main.Globals.

Contains all the global parameters of our model which

Globals() - Constructor for class main.Globals

GuiInterface - interface genegui.GuiInterface.

GuiInterface.java This interface provides all the methods that need to be implemeted by classes in the GUI that need to respond to changes in the node and effector templates, parameter set or over-all network or cell surface layout.

genegui - package genegui

getActiveDisplayMode() - Method in class genegui.NetworkViewer2

Returns the ActiveDisplayMode boolean value.

getActiveModelStateView() - Method in class genegui.ModelState

Gets the currently active (selected) ModelStateView.

getAffector() - Method in class genegui.InspectorList

getAffector() - Method in class main.AffectorTemplate

getAffectorDisplays() - Method in class genegui.NetworkPaintPanel.NodeDisplay

Returns an enumeration on all the AFfectorDisplays that are associated with this node (as inputs).

getAffectorName() - Method in class main.AffectorTemplate

getAffectorParameters() - Method in class main.AffectorTemplate

This function returns an enumeration of a vector containing the numbers of each of the affectors parameters (as Integers).

getAffectorSelectedColor() - Method in class genegui.NetworkPaintPanel

Returns the color of selected AffectorDisplays.

getAffectorTemplate() - Method in class genegui.NetworkPaintPanel.AffectorDisplay

Rerturns the AffectorTemplate that this AffectorDisplay represents.

getAffectors() - Method in class main.NodeTemplate

getAffectorsForNode(int) - Method in class main.Network

getAffectorsValue(int) - Method in class main.Node

getAffectorsValue(float[]) - Method in class main.Node

getCell() - Method in class genegui.InspectorList

getCell(Model) - Method in class main.NodeSpecifier

getCellIndex() - Method in class genegui.SingleCellSelector

Returns the selected cell index

getCellNum() - Method in class main.NodeSpecifier

getCellPosition() - Method in class genegui.CellState

Returns the location of the cell.

getCellShape() - Method in class main.Cell

Returns the cells shape.

getCellState(int) - Method in class genegui.ModelState

Returns the CellState for the cell with the given index.

getCellStateArray() - Method in class genegui.ModelState

Returns the CellStateArray - Used by serialization

getCells() - Method in class main.ModelRunner

getColor() - Method in class main.NodeTemplate

getCompareParamSetArray() - Static method in class main.Globals

getConfiguration() - Method in class genegui.MainGui

Returns the current program configuration object.

getCopyOfMatrix() - Method in class integrators.Integrator.NVmatrix

Use this if you want a freshly-made copy of the values matrix in the form of a 2D array of floats

getCopyOfMatrix(float[][]) - Method in class integrators.Integrator.NVmatrix

Use this one if you want the values matrix copied into a pre-allocated 2D array of floats

getCopyOfVector() - Method in class integrators.Integrator.NVvector

Use this if you want a freshly-made copy of the values vector in the form of an array of floats

getCopyOfVector(float[]) - Method in class integrators.Integrator.NVvector

Use this one if you want the values vector copied into a pre-allocated array of floats

getCurParamSetArray() - Static method in class main.Globals

getCurSet() - Method in class parameters.ParameterSetArray

getCurSetNum() - Method in class parameters.ParameterSetArray

getCurTag() - Method in class parameters.ParameterSetArray

getCurTagNum() - Method in class parameters.ParameterSetArray

getCurrentValues(NodeValues[]) - Method in class integrators.Integrator

getDefaultInitialValue(int) - Method in class initialconditions.InitialConditionSet

getDerivatives(NodeValues[]) - Method in class integrators.Integrator

getEnhancerTemplates() - Method in class main.AffectorTemplate

Returns an Enumeration on the enhancerTemplates Vector.

getErrorEstimate() - Method in class integrators.Integrator

Returns an estimate of the error introduced per timestep.

getEventSetDescriptors() - Method in class genegui.SuccessListBeanInfo

getFhatAndDfdyi(NodeValues[], NodeValues[]) - Method in class integrators.BackwardEulerIntegrator

getFhatAndDfdyi(NodeValues[], NodeValues[]) - Method in class integrators.SemiExplicitAPCIntegrator

getFieldName(int) - Method in class parameters.ParameterSet

getFieldPos(String) - Method in class parameters.ParameterSet

getFieldValue(int) - Method in class parameters.ParameterSet

getFieldValue(String) - Method in class parameters.ParameterSet

getFilename() - Method in class parameters.ParameterSetArray

getFrame() - Method in class genegui.Console

getFrame(Component) - Static method in class main.GeneralInput

getFuzzyParametersScore(float[]) - Method in class parameterrules.ParameterRuleSet

getFuzzyParametersScore(float[]) - Method in class parameters.ParameterSet

getFuzzyScore(float[]) - Method in class parameterrules.BoundaryRule

getFuzzyScore(float[]) - Method in class parameterrules.DimerHalfMaxRule

getFuzzyScore(float[]) - Method in class parameterrules.LessThanRule

getFuzzyScore(float[]) - Method in class parameterrules.MultiplyParameterRule

getFuzzyScore(float[]) - Method in class parameterrules.ParameterRule

This method should return 0 if the parameters in the input set pass the criteria in this rule.

getFuzzyScore(float[]) - Method in class parameterrules.ProductBetweenRule

getFuzzyScore(float[]) - Method in class parameterrules.RatioBetweenRule

getGeneNet() - Method in class genegui.MainGui

Returns the GeneNet object interfaced with by this GUI.

getGood(int) - Method in class stoppers.NoChangeStop

getGroupNum() - Method in class parameters.ParameterSet

getHeight() - Method in class genegui.Console

getHighThreshold() - Method in class parameters.ParameterSetArray

getHowStable() - Method in class stoppers.FPStripeStop

getHowStable() - Method in class stoppers.SimpleStop

getHybridityScore(ParameterSet, ParameterSet) - Method in class iterators.PopEvolveExpanderIterator

getIcon() - Method in class main.NodeTemplate

Returns the ImagIcon that is used to represnt this type of node for various editors and viewers.

getInitialConditions(Model) - Method in class initialconditions.InitialConditionStorage

getInitialValue(String) - Method in class main.Cell

getInitialValue(int) - Method in class main.Cell

getInitialValue(int) - Method in class main.Model

Returns the default initial value for this node as given by its initializers object.

getIntegrationAlgorithm() - Static method in class main.Globals

getIntegrationValue(int) - Method in class main.CalculatorNode

getIntegrationValue() - Method in class main.CalculatorNode

getIntegrationValue() - Method in class main.Node

getIntegrationValue(int) - Method in class main.Node

getIntegratorClass(int) - Static method in class integrators.IntegratorList

getIntegratorName(int) - Static method in class integrators.IntegratorList

getIntersectX() - Method in class main.AffectorTemplate

getIntersectY() - Method in class main.AffectorTemplate

getIterator() - Method in class main.GeneNet

Returns the ModelIterator.

getIteratorFile() - Method in class genegui.Configuration

getItsNum() - Method in class main.Cell

getLastOpenedDir() - Method in class genegui.Configuration

getLastSavedDir() - Method in class genegui.Configuration

getLineNo() - Method in class main.ModelLoadingException

getLowThreshold() - Method in class parameters.ParameterSetArray

getLowerBound() - Method in class initialconditions.InitialCondition

getLowerBound(int) - Method in class parameters.ParameterSet

getLowerBounds() - Method in class parameters.ParameterSet

getMainProgram() - Static method in class main.Globals

getMaxAmplitude() - Method in class main.NoiseGenerator

getMaxFrequency() - Method in class main.NoiseGenerator

getMethodDescriptors() - Method in class genegui.ModelStateBeanInfo

getMethodDescriptors() - Method in class genegui.SuccessListBeanInfo

getMinFrequency() - Method in class main.NoiseGenerator

getMode() - Method in class genegui.ModelStateToolBox

Gets the current mode (which tool is selected).

getModel() - Method in class genegui.ModelState

Returns the Model that this is a ModelState for.

getModel() - Method in class main.GeneNet

Returns the Model loaded in this GeneNet.

getModel() - Method in class main.ModelRunner

getModel() - Method in class parameters.ParameterSet

getModelFile() - Method in class genegui.Configuration

getModelFile() - Static method in class main.Globals

getModelName() - Static method in class main.Globals

getModelParameterSet() - Method in class main.Model

getModelState(int) - Method in class genegui.SuccessList

Returns the ModelState from pair index.

getModelState() - Method in class main.Model

Returns the ModelState Object associated with this model

getModelStates() - Method in class genegui.SuccessList

getNCValue(Node) - Method in class affectors.Affector

getNCValue(Node) - Method in class affectors.Affector_Template

If the Affector uses its own Node's concentration in making its calculation, then you this method should return the same value as getValue() divided by the concentration of the Affectors' Node.

getNCValue(Node) - Method in class affectors.Cleavage2A_ICAff

getNCValue(Node) - Method in class affectors.CleavageA_ECAff

getNCValue(Node) - Method in class affectors.CleavageA_ICAff

getNCValue(Node) - Method in class affectors.CleavageA_ICDipAff

getNCValue(Node) - Method in class affectors.CleaveA_Aff

getNCValue(Node) - Method in class affectors.ConversionEAff

getNCValue(Node) - Method in class affectors.DecayAff

getNCValue(Node) - Method in class affectors.DecayRegDownAff

getNCValue(Node) - Method in class affectors.DecayRegUpAff

getNCValue(Node) - Method in class affectors.Dephosphor1StepA_ICAff

getNCValue(Node) - Method in class affectors.DephosphorylateA_Aff

getNCValue(Node) - Method in class affectors.DephosphorylationA_ICAff

getNCValue(Node) - Method in class affectors.DimerizeAllMembrane_AAff

getNCValue(Node) - Method in class affectors.DimerizeCrossMembrane_AAff

getNCValue(Node) - Method in class affectors.DimerizeCytoMem_AAff

getNCValue(Node) - Method in class affectors.DimerizeCytoMem_BAff

getNCValue(Node) - Method in class affectors.DimerizeMemCyto_AAff

getNCValue(Node) - Method in class affectors.DimerizeMemCyto_BAff

getNCValue(Node) - Method in class affectors.Dimerize_AAff

getNCValue(Node) - Method in class affectors.DissociationA_Aff

getNCValue(Node) - Method in class affectors.DissociationCytoMemA_Aff

getNCValue(Node) - Method in class affectors.DissociationEC_Com_Aff

getNCValue(Node) - Method in class affectors.EndoEAff

getNCValue(Node) - Method in class affectors.EnhancerRegionAff

Overrides Affector.getNCValue() to return the value of the wrapped enhancer multiplied by the scaling characteristicTime / halfLife

getNCValue(Node) - Method in class affectors.EnzymeConversionEC_Sub_Aff

getNCValue(Node) - Method in class affectors.ExoIAff

getNCValue(Node) - Method in class affectors.LMxferEAff

getNCValue(Node) - Method in class affectors.MultiEnhancerAff

Overrides Affector.getNCValue() to multiply together the values from all the subsidiary affectors.

getNCValue(Node) - Method in class affectors.MxferOutAff

getNCValue(Node) - Method in class affectors.Phosphor1StepA_ICAff

getNCValue(Node) - Method in class affectors.PhosphorylateA_Aff

getNCValue(Node) - Method in class affectors.PhosphorylationA_ICAff

getNCValue(Node) - Method in class affectors.Product

Overrides Affector.getNCValue() to multiply together the values from all the subsidiary affectors.

getNCValue(Node) - Method in class affectors.ProductAff

Overrides Affector.getNCValue() to multiply together the values from all the subsidiary affectors.

getNCValue(Node) - Method in class affectors.RecycleAAff

getNCValue(Node) - Method in class affectors.SaturationEnhancerAff

Overrides Affector.getNCValue() to multiply together the values from all the subsidiary affectors.

getNCValue(Node) - Method in class affectors.SumAff

Overrides Affector.getNCValue() to multiply together the values from all the subsidiary affectors.

getNCValue(Node) - Method in class affectors.VonForresterB_Aff

getNCValue(Node) - Method in class affectors.VonForresterB_ECAff

getNCValue(Node) - Method in class affectors.VonForresterB_ICAff

getNCValue(Node) - Method in class affectors.XferOutAff

getName(int) - Method in class genegui.SuccessList

Returns the name of the ParameterSet.

getName() - Method in class main.Model

getName() - Method in class main.Network

getName() - Method in class main.NodeTemplate

getName() - Method in class parameters.Parameter

getName(int) - Method in class parameters.ParameterSet

getNames() - Method in class genegui.SuccessList

Returns a vector with the names of all the results.

getNeighborNode(int, String) - Method in class main.Cell

getNetwork() - Method in class main.GeneNet

Returns the Network for the Model loaded in this GeneNet.

getNetwork() - Method in class main.Model

getNetworkFile() - Method in class main.GeneNet

getNextSet() - Method in class parameters.ParameterSetArray

getNode() - Method in class genegui.InspectorList

getNode(String) - Method in class main.Cell

getNode(int) - Method in class main.Network

getNode(String) - Method in class main.Network

getNode(Model) - Method in class main.NodeSpecifier

getNodeColor(int) - Method in class genegui.ModelState

Returns the color for this type of node.

getNodeDisplay() - Method in class genegui.NetworkPaintPanel.AffectorDisplay

Returns the NodeDisplay for the NodeTemplate that this Affector template belongs to.

getNodeDisplays() - Method in class genegui.NetworkPaintPanel

Returns an array with all thye NodeDisplays

getNodeName() - Method in class initialconditions.InitialCondition

getNodeNames() - Method in class main.AffectorTemplate

This function is here so that viewers can examine an affector.

getNodeNum(String) - Method in class main.Cell

getNodeNum() - Method in class main.Node

getNodeNum() - Method in class main.NodeSpecifier

getNodeNum() - Method in class main.NodeTemplate

getNodeSelectedColor() - Method in class genegui.NetworkPaintPanel

Returns the color of selected NodeDisplays.

getNodeShift(Affector, int, int) - Method in class genegui.NetworkPaintPanel.NodeDisplay

When we move a node in the network viewer, we also move the attached nodes a bit.

getNodeTemplate() - Method in class genegui.NetworkPaintPanel.NodeDisplay

Returns the NodeTemplate for this NodeDisplay.

getNodeTemplates() - Method in class genegui.ModelState

Returns the array of NodeTemplates.

getNodeValue(int) - Method in class genegui.CellState

Returns the value of a single node for this cell.

getNodeValueArray() - Method in class genegui.CellState

Returns an array with the values of all the nodes for this cell.

getNodes() - Method in class affectors.Affector

This function is here so that viewers can examine an affector.

getNodes() - Method in class affectors.EnhancerRegionAff

getNodes() - Method in class main.Network

getNodesForCell() - Method in class main.Network

getNoise() - Method in class main.Node

getNoise(float) - Method in class main.NoiseGenerator

getNumAffectors() - Method in class main.Node

getNumAffectors() - Method in class main.NodeTemplate

getNumCells() - Method in class main.ModelRunner

getNumFrequencies() - Method in class main.NoiseGenerator

getNumFuncCalls() - Method in class parameters.ParameterSet

getNumIntegrators() - Static method in class integrators.IntegratorList

getNumNodes() - Method in class affectors.Affector

getNumNodes() - Method in class main.ModelRunner

getNumNodes() - Method in class main.Network

getNumParamSetArrays() - Static method in class main.Globals

getNumParameters() - Method in class affectors.Affector

getNumParameters() - Method in class main.AffectorTemplate

Returns the number of parameters that this affector has.

getNumParams() - Method in class parameters.ParameterSet

getNumSets() - Method in class parameters.ParameterSetArray

getNumValueFields() - Method in class parameters.ParameterSet

getNumberOfCells() - Method in class genegui.ModelState

Returns the number of cells in the model.

getNumberOfNodes() - Method in class genegui.ModelState

Returns the number of different types of nodes in the model.

getOtherSide(int) - Static method in class affectors.Affector

getOutputFileName() - Method in class iterators.ModelIterator

Returns the name of the iterator output file.

getParVals() - Method in class parameters.ParameterSet

This is for setting an Iterator's internal parameter vector p

getParamName(int) - Static method in class affectors.Affector

getParamPos(String) - Static method in class affectors.Affector

This function should only be called when constructing a model from the init() function of an iterator.

getParamSetArray(int) - Static method in class main.Globals

getParamSetArray(String) - Static method in class main.Globals

getParamValue(int) - Static method in class affectors.Affector

Use this instead of getting a whole Parameter object if all you want is the value of a parameter identified by its position.

getParamValue(String) - Static method in class affectors.Affector

Use this instead of getting a whole Parameter object if all you want is the named parameter's value.

getParamVariationMode(int) - Static method in class affectors.Affector

getParameter(String) - Static method in class affectors.Affector

Use this to read a Parameter object, identified by name, from the static arrays held by Affector.

getParameter(int) - Static method in class affectors.Affector

Use this to read a Parameter object, identified by number, from the static arrays held by Affector.

getParameter(int) - Method in class parameters.ParameterSet

getParameterNames() - Method in class genegui.SuccessList

getParameterSet(int) - Method in class genegui.SuccessList

Returns the ParameterSet from pair index.

getParameterSet() - Method in class iterators.ModelIterator

Returns the current ParameterSet for the Iterator

getPosition(String) - Method in class parameters.ParameterSet

Gets the position of a parameter called "name" in this sets params array.

getPreviousSet() - Method in class parameters.ParameterSetArray

getPrototype() - Method in class parameters.ParameterSet

getPrototype() - Method in class parameters.ParameterSetArray

getRunTime() - Static method in class main.Globals

getScore(int) - Method in class genegui.SuccessList

Returns the name of the ParameterSet.

getScore() - Method in class parameters.ParameterSet

getScore() - Method in class stoppers.MetaStop

getScore() - Method in class stoppers.MetaStopTwo

getScore() - Method in class stoppers.SimpleStop

getScores() - Method in class genegui.SuccessList

getSelectedCells() - Method in class genegui.ModelStateView

Returns an array of all the cells that are selected.

getSelectedNodes() - Method in class genegui.ModelStateView

Returns an array of the selected (visible) nodes.

getSeparatedDeriv(float[], float[]) - Method in class main.Node

getSetNum(int) - Method in class parameters.ParameterSetArray

getShow() - Method in class main.NodeTemplate

getSpacer(int) - Method in class genegui.IteratorViewer

getStartDir() - Method in class genegui.Configuration

getState(ParameterSet) - Method in class iterators.ModelIterator

getStdDev(double, double, int) - Static method in class main.MoreMath

Returns the standard deviation.

getStdDev(float, float, int) - Static method in class main.MoreMath

getStopTime() - Method in class stoppers.MetaStop

getStopTime() - Method in class stoppers.MetaStopTwo

getStopTime() - Method in class stoppers.SimpleStop

getStopper() - Method in class iterators.Function

getStopper() - Method in class iterators.ModelIterator

getStopper() - Method in class main.ModelRunner

getSubaffector(int) - Method in class affectors.EnhancerRegionAff

getSum() - Method in class main.CalculatorNode

getSum() - Method in class main.Node

getTag() - Method in class parameters.ParameterSet

getTime() - Method in class genegui.ModelState

Returns the ModelState time

getTimestep() - Method in class integrators.CashKarpIntegrator

getToolBox() - Method in class genegui.ModelState

Returns the one and only ModelStateToolBox attached to this ModelState

getType() - Method in class main.NodeTemplate

getUpperBound() - Method in class initialconditions.InitialCondition

getUpperBound(int) - Method in class parameters.ParameterSet

getUpperBounds() - Method in class parameters.ParameterSet

getUsingGUI() - Static method in class main.Globals

getValue(Node) - Method in class affectors.Affector

getValue(Node) - Method in class affectors.Affector_Template

getValue(Node) - Method in class affectors.Cleavage2A_ICAff

getValue(Node) - Method in class affectors.Cleavage2B_ICAff

getValue(Node) - Method in class affectors.CleavageA_ECAff

getValue(Node) - Method in class affectors.CleavageA_ICAff

getValue(Node) - Method in class affectors.CleavageA_ICDipAff

getValue(Node) - Method in class affectors.CleavageB_ECAff

getValue(Node) - Method in class affectors.CleavageB_ICAff

getValue(Node) - Method in class affectors.CleavageB_ICDipAff

getValue(Node) - Method in class affectors.CleaveA_Aff

getValue(Node) - Method in class affectors.CleaveB_Aff

getValue(Node) - Method in class affectors.CompAct2Aff

getValue(Node) - Method in class affectors.ConstantInputAff

getValue(Node) - Method in class affectors.ConstantLevelAff

getValue(Node) - Method in class affectors.ConversionEAff

getValue(Node) - Method in class affectors.ConversionIAff

getValue(Node) - Method in class affectors.DecayAff

getValue(Node) - Method in class affectors.DecayRegDownAff

getValue(Node) - Method in class affectors.DecayRegUpAff

getValue(Node) - Method in class affectors.DefinedValuesAff

getValue(Node) - Method in class affectors.DefinedValuesIndicatorAff

getValue(Node) - Method in class affectors.Dephosphor1StepA_ICAff

getValue(Node) - Method in class affectors.Dephosphor1StepB_ICAff

getValue(Node) - Method in class affectors.DephosphorylateA_Aff

getValue(Node) - Method in class affectors.DephosphorylateB_Aff

getValue(Node) - Method in class affectors.DephosphorylationA_ICAff

getValue(Node) - Method in class affectors.DephosphorylationB_ICAff

getValue(Node) - Method in class affectors.DimerizeAllMembrane_AAff

getValue(Node) - Method in class affectors.DimerizeAllMembrane_BAff

getValue(Node) - Method in class affectors.DimerizeCrossMembrane_AAff

getValue(Node) - Method in class affectors.DimerizeCrossMembrane_BAff

getValue(Node) - Method in class affectors.DimerizeCytoMem_AAff

getValue(Node) - Method in class affectors.DimerizeCytoMem_BAff

getValue(Node) - Method in class affectors.DimerizeCytoMem_CAff

getValue(Node) - Method in class affectors.DimerizeMemCyto_AAff

getValue(Node) - Method in class affectors.DimerizeMemCyto_BAff

getValue(Node) - Method in class affectors.DimerizeMemCyto_CAff

getValue(Node) - Method in class affectors.Dimerize_AAff

getValue(Node) - Method in class affectors.Dimerize_BAff

getValue(Node) - Method in class affectors.DissociationA_Aff

getValue(Node) - Method in class affectors.DissociationB_Aff

getValue(Node) - Method in class affectors.DissociationC_Aff

getValue(Node) - Method in class affectors.DissociationCytoMemA_Aff

getValue(Node) - Method in class affectors.DissociationCytoMemB_Aff

getValue(Node) - Method in class affectors.DissociationCytoMemC_Aff

getValue(Node) - Method in class affectors.DissociationEC_Com_Aff

getValue(Node) - Method in class affectors.DissociationEC_Lig_Aff

getValue(Node) - Method in class affectors.DissociationEC_Rec_Aff

getValue(Node) - Method in class affectors.EndoEAff

getValue(Node) - Method in class affectors.EndoIAff

getValue(Node) - Method in class affectors.EnhancerRegionAff

Overrides Affector.getValue() to return the value of the wrapped enhancer multiplied by the scaling characteristicTime / halfLife

getValue(Node) - Method in class affectors.EnzymeConversionEC_Pro_Aff

getValue(Node) - Method in class affectors.EnzymeConversionEC_Sub_Aff

getValue(Node) - Method in class affectors.ExoEAff

getValue(Node) - Method in class affectors.ExoIAff

getValue(Node) - Method in class affectors.Formula1Aff

getValue(Node) - Method in class affectors.HeatShockAff

getValue(Node) - Method in class affectors.LMxferEAff

getValue(Node) - Method in class affectors.LMxferIAff

getValue(Node) - Method in class affectors.MultiEnhancerAff

Overrides Affector.getValue() to multiply together the values from all the subsidiary affectors.

getValue(Node) - Method in class affectors.MxferInAff

getValue(Node) - Method in class affectors.MxferOutAff

getValue(Node) - Method in class affectors.NoChangeAff

getValue(Node) - Method in class affectors.Phosphor1StepA_ICAff

getValue(Node) - Method in class affectors.Phosphor1StepB_ICAff

getValue(Node) - Method in class affectors.PhosphorylateA_Aff

getValue(Node) - Method in class affectors.PhosphorylateB_Aff

getValue(Node) - Method in class affectors.PhosphorylationA_ICAff

getValue(Node) - Method in class affectors.PhosphorylationB_ICAff

getValue(Node) - Method in class affectors.PlaceHolderAff

getValue(Node) - Method in class affectors.Product

Overrides Affector.getValue() to multiply together the values from all the subsidiary affectors.

getValue(Node) - Method in class affectors.ProductAff

Overrides Affector.getValue() to multiply together the values from all the subsidiary affectors.

getValue(Node) - Method in class affectors.PsiAff

getValue(Node) - Method in class affectors.PsiECAff

getValue(Node) - Method in class affectors.RecycleAAff

getValue(Node) - Method in class affectors.RecycleBAff

getValue(Node) - Method in class affectors.SaturationEnhancerAff

Overrides Affector.getValue() to multiply together the values from all the subsidiary affectors.

getValue(Node) - Method in class affectors.SumAff

Overrides Affector.getValue() to multiply together the values from all the subsidiary affectors.

getValue(Node) - Method in class affectors.TlnAff

getValue(Node) - Method in class affectors.TlnRegUpAff

getValue(Node) - Method in class affectors.Txn1Aff

getValue(Node) - Method in class affectors.Txn1ECAff

getValue(Node) - Method in class affectors.Txn2aAff

getValue(Node) - Method in class affectors.Txn2aDipAff

getValue(Node) - Method in class affectors.Txn2bAff

getValue(Node) - Method in class affectors.Txn2bDipAff

getValue(Node) - Method in class affectors.Txn3aAff

getValue(Node) - Method in class affectors.Txn3bAff

getValue(Node) - Method in class affectors.Txn4Aff

getValue(Node) - Method in class affectors.Txn4DipAff

getValue(Node) - Method in class affectors.Txn5Aff

getValue(Node) - Method in class affectors.Txn6aAff

getValue(Node) - Method in class affectors.Txn6bAff

getValue(Node) - Method in class affectors.TxnLeakyCyceAff

getValue(Node) - Method in class affectors.TxnSiteActInhibit2Aff

getValue(Node) - Method in class affectors.TxnSiteActInhibit3Aff

getValue(Node) - Method in class affectors.TxnSiteActInhibitAff

getValue(Node) - Method in class affectors.TxnSiteActivatorAff

getValue(Node) - Method in class affectors.TxnSiteAddInhibitorAff

getValue(Node) - Method in class affectors.TxnSiteInhibitorAff

getValue(Node) - Method in class affectors.VonForresterA_Aff

getValue(Node) - Method in class affectors.VonForresterA_ECAff

getValue(Node) - Method in class affectors.VonForresterA_ICAff

getValue(Node) - Method in class affectors.VonForresterB_Aff

getValue(Node) - Method in class affectors.VonForresterB_ECAff

getValue(Node) - Method in class affectors.VonForresterB_ICAff

getValue(Node) - Method in class affectors.WhiteNoiseAff

getValue(Node) - Method in class affectors.XferInAff

getValue(Node) - Method in class affectors.XferOutAff

getValue() - Method in class initialconditions.InitialCondition

getValue() - Method in class iterators.ModelIterator

getValue(int) - Method in class main.CalculatorNode

getValue(int) - Method in class main.Cell

getValue(int) - Method in class main.Node

getValue(float[]) - Method in class main.Node

getValue() - Method in class parameters.Parameter

getValue(int) - Method in class parameters.ParameterSet

getValueMatrix() - Method in class integrators.Integrator.NVmatrix

Use this one if you just want a handle to the values vector

getValueVector() - Method in class integrators.Integrator.NVvector

Use this one if you just want a handle to the values vector

getValues() - Method in class main.Cell

Returns all the node values for a cell in the form of an array of floats

getVariationMode() - Method in class parameters.Parameter

getVariationMode(int) - Method in class parameters.ParameterSet

getXPos() - Method in class main.NodeTemplate

getYPos() - Method in class main.NodeTemplate

getYScale() - Method in class main.NodeTemplate

goToBeginning() - Method in class parameters.ParameterSetArray

goToSet(int) - Method in class parameters.ParameterSetArray

goToSet(ParameterSet) - Method in class parameters.ParameterSetArray

Moves the arrays pointer to the currently selected set to point to the input set.

H

HH - Static variable in class affectors.Affector

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

HIGH - Static variable in class stoppers.CellThresholdStop

HIGH - Static variable in class stoppers.MultiNodeThresholdStop

HTMLViewer - class genegui.HTMLViewer.

HTMLViewer.java A simple HTML Viewer for browsing through Ingeneue help files.

HTMLViewer(URL) - Constructor for class genegui.HTMLViewer

Simple constructor

HeatShockAff - class affectors.HeatShockAff.

This is for use by Experiments to simulate a heat shock pulse of some Node.

HeatShockAff(String, float, float) - Constructor for class affectors.HeatShockAff

HeatShockAff(String[]) - Constructor for class affectors.HeatShockAff

HeterodimerizeA_EC2Aff - class affectors.HeterodimerizeA_EC2Aff.

An old name for Dimerize_AAff

HeterodimerizeA_ECAff - class affectors.HeterodimerizeA_ECAff.

An old name for DimerizeCrossMembrane_AAff

HeterodimerizeA_ECAff() - Constructor for class affectors.HeterodimerizeA_ECAff

HeterodimerizeA_ECICAff - class affectors.HeterodimerizeA_ECICAff.

An old name for DimerizeMemeCyto_AAff

HeterodimerizeA_ECICAff() - Constructor for class affectors.HeterodimerizeA_ECICAff

HeterodimerizeA_EC_XAff - class affectors.HeterodimerizeA_EC_XAff.

An old name for DimerizeAllMembrane_AAff

HeterodimerizeA_EC_XAff() - Constructor for class affectors.HeterodimerizeA_EC_XAff

HeterodimerizeA_ICAff - class affectors.HeterodimerizeA_ICAff.

An old name for Dimerize_AAff

HeterodimerizeA_ICAff() - Constructor for class affectors.HeterodimerizeA_ICAff

HeterodimerizeB_EC2Aff - class affectors.HeterodimerizeB_EC2Aff.

An old name for Dimerize_BAff

HeterodimerizeB_EC2Aff() - Constructor for class affectors.HeterodimerizeB_EC2Aff

HeterodimerizeB_ECAff - class affectors.HeterodimerizeB_ECAff.

An old name for DimerizeCrossMembrane_BAff

HeterodimerizeB_ECAff() - Constructor for class affectors.HeterodimerizeB_ECAff

HeterodimerizeB_ECICAff - class affectors.HeterodimerizeB_ECICAff.

An old name for DimerizeMemCyto_BAff

HeterodimerizeB_ECICAff() - Constructor for class affectors.HeterodimerizeB_ECICAff

HeterodimerizeB_EC_XAff - class affectors.HeterodimerizeB_EC_XAff.

An old name for DimerizeAllMembrane_BAff

HeterodimerizeB_EC_XAff() - Constructor for class affectors.HeterodimerizeB_EC_XAff

HeterodimerizeB_ICAff - class affectors.HeterodimerizeB_ICAff.

An old name for Dimerize_BAff

HeterodimerizeB_ICAff() - Constructor for class affectors.HeterodimerizeB_ICAff

HeterodimerizeC_ECICAff - class affectors.HeterodimerizeC_ECICAff.

An old name for DimerizeMemCyto_CAff

HeterodimerizeC_ECICAff() - Constructor for class affectors.HeterodimerizeC_ECICAff

HuenIntegrator - class integrators.HuenIntegrator.

Deprecated.

HuenIntegrator() - Constructor for class integrators.HuenIntegrator

Deprecated. no-argument constructor allows instantiating a HuenIntegrator generically from its name alone, with default minimum step size of 10E-5 and with step size adaptation turned ON.

hiliteLine(int) - Method in class main.NetworkFile

I

ICSamplingFunction - class iterators.ICSamplingFunction.

ICSamplingFunction() - Constructor for class iterators.ICSamplingFunction

ICSamplingFunction(ModelRunner) - Constructor for class iterators.ICSamplingFunction

ICVaryingFunction - class iterators.ICVaryingFunction.

ICVaryingFunction() - Constructor for class iterators.ICVaryingFunction

ICVaryingFunction(ModelRunner) - Constructor for class iterators.ICVaryingFunction

INPUT - Static variable in class main.NodeTemplate

INTERFACE_ACTION - Static variable in class genegui.GeneNetInterface

INTERFACE_ACTION - Static variable in class genegui.InspectorList

IS_ITERATOR - Static variable in interface genegui.GuiInterface

IS_MODEL - Static variable in interface genegui.GuiInterface

ITERATOR_STARTED - Static variable in interface genegui.GuiInterface

ITERATOR_STOPPED - Static variable in interface genegui.GuiInterface

IncrementingACSC1 - class initialconditions.IncrementingACSC1.

An initial condition class that sets a middle cell to one value and then the cells immediately surrounding that middle cell to a second value.

IncrementingACSC1() - Constructor for class initialconditions.IncrementingACSC1

IncrementingACSC1(String, int, int, float, float) - Constructor for class initialconditions.IncrementingACSC1

IncrementingIC - class initialconditions.IncrementingIC.

Increments the value of its node along each row.

IncrementingIC() - Constructor for class initialconditions.IncrementingIC

IncrementingIC(String, int, int) - Constructor for class initialconditions.IncrementingIC

InitialCondition - class initialconditions.InitialCondition.

InitialCondition() - Constructor for class initialconditions.InitialCondition

InitialCondition(String, float) - Constructor for class initialconditions.InitialCondition

InitialConditionSet - class initialconditions.InitialConditionSet.

InitialConditionSet() - Constructor for class initialconditions.InitialConditionSet

InitialConditionStorage - class initialconditions.InitialConditionStorage.

InitialConditionStorage() - Constructor for class initialconditions.InitialConditionStorage

InitialConditionStorage(Model) - Constructor for class initialconditions.InitialConditionStorage

InspectorList - class genegui.InspectorList.

InspectorList() - Constructor for class genegui.InspectorList

IntegrateOneStep() - Method in class integrators.AdamsIntegrator

IntegrateOneStep() - Method in class integrators.BackwardEulerIntegrator

IntegrateOneStep() - Method in class integrators.CashKarpIntegrator

IntegrateOneStep() - Method in class integrators.HuenIntegrator

Deprecated.

IntegrateOneStep() - Method in class integrators.Integrator

Integrates across a single time step.

IntegrateOneStep() - Method in class integrators.MidpointIntegrator

Call IntegrateOneStep() to use the Modified Midpoint Method by itself; this call uses an estimate give in NRC based on a weighted sum of results from crossing the interval with n/2 substeps and then with n substeps...

IntegrateOneStep(int) - Method in class integrators.MidpointIntegrator

Call IntegrateOneStep(int) with the desired number of substeps as the argument when using the Modified Midpoint Method as part of another method, like the BulirschStoerIntegrator.

IntegrateOneStep() - Method in class integrators.SemiExplicitAPCIntegrator

Integrator - class integrators.Integrator.

Base class for objects that implement numerical integration routines.

Integrator() - Constructor for class integrators.Integrator

Integrator.NVmatrix - class integrators.Integrator.NVmatrix.

This class was intended for storing a Jacobian matrix, or something like that.

Integrator.NVvector - class integrators.Integrator.NVvector.

This utility class may be more convenient for some purposes than an array of NodeValues objects would be.

IntegratorList - class integrators.IntegratorList.

This class just holds a list of all available integrators.

IntegratorList() - Constructor for class integrators.IntegratorList

IteratorViewer - class genegui.IteratorViewer.

InteratorViewer.java

IteratorViewer(ModelIterator, MainGui) - Constructor for class genegui.IteratorViewer

Main constructor.

ItsIterator - Variable in class main.GeneNet

The iterator if any for this model

indent - Static variable in class main.GeneralInput

init(int, int, String[]) - Method in class affectors.Affector

init() - Method in class genegui.ParInspector

init() - Method in class genegui.ParameterViewer

Initialize the display

init(Model) - Method in class integrators.AdamsIntegrator

init(Model) - Method in class integrators.BackwardEulerIntegrator

init(Model) - Method in class integrators.CashKarpIntegrator

init(Model) - Method in class integrators.HuenIntegrator

Deprecated. Other than allocating the necessary storage arrays, HuenIntegrator.init() also sets the error tolerance to 10E-4 and minimum step size to 10E-5.

init(Model) - Method in class integrators.Integrator

Any object planning to use an Integrator of any kind MUST call its init(Model) method, which (among other things) is generally used to allocate storage arrays for the intermediates in an integration method.

init(Model) - Method in class integrators.MidpointIntegrator

init() allocates the necessary storage, nothing else.

init(Model) - Method in class integrators.SemiExplicitAPCIntegrator

init(Network, Model) - Method in class iterators.ACSCIterator

init(ModelRunner) - Method in class iterators.Function

init(ModelRunner) - Method in class iterators.ICSamplingFunction

init(ModelRunner) - Method in class iterators.ICVaryingFunction

init(Network, Model) - Method in class iterators.ModelIterator

init(Network, Model) - Method in class iterators.UberIterator

init(Network, Model) - Method in class iterators.VulvaClassifyIterator

init(int) - Method in class main.CalculatorNode

init() - Method in class main.Cell

init(boolean) - Method in class main.Cell

initialize network from a stored previous state (if from_last_state == true) else from stored ICs

init(Model) - Method in class main.Experiment

init(int) - Method in class main.Node

init(ParameterSet) - Method in class parameterrules.ParameterRule

Initializes refParam to point to a parameter set which will be used as reference herein.

init(ParameterSetArray) - Method in class stat.Stat

init(Model) - Method in class stoppers.CellThresholdStop

init(Model) - Method in class stoppers.FPStripeStop

init(Model) - Method in class stoppers.MultiNodeThresholdStop

init(Model) - Method in class stoppers.NeuroNoiseStop

init(Model) - Method in class stoppers.NeuroTest2Stop

init(Model) - Method in class stoppers.NeuroTest3Stop

init(Model) - Method in class stoppers.NoChangeStop

init(Model) - Method in class stoppers.SimpleStop

init(Model) - Method in class stoppers.StripeStop

init(Model) - Method in class stoppers.TwoCellDifferenceStop

initCells() - Method in class stoppers.FPStripeStop

initCells() - Method in class stoppers.MetaFPStripeStop

initCells() - Method in class stoppers.MetaStripeStop

initCells() - Method in class stoppers.SimpleStop

initCells() - Method in class stoppers.StripeStop

initialconditions - package initialconditions

inspectors - Variable in class genegui.GeneNetInterface

integrationAlgorithm - Static variable in class main.Globals

The integration algorithm to use in running models.

integrator - Variable in class main.ModelRunner

integrators - package integrators

integrators - Static variable in class integrators.IntegratorList

isClosed() - Method in class genegui.Console

isGood() - Method in class main.Model

isGood(float[]) - Method in class parameterrules.ParameterRule

Returns true if the parameters in the input set meet the criteria for this rule, false otherwise.

isIteratorRunning() - Method in class main.GeneNet

isLinearInTarget() - Method in class affectors.Affector

isModelRunning() - Method in class main.GeneNet

isPositionInside(int, int, int) - Method in class main.AffectorTemplate

isRunning() - Method in class iterators.ModelIterator

isRunning() - Method in class main.ModelRunner

Returns true if the model is currently running

isSaveExtra() - Method in class iterators.ModelIterator

If an iterator wants to save large amounts of information that doesn't fit into the tag format above, then it should return true in this method.

isSaveExtra() - Method in class iterators.PopEvolveExpanderIterator

Override to return true so we can save all the extra parameter sets we come up with.

isScriptRunning() - Static method in class main.Globals

isType(String) - Method in class integrators.Integrator

itemStateChanged(ItemEvent) - Method in class genegui.ParInspector

iterError(String) - Method in class iterators.ModelIterator

iterators - package iterators

K

KK - Static variable in class affectors.Affector

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

L

LINEAR - Static variable in class parameters.Parameter

LMxferEAff - class affectors.LMxferEAff.

This is one half of a pair of Affectors that moves things between neighboring faces of a cell.

LMxferEAff() - Constructor for class affectors.LMxferEAff

LMxferIAff - class affectors.LMxferIAff.

This is one half of a pair of Affectors that moves things between neighboring faces of a cell.

LMxferIAff() - Constructor for class affectors.LMxferIAff

LOAD_CAM_FILE - Static variable in class genegui.GeneNetInterface

LOAD_EXPERIMENT - Static variable in class genegui.GeneNetInterface

LOAD_EXPT_TEXT - Static variable in class genegui.GeneNetInterface

LOAD_MODEL - Static variable in class genegui.GeneNetInterface

LOAD_TEXT - Static variable in class genegui.GeneNetInterface

LOGARITHMIC - Static variable in class parameters.Parameter

LOW - Static variable in class stoppers.CellThresholdStop

LOW - Static variable in class stoppers.MultiNodeThresholdStop

LessThanRule - class parameterrules.LessThanRule.

Implements the rule that the "SmallerParameter" must be less than the "LargerParameter".

lineno() - Method in class main.BetterTokenizer

Return the current line number.

load(BetterTokenizer) - Method in class main.Model

loadICs(String, BetterTokenizer) - Method in class iterators.ICSamplingFunction

loadParameter(String, BetterTokenizer) - Method in class initialconditions.CellIC

loadParameter(String, BetterTokenizer) - Method in class initialconditions.CenterIC

loadParameter(String, BetterTokenizer) - Method in class initialconditions.ColumnIC

loadParameter(String, BetterTokenizer) - Method in class initialconditions.IncrementingACSC1

loadParameter(String, BetterTokenizer) - Method in class initialconditions.IncrementingIC

loadParameter(String, BetterTokenizer) - Method in class initialconditions.InitialCondition

loadParameter(String, BetterTokenizer) - Method in class initialconditions.InitialConditionSet

loadParameter(String, BetterTokenizer) - Method in class initialconditions.NeuroNoiseIC

loadParameter(String, BetterTokenizer) - Method in class initialconditions.RowIC

loadParameter(String, BetterTokenizer) - Method in class initialconditions.SequenceACSC1

loadParameter(String, BetterTokenizer) - Method in class iterators.ACSCIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.ACSC_SwitchIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.EllipIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.FindVolumeIterator

Loads parameters specific to this iterator.

loadParameter(String, BetterTokenizer) - Method in class iterators.Function

loadParameter(String, BetterTokenizer) - Method in class iterators.ICSamplingFunction

loadParameter(String, BetterTokenizer) - Method in class iterators.ICVaryingFunction

loadParameter(String, BetterTokenizer) - Method in class iterators.MatingIterator

Loads parameters specific to this iterator.

loadParameter(String, BetterTokenizer) - Method in class iterators.ModelIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.PhasePortraitIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.PopEvolveExpanderIterator

Loads parameters specific to this iterator.

loadParameter(String, BetterTokenizer) - Method in class iterators.PowellIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.RandInitRunIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.SteepestDescentIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.SurfaceIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.TransectIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.UberIterator

loadParameter(String, BetterTokenizer) - Method in class iterators.VulvaClassifyIterator

loadParameter(String, BetterTokenizer) - Method in class main.CalculatorNode

loadParameter(String, BetterTokenizer) - Method in class main.Experiment

loadParameter(String, BetterTokenizer) - Method in class main.NodeTemplate

loadParameter(String, BetterTokenizer) - Method in class parameterrules.BoundaryRule

loadParameter(String, BetterTokenizer) - Method in class parameterrules.DimerHalfMaxRule

loadParameter(String, BetterTokenizer) - Method in class parameterrules.LessThanRule

loadParameter(String, BetterTokenizer) - Method in class parameterrules.MultiplyParameterRule

loadParameter(String, BetterTokenizer) - Method in class parameterrules.ParameterRule

Override this function for each parameter rule to load in setup info specific to that rule.

loadParameter(String, BetterTokenizer) - Method in class parameterrules.ParameterRuleSet

Loads a parameter rule from a stream.

loadParameter(String, BetterTokenizer) - Method in class parameterrules.ProductBetweenRule

loadParameter(String, BetterTokenizer) - Method in class parameterrules.RatioBetweenRule

loadParameter(String, BetterTokenizer) - Method in class stoppers.CellSurround2Stop

loadParameter(String, BetterTokenizer) - Method in class stoppers.CellSurroundStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.CellThresholdStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.FPStripeStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.FindMaxRatioStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.MetaFPStripeStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.MetaStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.MetaStopTwo

loadParameter(String, BetterTokenizer) - Method in class stoppers.MetaStripeStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.MultiNodeThresholdStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.NeuroNoiseStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.NeuroTest2Stop

loadParameter(String, BetterTokenizer) - Method in class stoppers.NeuroTest3Stop

loadParameter(String, BetterTokenizer) - Method in class stoppers.NoChangeStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.OscillatingStripeStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.OscillatorStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.OscillatorStopSpecial

loadParameter(String, BetterTokenizer) - Method in class stoppers.PulseStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.SimpleStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.StripeStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.ThresholdStop

loadParameter(String, BetterTokenizer) - Method in class stoppers.TwoCellDifferenceStop

loadParameterValues(BetterTokenizer, boolean) - Method in class parameters.ParameterSet

Loads a set of parameters from a stream.

loadParameters(BetterTokenizer) - Method in class initialconditions.InitialCondition

loadParameters(BetterTokenizer, Network) - Method in class initialconditions.InitialConditionSet

loadParameters(BetterTokenizer) - Method in class iterators.ACSCIterator

loadParameters(BetterTokenizer) - Method in class iterators.ACSC_SwitchIterator

loadParameters(BetterTokenizer) - Method in class iterators.Function

loadParameters(BetterTokenizer) - Method in class iterators.ICSamplingFunction

loadParameters(BetterTokenizer) - Method in class iterators.ICVaryingFunction

loadParameters(BetterTokenizer) - Method in class iterators.ModelIterator

loadParameters(BetterTokenizer) - Method in class iterators.PowellIterator

loadParameters(BetterTokenizer) - Method in class iterators.RandInitRunIterator

loadParameters(BetterTokenizer) - Method in class iterators.SteepestDescentIterator

loadParameters(BetterTokenizer) - Method in class iterators.TransectIterator

loadParameters(BetterTokenizer) - Method in class iterators.UberIterator

loadParameters(BetterTokenizer) - Method in class iterators.VulvaClassifyIterator

loadParameters(BetterTokenizer) - Method in class main.Experiment

loadParameters(BetterTokenizer) - Method in class parameterrules.DimerHalfMaxRule

Overridden to do error checking, making sure that all parameters are specified.

loadParameters(BetterTokenizer) - Method in class parameterrules.ParameterRule

The main method for loading paramaters from a stream.

loadParameters(BetterTokenizer) - Method in class parameterrules.ParameterRuleSet

Loads a set of parameter rules from a stream.

loadParameters(BetterTokenizer) - Method in class parameters.Parameter

This loadParameters calls the other one with need_all = true

loadParameters(BetterTokenizer, boolean) - Method in class parameters.Parameter

This function is for loading parameters from a file.

loadParameters(BetterTokenizer) - Method in class parameters.ParameterSet

This function loads a parameter set from an output file, tagged with the FPARS tag.

loadParameters(BetterTokenizer) - Method in class parameters.ParameterSetArray

loadParameters(BetterTokenizer) - Method in class stoppers.FPStripeStop

loadParameters(BetterTokenizer) - Method in class stoppers.MetaStop

loadParameters(BetterTokenizer) - Method in class stoppers.MetaStopTwo

loadParameters(BetterTokenizer) - Method in class stoppers.SimpleStop

loadParameters(BetterTokenizer) - Method in class stoppers.StripeStop

loadValueFieldNames(BetterTokenizer) - Method in class parameters.ParameterSet

Value Fields

lowerBound - Variable in class parameters.Parameter

The highest value this parameter can every have.

lowerCaseMode(boolean) - Method in class main.BetterTokenizer

Determines whether or not word token are automatically lowercased.

M

MATHTYPE - Static variable in class affectors.Affector

Position meanings for Type[].

MODEL_STARTED - Static variable in interface genegui.GuiInterface

MODEL_STOPPED - Static variable in interface genegui.GuiInterface

MODE_APPLY - Static variable in class genegui.ModelStateToolBox

MODE_GRADIENT - Static variable in class genegui.ModelStateToolBox

MODE_MAGNIFY - Static variable in class genegui.ModelStateToolBox

MODE_MARQUEE - Static variable in class genegui.ModelStateToolBox

MODE_SELECT - Static variable in class genegui.ModelStateToolBox

MODE_STRIPE - Static variable in class genegui.ModelStateToolBox

MainGui - class genegui.MainGui.

MainGui.java

MainGui(GeneNet) - Constructor for class genegui.MainGui

Simple constructor

MatingIterator - class iterators.MatingIterator.

MatingIterator() - Constructor for class iterators.MatingIterator

MetaFPStripeStop - class stoppers.MetaFPStripeStop.

MetaFPStripeStop() - Constructor for class stoppers.MetaFPStripeStop

MetaStop - class stoppers.MetaStop.

Use this Stopper to combine together several simple Stoppers to look for more complicated patterns.

MetaStop() - Constructor for class stoppers.MetaStop

MetaStopTwo - class stoppers.MetaStopTwo.

MetaStopTwo() - Constructor for class stoppers.MetaStopTwo

MetaStripeStop - class stoppers.MetaStripeStop.

MetaStripeStop() - Constructor for class stoppers.MetaStripeStop

MidpointIntegrator - class integrators.MidpointIntegrator.

Modified Midpoint Method as described in Numerical Recipes in C; this is NOT a translation of their code (which I didn't even look at), but merely my implementation of the recipe outlined in the text.

MidpointIntegrator() - Constructor for class integrators.MidpointIntegrator

no-argument constructor allows instantiating a MidpointIntegrator generically from its name alone, with default number of substeps = 8.

Model - class main.Model.

Model() - Constructor for class main.Model

Note - after making a new Model, you should immediately call the load() function.

ModelIterator - class iterators.ModelIterator.

ModelIterator() - Constructor for class iterators.ModelIterator

ModelLoadingException - exception main.ModelLoadingException.

ModelLoadingException() - Constructor for class main.ModelLoadingException

ModelLoadingException(String) - Constructor for class main.ModelLoadingException

ModelLoadingException(String, int) - Constructor for class main.ModelLoadingException

ModelLoadingException(int) - Constructor for class main.ModelLoadingException

ModelRunner - class main.ModelRunner.

ModelRunner(Model, SimpleStop) - Constructor for class main.ModelRunner

ModelState - class genegui.ModelState.

ModelState.java Maintains a ModelState to be used for specifying intial states and stoppers.

ModelState() - Constructor for class genegui.ModelState

Simple constructor does little to be proud of.

ModelState(Model) - Constructor for class genegui.ModelState

Constructor initializes the ModelState based upon a passed Model.

ModelStateBeanInfo - class genegui.ModelStateBeanInfo.

ModelStateBeanInfo() - Constructor for class genegui.ModelStateBeanInfo

ModelStateChangeListener - interface genegui.ModelStateChangeListener.

Interface to be implemented by anything that is viewing the state of an entire model.

ModelStateEditor - class genegui.ModelStateEditor.

ModelStateEditor.java The ModelStateEditor allows the user to define node states for each cell in the model.

ModelStateEditor(Model, MainGui) - Constructor for class genegui.ModelStateEditor

ModelStateNodePalette - class genegui.ModelStateNodePalette.

ModelStateNodePalette.java

ModelStateNodePalette(ModelState, MainGui) - Constructor for class genegui.ModelStateNodePalette

Primary constructor builds the visual appearance for the palette and makes the menu bar.

ModelStateToolBox - class genegui.ModelStateToolBox.

ModelStateToolBox.java

ModelStateToolBox() - Constructor for class genegui.ModelStateToolBox

Simple constructor.

ModelStateView - class genegui.ModelStateView.

ModelStateView.java Constructs a JWindow for viewing all the cells in a model.

ModelStateView(ModelState, ModelStateEditor, MainGui) - Constructor for class genegui.ModelStateView

Primary constructor builds the visual appearance of the viewer and establishes mouse listeners.

MoreMath - class main.MoreMath.

This class includes a bunch of extra mathematical functions and other math tidbits that are useful to have around.

MoreMath() - Constructor for class main.MoreMath

MoreMath.Comparer - interface main.MoreMath.Comparer.

MoreMath.PartialDerivRec - class main.MoreMath.PartialDerivRec.

A record class that's handy when assembling a Jacobian matrix from the Affectors' formulas rather than numerically.

MoreMath.PartialDerivRec() - Constructor for class main.MoreMath.PartialDerivRec

MultiEnhancerAff - class affectors.MultiEnhancerAff.

This is a meta-affector which sums together transcriptional activation terms while keeping the total transcription rate less than or equal to 1.

MultiEnhancerAff() - Constructor for class affectors.MultiEnhancerAff

MultiFloatReturn - class iterators.MultiFloatReturn.

MultiFloatReturn() - Constructor for class iterators.MultiFloatReturn

MultiFloatReturn(float) - Constructor for class iterators.MultiFloatReturn

MultiFloatReturn(float, float) - Constructor for class iterators.MultiFloatReturn

MultiNodeThresholdStop - class stoppers.MultiNodeThresholdStop.

MultiNodeThresholdStop() - Constructor for class stoppers.MultiNodeThresholdStop

MultiNodeThresholdStop(float) - Constructor for class stoppers.MultiNodeThresholdStop

MultiplyParameterRule - class parameterrules.MultiplyParameterRule.

Implements the manipulation the Parameter's value is multiplied by a constant before being used in a model.

MxferInAff - class affectors.MxferInAff.

This is one half of a pair of Affectors that moves things from a face of one cell to the opposing face of a neighboring cell.

MxferInAff() - Constructor for class affectors.MxferInAff

MxferOutAff - class affectors.MxferOutAff.

This is one half of a pair of Affectors that moves things from a face of one cell to the opposing face of a neighboring cell.

MxferOutAff() - Constructor for class affectors.MxferOutAff

main - package main

main(String[]) - Static method in class main.GeneNet

mainProgram - Static variable in class main.Globals

makeAffector(Cell, int) - Method in class main.AffectorTemplate

makeFirstPoint(ParameterSet, int) - Method in class iterators.UberIterator

makeNewPoint(ParameterSet, int) - Method in class iterators.UberIterator

makeNewPoint(int, ParameterSet) - Method in class parameters.ParameterSet

makeNewPoint(int) - Method in class parameters.ParameterSet

makeNode() - Method in class main.NodeTemplate

makePhasePortraitDlog() - Method in class genegui.InspectorList

makeTimeGraph() - Method in class genegui.InspectorList

makeWindows() - Method in class genegui.InspectorList

maxNumNodes - Static variable in class main.Globals

The maximum number of nodes - like maxNumParams, we should clean this out of the code eventually

maxNumParams - Static variable in class main.Globals

The maximum number of parameters for all the affectors

model - Variable in class iterators.ModelIterator

model - Variable in class main.GeneNet

modelChangeTime - Static variable in class main.Globals

The lastModified time for current model file

modelFileViewerFrame - Variable in class genegui.InspectorList

modelFilename - Static variable in class main.Globals

The name of the currently loaded model file

moveIntersectPos(int, int) - Method in class main.AffectorTemplate

moveModelStateViewToFront(ModelStateView) - Method in class genegui.ModelStateEditor

Moves a ModelStateView to the "front" which in this case is still behind the ToolBox and NodePalette which should always be on top.

moveViewerPanelDown(CellSurfaceViewer.SingleNodeViewerPanel) - Method in class genegui.CellSurfaceViewer

Moves nodeViewerPanel down a space.

moveViewerPanelUp(CellSurfaceViewer.SingleNodeViewerPanel) - Method in class genegui.CellSurfaceViewer

Moves nodeViewerPanel up a space

N

NDesc - Variable in class affectors.Affector

NEW - Static variable in interface genegui.GuiInterface

NEW_RUN - Static variable in class main.Model

NOT_SET - Static variable in class parameters.Parameter

NetInput - class main.NetInput.

Network - class main.Network.

NetworkFile - class main.NetworkFile.

NetworkFile() - Constructor for class main.NetworkFile

NetworkPaintPanel - class genegui.NetworkPaintPanel.

NetworkPaintPanel.java A JPanel with paint over-ridden for painting the nextwork connections.

NetworkPaintPanel(NetworkViewer2) - Constructor for class genegui.NetworkPaintPanel

NetworkPaintPanel.AffectorDisplay - class genegui.NetworkPaintPanel.AffectorDisplay.

AffectorDisplay.java An inner class for representing affector nodes.

NetworkPaintPanel.AffectorDisplay(AffectorTemplate, NetworkPaintPanel.NodeDisplay) - Constructor for class genegui.NetworkPaintPanel.AffectorDisplay

Simple constructor.

NetworkPaintPanel.NodeDisplay - class genegui.NetworkPaintPanel.NodeDisplay.

NodeDisplay.java Inner class used for representing a network node.

NetworkPaintPanel.NodeDisplay(NodeTemplate) - Constructor for class genegui.NetworkPaintPanel.NodeDisplay

Simple constructor.

NetworkViewer2 - class genegui.NetworkViewer2.

A total re-write of the original NetworkViewer.

NetworkViewer2(Model, MainGui) - Constructor for class genegui.NetworkViewer2

Main constructor.

NeuroNoiseIC - class initialconditions.NeuroNoiseIC.

Input Parameters:
Node
Value
LowToHighDifference
StartLowCell
StepSize
NumRows

NeuroNoiseIC() - Constructor for class initialconditions.NeuroNoiseIC

NeuroNoiseStop - class stoppers.NeuroNoiseStop.

Specially made stopping class for exploring switching behavior in the neurogenic network.

NeuroNoiseStop() - Constructor for class stoppers.NeuroNoiseStop

NeuroNoiseStop(float) - Constructor for class stoppers.NeuroNoiseStop

NeuroTest2Stop - class stoppers.NeuroTest2Stop.

NeuroTest2Stop() - Constructor for class stoppers.NeuroTest2Stop

NeuroTest2Stop(float) - Constructor for class stoppers.NeuroTest2Stop

NeuroTest3Stop - class stoppers.NeuroTest3Stop.

NeuroTest3Stop() - Constructor for class stoppers.NeuroTest3Stop

NeuroTest3Stop(float) - Constructor for class stoppers.NeuroTest3Stop

NoChangeAff - class affectors.NoChangeAff.

Returns zero as the derivative; use to lock a Node at a constant level, such as an initial condition that should persist indefinitely.

NoChangeAff() - Constructor for class affectors.NoChangeAff

NoChangeStop - class stoppers.NoChangeStop.

NoChangeStop() - Constructor for class stoppers.NoChangeStop

NoChangeStop(float) - Constructor for class stoppers.NoChangeStop

Node - class main.Node.

A node is one of the state variables in the model: an mRNA, protein, protein complex, protein at a membrane, etc.

NodeSpecifier - class main.NodeSpecifier.

NodeSpecifier(Cell, Node) - Constructor for class main.NodeSpecifier

NodeSpecifier(int, int) - Constructor for class main.NodeSpecifier

NodeStateChangeListener - interface genegui.NodeStateChangeListener.

Interface to be implemented by anything that is viewing the state of cells and their node values, eg.

NodeStateViewer - class genegui.NodeStateViewer.

NodeStateViewer.java This viewer displays all the values for all the nodes of a selected cell.

NodeStateViewer(ModelState, MainGui, String) - Constructor for class genegui.NodeStateViewer

Primary constructor.

NodeTemplate - class main.NodeTemplate.

NodeTemplate(String, int) - Constructor for class main.NodeTemplate

NodeValues - class integrators.NodeValues.

Most Integrator functions use this utility class to build convenient arrays of Node values.

NodeValues() - Constructor for class integrators.NodeValues

NodeValues(int) - Constructor for class integrators.NodeValues

NodeViewPanel - class genegui.NodeViewPanel.

NodeViewPanel.java A JPanel extendsion for showing/editing the properties of NodeTemplates.

NodeViewPanel(NodeTemplate, MainGui) - Constructor for class genegui.NodeViewPanel

NoiseGenerator - class main.NoiseGenerator.

NoiseGenerator() - Constructor for class main.NoiseGenerator

nParsTV - Variable in class iterators.ModelIterator

name - Variable in class parameters.Parameter

The name of this parameter.

neighbors - Variable in class main.Cell

The cell's neighbors - set up by the init object

net - Variable in class main.Model

netViewerFrame - Variable in class genegui.InspectorList

network - Variable in class iterators.ModelIterator

networkIO(int, File) - Method in class genegui.AffectorViewPanel

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.CellSurfaceViewer

Method for invoking general network IO operations.

networkIO(int, File) - Method in interface genegui.GuiInterface

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.MainGui

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.ModelStateEditor

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.ModelStateNodePalette

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.ModelStateView

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.NetworkViewer2

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.NodeStateViewer

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.NodeViewPanel

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.ParameterViewer

Method for invoking general network IO operations.

networkIO(int, File) - Method in class genegui.TimeGraph

Method for invoking general network IO operations.

networkIO(int, File) - Method in class main.GeneNet

Method for invoking general network IO operations.

nextToken() - Method in class main.BetterTokenizer

* Parses the next token from the input stream of this tokenizer.

nextToken(BetterTokenizer) - Static method in class main.GeneralInput

nextWordToken(BetterTokenizer) - Static method in class main.GeneralInput

nodePeek(String) - Method in class main.Cell

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.AffectorViewPanel

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.CellSurfaceViewer

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in interface genegui.GuiInterface

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.MainGui

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.ModelStateEditor

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.ModelStateNodePalette

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.ModelStateView

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.NetworkViewer2

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.NodeStateViewer

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.NodeViewPanel

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.ParameterViewer

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class genegui.TimeGraph

Called when a change is made to the passed NodeTemplate

nodeTemplateChanged(int, NodeTemplate, GuiInterface) - Method in class main.GeneNet

Called when a change is made to the passed NodeTemplate

nodes - Variable in class main.Cell

nodes - Variable in class main.Network

noiseAware - Variable in class initialconditions.CellIC

noiseAware - Variable in class initialconditions.CenterIC

noiseAware - Variable in class initialconditions.ColumnIC

noiseAware - Variable in class initialconditions.InitialCondition

noiseAware - Variable in class initialconditions.RowIC

nonFatalError(String) - Static method in class genegui.ErrorPopUp

nonFatalErrorQuery(String) - Static method in class genegui.ErrorPopUp

numCells - Variable in class iterators.ModelIterator

numCells - Variable in class main.Model

numFunctionCalls - Variable in class iterators.ModelIterator

numGroups - Variable in class parameters.ParameterSetArray

numIntegratorSteps - Static variable in class main.Globals

Something for the integrator (?)

numNodes - Variable in class main.Network

numParams - Variable in class parameterrules.ParameterRule

numParams - Variable in class parameters.ParameterSet

Note that not all params below numParams neccesarily exist.

numSides - Variable in class integrators.NodeValues

numSides - Variable in class main.Node

nval - Variable in class main.BetterTokenizer

If the current token is a number, this field contains the value * of that number.

O

OPEN - Static variable in interface genegui.GuiInterface

OPTIONS_TEXT - Static variable in class genegui.GeneNetInterface

OptionsPanelInterface - interface genegui.OptionsPanelInterface.

Interface for communicating with either TimeGraph of Graph Panel class

OscillatingStripeStop - class stoppers.OscillatingStripeStop.

OscillatingStripeStop() - Constructor for class stoppers.OscillatingStripeStop

OscillatingStripeStop(float) - Constructor for class stoppers.OscillatingStripeStop

OscillatorStop - class stoppers.OscillatorStop.

OscillatorStop() - Constructor for class stoppers.OscillatorStop

OscillatorStop(float) - Constructor for class stoppers.OscillatorStop

OscillatorStopSpecial - class stoppers.OscillatorStopSpecial.

OscillatorStopSpecial() - Constructor for class stoppers.OscillatorStopSpecial

OscillatorStopSpecial(float) - Constructor for class stoppers.OscillatorStopSpecial

object - Variable in class genegui.Pointer

openAFile(String, String) - Method in class genegui.MainGui

ordinaryChar(int) - Method in class main.BetterTokenizer

* Specifies that the character argument is "ordinary" * in this tokenizer.

ordinaryChars(int, int) - Method in class main.BetterTokenizer

* Specifies that all characters c in the range * low <= c <= high * are "ordinary" in this tokenizer.

origStopper - Variable in class iterators.ModelIterator

out - Variable in class main.Model

outFileName - Variable in class iterators.ModelIterator

P

PARAMETER_ADDED - Static variable in interface genegui.GuiInterface

Static values for parameter set change operation

PARAMETER_CHANGED - Static variable in interface genegui.GuiInterface

PARAMETER_REMOVED - Static variable in interface genegui.GuiInterface

PARAMETER_SET_CHANGED - Static variable in interface genegui.GuiInterface

PDesc - Variable in class affectors.Affector

PHASE_PORTRAIT - Static variable in class genegui.GeneNetInterface

POSITION_NOT_SET - Static variable in class main.NodeTemplate

PRODUCTION - Static variable in class affectors.Affector

Type.[TERMTYPE] values;

PROTEIN - Static variable in class main.NodeTemplate

ParInspector - class genegui.ParInspector.

ParInspector() - Constructor for class genegui.ParInspector

ParamTendenciesStat - class stat.ParamTendenciesStat.

Saves a parameter set with the minimum and maximum values set to encompass the most common values for each parameter in all the loaded sets.

ParamTendenciesStat() - Constructor for class stat.ParamTendenciesStat

Parameter - class parameters.Parameter.

This class holds the value of a given parameter, its upper and lower bounds, and whether it should vary linearly or logarithmically.

Parameter() - Constructor for class parameters.Parameter

Parameter(String) - Constructor for class parameters.Parameter

This initializer is for use when reading from a file, where the creation of this Parameter object will happen after the parameter name is already known.

Parameter(String, float, float, float, int) - Constructor for class parameters.Parameter

Parameter(Parameter) - Constructor for class parameters.Parameter

ParameterRule - class parameterrules.ParameterRule.

ParameterRuleSet - class parameterrules.ParameterRuleSet.

ParameterRuleSet(ParameterSet) - Constructor for class parameterrules.ParameterRuleSet

ParameterSet - class parameters.ParameterSet.

ParameterSet.java This class stores a set of Parameter objects, along with variables that might be associated with such a set.

ParameterSet() - Constructor for class parameters.ParameterSet

ParameterSet(String) - Constructor for class parameters.ParameterSet

If you call a constructor with a prototype set, the only parameters that can be added to this set are those that are in the prototype.

ParameterSet(ParameterSet) - Constructor for class parameters.ParameterSet

ParameterSet(ParameterSet, int, String) - Constructor for class parameters.ParameterSet

ParameterSetArray - class parameters.ParameterSetArray.

ParameterSetArray() - Constructor for class parameters.ParameterSetArray

ParameterSetArray(ParameterSet) - Constructor for class parameters.ParameterSetArray

ParameterViewer - class genegui.ParameterViewer.

ParameterViewer.java A corgial re-write of the ParInsepctor with a new name and some enhancements.

ParameterViewer(MainGui, String, boolean) - Constructor for class genegui.ParameterViewer

Simple constructor.

PhasePortraitDlog - class genegui.PhasePortraitDlog.

PhasePortraitIterator - class iterators.PhasePortraitIterator.

PhasePortraitIterator() - Constructor for class iterators.PhasePortraitIterator

Phi(float, float, float) - Method in class affectors.Affector

Phosphor1StepA_ICAff - class affectors.Phosphor1StepA_ICAff.

This is one half of an affector that phosphrylates a single node.

Phosphor1StepA_ICAff() - Constructor for class affectors.Phosphor1StepA_ICAff

Phosphor1StepB_ICAff - class affectors.Phosphor1StepB_ICAff.

This is one half of an affector that phosphrylates a single node.

Phosphor1StepB_ICAff() - Constructor for class affectors.Phosphor1StepB_ICAff

PhosphorylateA_Aff - class affectors.PhosphorylateA_Aff.

This is one half of an affector that phosphorylates a single node based on a kinase activity.

PhosphorylateA_Aff() - Constructor for class affectors.PhosphorylateA_Aff

PhosphorylateB_Aff - class affectors.PhosphorylateB_Aff.

This is one half of an affector that phosphorylates a single node based on a kinase activity.

PhosphorylateB_Aff() - Constructor for class affectors.PhosphorylateB_Aff

PhosphorylationA_ICAff - class affectors.PhosphorylationA_ICAff.

This is one half of an affector that phosphorylates a single node.

PhosphorylationA_ICAff() - Constructor for class affectors.PhosphorylationA_ICAff

PhosphorylationB_ICAff - class affectors.PhosphorylationB_ICAff.

This is one half of an affector that phosphrylates a single node.

PhosphorylationB_ICAff() - Constructor for class affectors.PhosphorylationB_ICAff

PlaceHolderAff - class affectors.PlaceHolderAff.

Placeholder affector for use with creating dummy (i.e.

PlaceHolderAff() - Constructor for class affectors.PlaceHolderAff

Constructor for this Affector.

Pointer - class genegui.Pointer.

This is here solely to be able to pass null objects around in events.

Pointer(Object) - Constructor for class genegui.Pointer

PopEvolveExpanderIterator - class iterators.PopEvolveExpanderIterator.

PopEvolveExpanderIterator() - Constructor for class iterators.PopEvolveExpanderIterator

PowellIterator - class iterators.PowellIterator.

PowellIterator() - Constructor for class iterators.PowellIterator

Product - class affectors.Product.

This is a special "meta-affector".

Product() - Constructor for class affectors.Product

ProductAff - class affectors.ProductAff.

This is a special "meta-affector".

ProductAff() - Constructor for class affectors.ProductAff

ProductBetweenRule - class parameterrules.ProductBetweenRule.

Implements the rule that the product of all the input parameters has to lie between lowerBound <= product <= upperBound.

Psi(float, float, float) - Method in class affectors.Affector

PsiAff - class affectors.PsiAff.

We call our basic upside-down sigmoid function "Psi".

PsiAff() - Constructor for class affectors.PsiAff

PsiECAff - class affectors.PsiECAff.

This is similar to the Psi function except the inhibitor is in a neighboring cell from the one that contains the target Node.

PsiECAff() - Constructor for class affectors.PsiECAff

PulseStop - class stoppers.PulseStop.

PulseStop.java Detects a square-wave-like pulse for a node.

PulseStop() - Constructor for class stoppers.PulseStop

No arg constructor for instantiating by name

PulseStop(float) - Constructor for class stoppers.PulseStop

p - Variable in class iterators.ModelIterator

local copy of Parameters.

pack() - Method in class genegui.TimeGraph

Over-ride pack to keep current width settings and to keep display from getting to tall for the screen.

paint(Graphics) - Method in class genegui.NetworkPaintPanel.AffectorDisplay

Paints the affector.

paint(Graphics) - Method in class genegui.NetworkPaintPanel.NodeDisplay

Over-ride the paint method to paint the offscreen image.

paint(Graphics) - Method in class genegui.NetworkPaintPanel

Over-rides paint to paint the connections bewteen nodes and affectors

paint(Graphics, int, Network, AffectorTemplate) - Method in class main.AffectorTemplate

paintAll() - Method in class genegui.CellSurfaceViewer

Forces all panels to repaint.

paintOffScreen(boolean) - Method in class genegui.NetworkPaintPanel.NodeDisplay

Paints the node image in an offscreen buffer

paintOutgoingLines(Graphics, Network, int, int, NodeTemplate, int, AffectorTemplate) - Method in class main.AffectorTemplate

paramNums - Variable in class parameterrules.ParameterRule

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.AffectorViewPanel

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.CellSurfaceViewer

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in interface genegui.GuiInterface

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.MainGui

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.ModelStateEditor

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.ModelStateNodePalette

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.ModelStateView

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.NetworkViewer2

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.NodeStateViewer

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.NodeViewPanel

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.ParameterViewer

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class genegui.TimeGraph

Called when a change is made to a parameter or the whole parameter set

parameterSetChanged(int, int, GuiInterface) - Method in class main.GeneNet

Called when a change is made to a parameter or the whole parameter set

parameterrules - package parameterrules

parameters - package parameters

params - Variable in class parameters.ParameterSet

Get the position of a parameter in this array using the getPosition function

parsTV - Variable in class iterators.ModelIterator

Local copy of Parameters.nParsTV

parseNumbers() - Method in class main.BetterTokenizer

* Specifies that numbers should be parsed by this tokenizer.

pickNewParameterValue(float[], int, float, float, int, ParameterSet) - Method in class parameterrules.ParameterRule

Picks a new parameter value in the range min to max.

pickRandomLinear(float, float) - Static method in class main.MoreMath

pickRandomLogarithmic(float, float) - Static method in class main.MoreMath

print(char) - Method in class genegui.Console

print(char[]) - Method in class genegui.Console

print(double) - Method in class genegui.Console

print(float) - Method in class genegui.Console

print(int) - Method in class genegui.Console

print(long) - Method in class genegui.Console

print(Object) - Method in class genegui.Console

print(String) - Method in class genegui.Console

print() - Method in class initialconditions.CellIC

print() - Method in class initialconditions.ColumnIC

print() - Method in class initialconditions.InitialCondition

print() - Method in class initialconditions.RowIC

print(String) - Method in class iterators.ModelIterator

printComponents(Component) - Static method in class main.GeneralInput

printGeneral(String) - Static method in class main.GlobalIO

printGeneral(String, boolean) - Static method in class main.GlobalIO

printScript(String) - Static method in class main.GlobalIO

println() - Method in class genegui.Console

println(char) - Method in class genegui.Console

println(char[]) - Method in class genegui.Console

println(double) - Method in class genegui.Console

println(float) - Method in class genegui.Console

println(int) - Method in class genegui.Console

println(long) - Method in class genegui.Console

println(Object) - Method in class genegui.Console

println(String) - Method in class genegui.Console

println(String) - Method in class iterators.ModelIterator

println() - Method in class iterators.ModelIterator

printlnGeneral(String) - Static method in class main.GlobalIO

printlnGeneral(String, boolean) - Static method in class main.GlobalIO

printlnScript(String) - Static method in class main.GlobalIO

ps - Variable in class iterators.ModelIterator

The general purpose output file from an iterator.

pushBack() - Method in class main.BetterTokenizer

Causes the next call to the nextToken method of this * tokenizer to return the current value in the ttype * field, and not to modify the value in the nval or * sval field.

Q

QUIT_TEXT - Static variable in class genegui.GeneNetInterface

quit() - Method in class iterators.ModelIterator

quit() - Method in class iterators.UberIterator

quoteChar(int) - Method in class main.BetterTokenizer

* Specifies that matching pairs of this character delimit string * constants in this tokenizer.

R

RATIO - Static variable in class main.NodeTemplate

REMOVED - Static variable in interface genegui.GuiInterface

REMOVE_EXPERIMENT_TEXT - Static variable in class genegui.GeneNetInterface

REMOVING_PARAM_SET_STRING - Static variable in class parameters.ParameterSetArray

RESET_ITERATOR - Static variable in interface genegui.GuiInterface

RESET_MODEL - Static variable in interface genegui.GuiInterface

RESET_MODEL_TEXT - Static variable in class genegui.GeneNetInterface

RETURNS_DERIV - Static variable in class affectors.Affector

Type.[CERTIFICATION] values; in the constructor of a subclass, once you have made sure the formula in getValue (and getNCValue if necessary) is correct, set this.Type.[CERTIFICATION]=Affector.RETURNS_DERIV, and once your subclass knows how to return a list of partial derivatives, set it to RETURNS_PARTIALS.

RETURNS_PARTIALS - Static variable in class affectors.Affector

Type.[CERTIFICATION] values; in the constructor of a subclass, once you have made sure the formula in getValue (and getNCValue if necessary) is correct, set this.Type.[CERTIFICATION]=Affector.RETURNS_DERIV, and once your subclass knows how to return a list of partial derivatives, set it to RETURNS_PARTIALS.

RNA - Static variable in class main.NodeTemplate

RUN_FIXED_POINT_TEXT - Static variable in class genegui.GeneNetInterface

RUN_ITERATOR - Static variable in interface genegui.GuiInterface

RUN_ITERATOR_TEXT - Static variable in class genegui.GeneNetInterface

RUN_MODEL - Static variable in interface genegui.GuiInterface

Static values for runControl operations

RUN_MODEL_TEXT - Static variable in class genegui.GeneNetInterface

RandInitRunIterator - class iterators.RandInitRunIterator.

RandInitRunIterator() - Constructor for class iterators.RandInitRunIterator

RatioBetweenRule - class parameterrules.RatioBetweenRule.

Implements the rule that the ratio of two products of input parameters has to lie between lowerBound <= ratio <= upperBound.

RecycleAAff - class affectors.RecycleAAff.

One half of a pair of affectors which recycles proteins from one state back to another.

RecycleAAff() - Constructor for class affectors.RecycleAAff

RecycleBAff - class affectors.RecycleBAff.

The other half of a pair of affectors which recycles proteins from one state back to another.

RecycleBAff() - Constructor for class affectors.RecycleBAff

RefreshReject - Variable in class genegui.NetworkViewer2

Controls the rate at which the display refreshes by rejecting changes in size below the RefreshReject

RowIC - class initialconditions.RowIC.

RowIC() - Constructor for class initialconditions.RowIC

RowIC(String, float, int) - Constructor for class initialconditions.RowIC

randNeg(int) - Static method in class main.MoreMath

random() - Static method in class main.MoreMath

random(int) - Static method in class main.MoreMath

randomInt(int, int) - Static method in class main.MoreMath

Returns an integer between min and max - 1.

randomize(int[]) - Static method in class main.MoreMath

Randomizes the elements in the array.

readCalculators(BetterTokenizer, Network) - Method in class main.NetInput

readDefaultParameterValues(BetterTokenizer, Network) - Method in class main.NetInput

readGenes(BetterTokenizer, Network) - Method in class main.NetInput

readInteractions(BetterTokenizer, Network) - Method in class main.NetInput

readParameterValues(BetterTokenizer, Network) - Method in class main.NetInput

readRandomPicks(BetterTokenizer, Network) - Method in class main.NetInput

readSetup(BetterTokenizer, String) - Method in class main.AffectorTemplate

readSetup(BetterTokenizer) - Method in class main.NodeTemplate

readText(InputStream) - Method in class main.NetworkFile

Reads in a model file from a stream, which will usually be a file stream.

remove(int) - Method in class parameters.ParameterSetArray

removeActionListener(ActionListener) - Method in class genegui.GeneNetInterface

removeActionListener(ActionListener) - Method in class genegui.InspectorList

removeActionListener(ActionListener) - Method in class main.NetworkFile

removeActionListener(ActionListener) - Method in class parameters.ParameterSetArray

removeAll() - Method in class parameters.ParameterSetArray

removeAllModelStateViews() - Method in class genegui.ModelState

Removes all ModelStateViews, disposing of them and clearing the local list.

removeExpAffectors() - Method in class main.Node

removeGUIListener(GuiInterface) - Method in class genegui.MainGui

Removes the pass NettoGUI listener from the listener list.

removeInternalFrame(JInternalFrame) - Method in class genegui.MainGui

Removes an internal frame from the GUI

removeModelStateChangeListener(ModelStateChangeListener) - Method in class genegui.ModelState

Called to remove a ModelStateChangeListener.

removeModelStateView(ModelStateView) - Method in class genegui.ModelState

Called to remove a ModelStateView from the local list.

removeNetworkListener(NetworkEventListener) - Method in class main.GeneNet

removeNetworkListener(NetworkEventListener) - Method in class main.Network

removeNodeViewerPanel(CellSurfaceViewer.SingleNodeViewerPanel) - Method in class genegui.CellSurfaceViewer

Removes a SingleNodeViewerPanel from the CellViewer.

removeParamSetArray(ParameterSetArray) - Static method in class main.Globals

removeParameter(String) - Method in class parameters.ParameterSet

removeStateChangeListener(NodeStateChangeListener, int) - Method in class genegui.ModelState

Removes a NodeStateChangeListener from the ModelState.

reportRunCount(int) - Method in class genegui.IteratorViewer

reportSuccessCount(ModelState, ParameterSet, int, float) - Method in class genegui.IteratorViewer

reset() - Method in class genegui.CellState

Resets all node values for this cell to 0.

reset() - Method in class genegui.ModelState

Resets the values of all nodes for all cells to 0.

reset() - Method in class genegui.ModelStateNodePalette

Clears the current setting of the node palette disabling all the node planes and blanking all displays.

reset() - Method in class genegui.ModelStateView

Resets the ModelStateView by switching off all cell-selections, turning off all visible nodes.

reset() - Method in class integrators.AdamsIntegrator

reset() - Method in class integrators.BackwardEulerIntegrator

reset() - Method in class integrators.CashKarpIntegrator

reset() - Method in class integrators.HuenIntegrator

Deprecated. Resets timestep to default, and cleans up various internal flags; call before starting a new run.

reset() - Method in class integrators.Integrator

Should be called after the Integrator has crossed an entire interval.

reset() - Method in class integrators.SemiExplicitAPCIntegrator

reset() - Method in class iterators.EllipIterator

reset() - Method in class iterators.MatingIterator

reset() - Method in class iterators.ModelIterator

Called before each run of an iterator.

reset() - Method in class iterators.PopEvolveExpanderIterator

reset() - Method in class iterators.PowellIterator

reset() - Method in class iterators.UberIterator

reset() - Method in class main.NoiseGenerator

reset() - Method in class stoppers.CellSurround2Stop

reset() - Method in class stoppers.CellSurroundStop

reset() - Method in class stoppers.CellThresholdStop

reset() - Method in class stoppers.MetaFPStripeStop

reset() - Method in class stoppers.MetaStop

reset() - Method in class stoppers.MetaStopTwo

reset() - Method in class stoppers.MetaStripeStop

reset() - Method in class stoppers.MultiNodeThresholdStop

reset() - Method in class stoppers.NeuroNoiseStop

reset() - Method in class stoppers.NeuroTest2Stop

reset() - Method in class stoppers.NeuroTest3Stop

reset() - Method in class stoppers.NoChangeStop

reset() - Method in class stoppers.OscillatingStripeStop

reset() - Method in class stoppers.OscillatorStop

reset() - Method in class stoppers.OscillatorStopSpecial

reset() - Method in class stoppers.PulseStop

reset() - Method in class stoppers.SimpleStop

reset() - Method in class stoppers.ThresholdStop

reset() - Method in class stoppers.TwoCellDifferenceStop

resetStopper() - Method in class iterators.ModelIterator

resetSyntax() - Method in class main.BetterTokenizer

* Resets this tokenizer's syntax table so that all characters are * "ordinary." See the ordinaryChar method * for more information on a character being ordinary.

resizeDisplay() - Method in class genegui.NetworkPaintPanel

Resizes the network display to make it fit neatly within the bounds of the panel less the Insets.

rng - Static variable in class main.Globals

rules - Variable in class parameterrules.ParameterRuleSet

run() - Method in class genegui.ParInspector

run() - Method in class iterators.ModelIterator

run() - Method in class main.GeneNet

run() - Method in class main.ModelRunner

No other class should call run() directly.

run() - Method in class stat.CrossCorrStat

run() - Method in class stat.Stat

runControl(int) - Method in class genegui.AffectorViewPanel

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.CellSurfaceViewer

Method for controling model/iterator runs.

runControl(int) - Method in interface genegui.GuiInterface

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.MainGui

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.ModelStateEditor

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.ModelStateNodePalette

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.ModelStateView

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.NetworkViewer2

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.NodeStateViewer

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.NodeViewPanel

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.ParameterViewer

Method for controling model/iterator runs.

runControl(int) - Method in class genegui.TimeGraph

Method for controling model/iterator runs.

runControl(int) - Method in class main.GeneNet

Method for controling model/iterator runs.

runReset() - Method in class genegui.IteratorViewer

runStarted() - Method in class genegui.IteratorViewer

runStatus(int) - Method in class genegui.AffectorViewPanel

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.CellSurfaceViewer

Method for reporting status of the model/iterator runs

runStatus(int) - Method in interface genegui.GuiInterface

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.MainGui

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.ModelStateEditor

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.ModelStateNodePalette

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.ModelStateView

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.NetworkViewer2

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.NodeStateViewer

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.NodeViewPanel

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.ParameterViewer

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class genegui.TimeGraph

Method for reporting status of the model/iterator runs

runStatus(int) - Method in class main.GeneNet

Method for reporting status of the model/iterator runs

runStopped() - Method in class genegui.IteratorViewer

runThread - Variable in class iterators.ModelIterator

runThread - Variable in class main.ModelRunner

runTime - Static variable in class main.Globals

The amount of time to run a model when the user selects Run from the menu.

runner - Variable in class iterators.Function

running - Variable in class iterators.ModelIterator

running - Variable in class main.ModelRunner

S

SAVE - Static variable in interface genegui.GuiInterface

SAVE_MODEL - Static variable in class genegui.GeneNetInterface

SAVE_MODEL_TEXT - Static variable in class genegui.GeneNetInterface

STEADYSTATE - Static variable in class main.NodeTemplate

STEP_ITERATOR - Static variable in interface genegui.GuiInterface

STEP_MODEL - Static variable in interface genegui.GuiInterface

STEP_MODEL_TEXT - Static variable in class genegui.GeneNetInterface

STOP_ITERATOR - Static variable in interface genegui.GuiInterface

STOP_TEXT - Static variable in class genegui.GeneNetInterface

SUM - Static variable in class main.NodeTemplate

SaturationEnhancerAff - class affectors.SaturationEnhancerAff.

This is the wrapper for meta-affectors which need to be put through a saturating function.

SaturationEnhancerAff() - Constructor for class affectors.SaturationEnhancerAff

SemiExplicitAPCIntegrator - class integrators.SemiExplicitAPCIntegrator.

The SemiExplicitAPCIntegrator implements a custom-modified fourth-order Adams-Bashforth-Moulton predictor-corrector method, with a special way of writing the corrector formula that, dependent on the parameters of the underlying equations, allows the fixed-point iteration to converge for larger values of the partial derivatives of the system than would be possible for the straight Adams method.

SemiExplicitAPCIntegrator() - Constructor for class integrators.SemiExplicitAPCIntegrator

SequenceACSC1 - class initialconditions.SequenceACSC1.

An initial condition class that sets a middle cell to one value and then the cells immediately surrounding that middle cell to a second value.

SequenceACSC1() - Constructor for class initialconditions.SequenceACSC1

SequenceACSC1(String, int, float, float) - Constructor for class initialconditions.SequenceACSC1

SimpleStop - class stoppers.SimpleStop.

SimpleStop() - Constructor for class stoppers.SimpleStop

SimpleStop(float) - Constructor for class stoppers.SimpleStop

SingleCellSelector - class genegui.SingleCellSelector.

SingleCellSelector(ModelState, int, ActionListener) - Constructor for class genegui.SingleCellSelector

Constructor

Stat - class stat.Stat.

Stat is the base class for statistical output classes from GeneNet.

Stat() - Constructor for class stat.Stat

SteepestDescentIterator - class iterators.SteepestDescentIterator.

SteepestDescentIterator() - Constructor for class iterators.SteepestDescentIterator

StripeStop - class stoppers.StripeStop.

StripeStop() - Constructor for class stoppers.StripeStop

SuccessList - class genegui.SuccessList.

SuccessList.java Accumulates a list of "successful" runs.

SuccessList() - Constructor for class genegui.SuccessList

Simple constructor.

SuccessListBeanInfo - class genegui.SuccessListBeanInfo.

SuccessListBeanInfo() - Constructor for class genegui.SuccessListBeanInfo

SumAff - class affectors.SumAff.

This is a special "meta-affector".

SumAff() - Constructor for class affectors.SumAff

SummaryStat - class stat.SummaryStat.

Calculates a number of summary statistics for the parameter sets, including average, std.

SummaryStat() - Constructor for class stat.SummaryStat

SurfaceIterator - class iterators.SurfaceIterator.

Use this to find the surface around a particular instance of the network.

SurfaceIterator() - Constructor for class iterators.SurfaceIterator

save() - Method in class genegui.IteratorViewer

save(PrintWriter) - Method in class main.Cell

saveDataSets(File) - Method in class genegui.TimeGraph

Saves all Data from all data sets to an external file

saveExtra(PrintWriter) - Method in class iterators.ModelIterator

Called when the iterator finishes running if isSaveExtra returns true.

saveHeadings(PrintWriter) - Method in class main.Cell

saveNetworkFile(PrintWriter) - Method in class main.Model

saveOutput(PrintWriter, String) - Method in class iterators.ACSCIterator

saveOutput(PrintWriter, String) - Method in class iterators.ACSC_SwitchIterator

saveOutput(PrintWriter, String) - Method in class iterators.ModelIterator

Saves tagged output from this iterator to a cam file.

saveOutput(PrintWriter, String) - Method in class iterators.TransectIterator

saveOutput(PrintWriter, String) - Method in class stoppers.NeuroNoiseStop

saveOutput(PrintWriter, String) - Method in class stoppers.NeuroTest2Stop

saveOutput(PrintWriter, String) - Method in class stoppers.NeuroTest3Stop

saveOutput(PrintWriter, String) - Method in class stoppers.SimpleStop

This function is called to save information to a cam file.

saveOutputTags(PrintWriter, String) - Method in class iterators.ACSCIterator

saveOutputTags(PrintWriter, String) - Method in class iterators.ACSC_SwitchIterator

saveOutputTags(PrintWriter, String) - Method in class iterators.ModelIterator

This is called when a cam file is being set up.

saveOutputTags(PrintWriter, String) - Method in class iterators.TransectIterator

saveOutputTags() - Method in class iterators.UberIteratorFunction

Save out a list of all the types of data that might be output together with a good parameter set.

saveOutputTags(PrintWriter, String) - Method in class stoppers.NeuroNoiseStop

saveOutputTags(PrintWriter, String) - Method in class stoppers.NeuroTest2Stop

saveOutputTags(PrintWriter, String) - Method in class stoppers.NeuroTest3Stop

saveOutputTags(PrintWriter, String) - Method in class stoppers.SimpleStop

This function is called when a cam file is being set up.

saveParameters(PrintWriter, String) - Method in class parameters.ParameterSetArray

scoreBullseye(Cell[], float) - Method in class stoppers.CellSurroundStop

scoreStripe(Cell[], float) - Method in class stoppers.OscillatingStripeStop

scriptRunning - Static variable in class main.Globals

True when a script is running.

selectCell(int, boolean) - Method in class genegui.ModelStateView

Sets a single cell as being selected.

setActiveModelStateNodePalette(ModelStateNodePalette) - Method in class genegui.ModelState

Sets the one and only ModelStateNodePalette attached to thsi ModelState.

setActiveModelStateView(ModelStateView) - Method in class genegui.ModelState

Sets the ModelStateView that is currently active (selected).

setAdaptiveStepsizing(boolean) - Method in class integrators.HuenIntegrator

Deprecated. Turn on or off the recursion this simple-minded method uses to try and make the error estimate acceptable.

setAffector(AffectorTemplate) - Method in class genegui.InspectorList

setAffectorSelectedColor(Color) - Method in class genegui.NetworkPaintPanel

Sets the color of selected AffectorDisplays.

setAffectors(Vector, Cell) - Method in class main.Node

setArrangeByModel(boolean) - Method in class parameters.ParameterSet

Set to true if parameters should be put into the same order in this parameter set as they are in the model.

setAtDefaultLocation(JInternalFrame) - Method in class genegui.MainGui

Places the JInternalFrame at its default location.

setBounds(float, float) - Method in class parameters.Parameter

setCalculatorNode(boolean) - Method in class main.NodeTemplate

setCell(int) - Method in class genegui.InspectorList

setCell(int) - Method in class genegui.NodeStateViewer

Sets the index of the cell whose nodes are being displayed/altered.

setCellPosition(Point2D.Float) - Method in class genegui.CellState

Sets the location of the cell.

setCellState(CellState) - Method in class genegui.CellState

Sets the state of this cell by copying it from the another cell state passed as an argument.

setCellState(int, CellState) - Method in class genegui.ModelState

Sets the CellState for the given cell to that of a new CellState.

setCellStateArray(CellState[]) - Method in class genegui.ModelState

Replaces the entire CellStateArray with a new one.

setColor(Color) - Method in class main.NodeTemplate

setColorMapValues(int, float, float, float) - Method in class genegui.NetworkPaintPanel

Sets the parameters that control how colors are mapped during active display mode.

setCompareParamSetArray(ParameterSetArray) - Static method in class main.Globals

setCompareParamSetArray(String) - Static method in class main.Globals

setContainsTarget(boolean) - Method in class affectors.Affector

setCurParamSetArray(ParameterSetArray) - Static method in class main.Globals

setCurParamSetArray(String) - Static method in class main.Globals

setCurTag(String) - Method in class parameters.ParameterSetArray

setCutoff(float) - Method in class stoppers.MetaStop

setCutoff(float) - Method in class stoppers.MetaStopTwo

setCutoff(float) - Method in class stoppers.SimpleStop

setDefaultInitialValue(int, float, Cell[]) - Method in class initialconditions.InitialConditionSet

setDefaultStepSize(float) - Method in class integrators.Integrator

Set the default step size; this is usually only used by Integrator.reset() to return the Integrator to it's defualt state after an entire integration.

setDescriptions(String, String[], String[]) - Method in class affectors.Affector

setEpsilon(float) - Method in class stoppers.CellThresholdStop

setEpsilon(float) - Method in class stoppers.MultiNodeThresholdStop

setErrorTolerance(float) - Method in class integrators.Integrator

Set the per-step error tolerance; different methods make different use of this value, so see documentation of each Integrator subclass to determine how best to set this, or whether the default value is appropriate.

setEvaluating(boolean) - Method in class stoppers.FPStripeStop

setEvaluating(boolean) - Method in class stoppers.SimpleStop

setFPStabilizer(float) - Method in class iterators.UberIteratorFunction

setFieldValue(int, float) - Method in class parameters.ParameterSet

setFieldValue(String, float) - Method in class parameters.ParameterSet

setFilename(String) - Method in class parameters.ParameterSetArray

setFinalValues(NodeValues[]) - Method in class integrators.Integrator

setFinalValues(float[]) - Method in class main.Node

setFirstWheel(ParameterSetArray) - Method in class iterators.MatingIterator

setFrom(Cell[], boolean) - Method in class initialconditions.CellIC

setFrom(Cell[], boolean) - Method in class initialconditions.ColumnIC

setFrom(Cell[], boolean) - Method in class initialconditions.InitialCondition

setFrom(Cell[]) - Method in class initialconditions.InitialConditionSet

setFrom(Cell[], boolean) - Method in class initialconditions.InitialConditionSet

setFrom(Cell[], boolean) - Method in class initialconditions.RowIC

setFrom(ParameterSet) - Method in class parameters.ParameterSet

Sets parameters in this set from the set that's passed in, for all parameters that appear in both

setFrom(float[]) - Method in class parameters.ParameterSet

And this is for setting par values from the same vector.

setFromFinalValues() - Method in class main.CalculatorNode

setFunction(Function) - Method in class iterators.ModelIterator

setGlobalOutfile(String) - Static method in class main.GlobalIO

setGraphIndex(int) - Method in class genegui.TimeGraph

Sets the DataSetIndex, which determines which DataSet is being displayed.

setGridOn(boolean) - Method in interface genegui.OptionsPanelInterface

Turns grid display on or off.

setGridOn(boolean) - Method in class genegui.TimeGraph

Turns grid display on or off.

setGridSpacing(int) - Method in interface genegui.OptionsPanelInterface

Set spacing for grid pattern.

setGridSpacing(int) - Method in class genegui.TimeGraph

Set spacing for grid pattern.

setGroupNum(int) - Method in class parameters.ParameterSet

setHighThreshold(float) - Method in class parameters.ParameterSetArray

setIcon(boolean) - Method in class genegui.CellSurfaceViewer

Over-ride native method to allow the small version of the window

setIcon(boolean) - Method in class genegui.ParameterViewer

Over-ride native method to allow the small version of the window

setIcon(boolean) - Method in class genegui.TimeGraph

Over-ride native method to allow the small version of the window

setInitialConditions(Model) - Method in class initialconditions.InitialConditionStorage

setInitialValue(String, float) - Method in class main.Cell

setInitialValue(int, float) - Method in class main.Cell

setInitialValue(int, float) - Method in class main.Model

Calls setDefaultInitialValue with given parameters in its initializers object.

setIntegrationAlgorithm(String) - Static method in class main.Globals

setIntegrationValues(NodeValues[]) - Method in class integrators.Integrator

setIntegrationValues(float[]) - Method in class main.Node

setIntersectX(int) - Method in class main.AffectorTemplate

setIntersectY(int) - Method in class main.AffectorTemplate

setInterval(float) - Method in class stoppers.CellThresholdStop

setInterval(float) - Method in class stoppers.MultiNodeThresholdStop

setIteratorFile(String) - Method in class genegui.Configuration

setIteratorViewer(IteratorViewer) - Method in class iterators.ModelIterator

Sets the IteratorViewer that this iterator reports to.

setItsNum(int) - Method in class main.Cell

setLabelsAndTypes() - Method in class affectors.Affector

setLabelsAndTypes() - Method in class affectors.Affector_Template

setLabelsAndTypes() - Method in class affectors.Cleavage2A_ICAff

setLabelsAndTypes() - Method in class affectors.Cleavage2B_ICAff

setLabelsAndTypes() - Method in class affectors.CleavageA_ECAff

setLabelsAndTypes() - Method in class affectors.CleavageA_ICAff

setLabelsAndTypes() - Method in class affectors.CleavageA_ICDipAff

setLabelsAndTypes() - Method in class affectors.CleavageB_ECAff

setLabelsAndTypes() - Method in class affectors.CleavageB_ICAff

setLabelsAndTypes() - Method in class affectors.CleavageB_ICDipAff

setLabelsAndTypes() - Method in class affectors.CleaveA_Aff

setLabelsAndTypes() - Method in class affectors.CleaveB_Aff

setLabelsAndTypes() - Method in class affectors.CompAct2Aff

setLabelsAndTypes() - Method in class affectors.ConstantInputAff

setLabelsAndTypes() - Method in class affectors.ConstantLevelAff

setLabelsAndTypes() - Method in class affectors.ConversionEAff

setLabelsAndTypes() - Method in class affectors.ConversionIAff

setLabelsAndTypes() - Method in class affectors.DecayAff

setLabelsAndTypes() - Method in class affectors.DecayRegDownAff

setLabelsAndTypes() - Method in class affectors.DecayRegUpAff

setLabelsAndTypes() - Method in class affectors.DefinedValuesAff

setLabelsAndTypes() - Method in class affectors.DefinedValuesIndicatorAff

setLabelsAndTypes() - Method in class affectors.Dephosphor1StepA_ICAff

setLabelsAndTypes() - Method in class affectors.Dephosphor1StepB_ICAff

setLabelsAndTypes() - Method in class affectors.DephosphorylateA_Aff

setLabelsAndTypes() - Method in class affectors.DephosphorylateB_Aff

setLabelsAndTypes() - Method in class affectors.DephosphorylationA_ICAff

setLabelsAndTypes() - Method in class affectors.DephosphorylationB_ICAff

setLabelsAndTypes() - Method in class affectors.DimerizeAllMembrane_AAff

setLabelsAndTypes() - Method in class affectors.DimerizeAllMembrane_BAff

setLabelsAndTypes() - Method in class affectors.DimerizeCrossMembrane_AAff

setLabelsAndTypes() - Method in class affectors.DimerizeCrossMembrane_BAff

setLabelsAndTypes() - Method in class affectors.DimerizeCytoMem_AAff

setLabelsAndTypes() - Method in class affectors.DimerizeCytoMem_BAff

setLabelsAndTypes() - Method in class affectors.DimerizeCytoMem_CAff

setLabelsAndTypes() - Method in class affectors.DimerizeMemCyto_AAff

setLabelsAndTypes() - Method in class affectors.DimerizeMemCyto_BAff

setLabelsAndTypes() - Method in class affectors.DimerizeMemCyto_CAff

setLabelsAndTypes() - Method in class affectors.Dimerize_AAff

setLabelsAndTypes() - Method in class affectors.Dimerize_BAff

setLabelsAndTypes() - Method in class affectors.DissociationA_Aff

setLabelsAndTypes() - Method in class affectors.DissociationB_Aff

setLabelsAndTypes() - Method in class affectors.DissociationC_Aff

setLabelsAndTypes() - Method in class affectors.DissociationCytoMemA_Aff

setLabelsAndTypes() - Method in class affectors.DissociationCytoMemB_Aff

setLabelsAndTypes() - Method in class affectors.DissociationCytoMemC_Aff

setLabelsAndTypes() - Method in class affectors.DissociationEC_Com_Aff

setLabelsAndTypes() - Method in class affectors.DissociationEC_Lig_Aff

setLabelsAndTypes() - Method in class affectors.DissociationEC_Rec_Aff

setLabelsAndTypes() - Method in class affectors.EndoEAff

setLabelsAndTypes() - Method in class affectors.EndoIAff

setLabelsAndTypes() - Method in class affectors.EnhancerRegionAff

half life param

setLabelsAndTypes() - Method in class affectors.EnzymeConversionEC_Pro_Aff

setLabelsAndTypes() - Method in class affectors.EnzymeConversionEC_Sub_Aff

setLabelsAndTypes() - Method in class affectors.ExoEAff

setLabelsAndTypes() - Method in class affectors.ExoIAff

setLabelsAndTypes() - Method in class affectors.Formula1Aff

setLabelsAndTypes() - Method in class affectors.HeatShockAff

setLabelsAndTypes() - Method in class affectors.LMxferEAff

setLabelsAndTypes() - Method in class affectors.LMxferIAff

setLabelsAndTypes() - Method in class affectors.MultiEnhancerAff

setLabelsAndTypes() - Method in class affectors.MxferInAff

setLabelsAndTypes() - Method in class affectors.MxferOutAff

setLabelsAndTypes() - Method in class affectors.NoChangeAff

setLabelsAndTypes() - Method in class affectors.Phosphor1StepA_ICAff

setLabelsAndTypes() - Method in class affectors.Phosphor1StepB_ICAff

setLabelsAndTypes() - Method in class affectors.PhosphorylateA_Aff

setLabelsAndTypes() - Method in class affectors.PhosphorylateB_Aff

setLabelsAndTypes() - Method in class affectors.PhosphorylationA_ICAff

setLabelsAndTypes() - Method in class affectors.PhosphorylationB_ICAff

setLabelsAndTypes() - Method in class affectors.PlaceHolderAff

setLabelsAndTypes() - Method in class affectors.Product

setLabelsAndTypes() - Method in class affectors.ProductAff

setLabelsAndTypes() - Method in class affectors.PsiAff

setLabelsAndTypes() - Method in class affectors.PsiECAff

setLabelsAndTypes() - Method in class affectors.RecycleAAff

setLabelsAndTypes() - Method in class affectors.RecycleBAff

setLabelsAndTypes() - Method in class affectors.SaturationEnhancerAff

setLabelsAndTypes() - Method in class affectors.SumAff

setLabelsAndTypes() - Method in class affectors.TlnAff

setLabelsAndTypes() - Method in class affectors.TlnRegUpAff

setLabelsAndTypes() - Method in class affectors.Txn1Aff

setLabelsAndTypes() - Method in class affectors.Txn1ECAff

setLabelsAndTypes() - Method in class affectors.Txn2aAff

setLabelsAndTypes() - Method in class affectors.Txn2aDipAff

setLabelsAndTypes() - Method in class affectors.Txn2bAff

setLabelsAndTypes() - Method in class affectors.Txn2bDipAff

setLabelsAndTypes() - Method in class affectors.Txn3aAff

setLabelsAndTypes() - Method in class affectors.Txn3bAff

setLabelsAndTypes() - Method in class affectors.Txn4Aff

setLabelsAndTypes() - Method in class affectors.Txn4DipAff

setLabelsAndTypes() - Method in class affectors.Txn5Aff

setLabelsAndTypes() - Method in class affectors.Txn6aAff

setLabelsAndTypes() - Method in class affectors.Txn6bAff

setLabelsAndTypes() - Method in class affectors.TxnLeakyCyceAff

setLabelsAndTypes() - Method in class affectors.TxnSiteActInhibit2Aff

setLabelsAndTypes() - Method in class affectors.TxnSiteActInhibit3Aff

setLabelsAndTypes() - Method in class affectors.TxnSiteActInhibitAff

setLabelsAndTypes() - Method in class affectors.TxnSiteActivatorAff

setLabelsAndTypes() - Method in class affectors.TxnSiteAddInhibitorAff

setLabelsAndTypes() - Method in class affectors.TxnSiteInhibitorAff

setLabelsAndTypes() - Method in class affectors.VonForresterA_Aff

setLabelsAndTypes() - Method in class affectors.VonForresterA_ECAff

setLabelsAndTypes() - Method in class affectors.VonForresterA_ICAff

setLabelsAndTypes() - Method in class affectors.VonForresterB_Aff

setLabelsAndTypes() - Method in class affectors.VonForresterB_ECAff

setLabelsAndTypes() - Method in class affectors.VonForresterB_ICAff

setLabelsAndTypes() - Method in class affectors.WhiteNoiseAff

setLabelsAndTypes() - Method in class affectors.XferInAff

setLabelsAndTypes() - Method in class affectors.XferOutAff

setLastOpenedDir(String) - Method in class genegui.Configuration

setLastSavedDir(String) - Method in class genegui.Configuration

setLegendOn(boolean) - Method in interface genegui.OptionsPanelInterface

Turns legend display on or off.

setLegendOn(boolean) - Method in class genegui.TimeGraph

Turns legend display on or off.

setLocation(int, int) - Method in class genegui.Console

setLocation(Point2D.Float) - Method in class main.Cell

Sets the location of the cell

setLowThreshold(float) - Method in class parameters.ParameterSetArray

setLowerBound(int, float) - Method in class parameters.ParameterSet

setMainProgram(GeneNet) - Static method in class main.Globals

setMaxAmplitude(float) - Method in class main.NoiseGenerator

setMaxFrequency(float) - Method in class main.NoiseGenerator

setMaximum(boolean) - Method in class genegui.CellSurfaceViewer

Over-ride native method to allow the normal version of the window

setMaximum(boolean) - Method in class genegui.ParameterViewer

Over-ride native method to allow the normal version of the window

setMaximum(boolean) - Method in class genegui.TimeGraph

Over-ride native method to allow the normal version of the window

setMessagesText(String) - Method in class genegui.IteratorViewer

setMinFrequency(float) - Method in class main.NoiseGenerator

setMinStepSize(float) - Method in class integrators.HuenIntegrator

Deprecated. Set the minimum timestep.

setMode(int) - Method in class stoppers.CellThresholdStop

setMode(int) - Method in class stoppers.MultiNodeThresholdStop

setModel(Model) - Method in class genegui.CellSurfaceViewer

Sets the model.

setModel(Model) - Method in class genegui.GeneNetInterface

Call this when the currently loaded model changes

setModel(Model) - Method in class genegui.InspectorList

setModel(Model) - Method in class genegui.ModelState

Sets the model.

setModel(Cell[]) - Method in class initialconditions.CellIC

setModel(Cell[]) - Method in class initialconditions.CenterIC

setModel(Cell[]) - Method in class initialconditions.ColumnIC

setModel(Cell[]) - Method in class initialconditions.IncrementingACSC1

setModel(Cell[]) - Method in class initialconditions.IncrementingIC

setModel(Cell[]) - Method in class initialconditions.InitialCondition

setModel(Cell[]) - Method in class initialconditions.InitialConditionSet

setModel(Cell[]) - Method in class initialconditions.NeuroNoiseIC

setModel(Cell[]) - Method in class initialconditions.RowIC

setModel(Cell[]) - Method in class initialconditions.SequenceACSC1

setModel(Cell[]) - Method in class iterators.ICSamplingFunction

setModel() - Method in class parameters.ParameterSet

Sets the currently loaded model according to the parameters in this parameter set.

setModelFile(String) - Method in class genegui.Configuration

setModelFile(String, long) - Static method in class main.Globals

setModelState(ModelState) - Method in class genegui.CellSurfaceViewer

Sets the ModelState that this CellViewer reads from when painting.

setModelState(ModelState) - Method in class genegui.NodeStateViewer

Sets a new ModelState.

setModelState(ModelState) - Method in class genegui.TimeGraph

Sets the ModelState that this CellViewer reads from when painting.

setModelState(ModelState) - Method in class main.Model

Sets a ModelState object for this Model.

setModelStateEditor(ModelStateEditor) - Method in class genegui.ModelState

Sets a ModelStateEditor to be used with this ModelState if there is one

setModelStates(Vector) - Method in class genegui.SuccessList

setName(String) - Method in class main.Network

setName(String) - Method in class main.NodeTemplate

setNetwork(Network) - Method in class genegui.CellSurfaceViewer

Sets the network used by all cells.

setNetwork(Network) - Method in class genegui.GeneNetInterface

Call this when the currently loaded model (network) changes

setNetwork(Network) - Method in class genegui.InspectorList

setNetwork(Network) - Method in class genegui.NetworkPaintPanel

Sets the network and rebuilds the display

setNetwork(Network) - Method in class initialconditions.InitialConditionSet

setNode(int) - Method in class genegui.InspectorList

setNodeNum(int) - Method in class main.NodeTemplate

setNodeSelected(int, boolean) - Method in class genegui.ModelStateView

Sets a node as being selected (viewed) by this viewer.

setNodeSelectedColor(Color) - Method in class genegui.NetworkPaintPanel

Sets the color of selected NodeDisplays.

setNodeTemplates(NodeTemplate[]) - Method in class genegui.ModelState

Sets the node template array.

setNodeValue(int, float) - Method in class genegui.CellState

Sets the value of a node for this cell.

setNodeValueArray(float[]) - Method in class genegui.CellState

Sets the values of all the nodes for this cell based upon an array of values passed to it.

setNoise(float) - Method in class main.Node

setNumFrequencies(int) - Method in class main.NoiseGenerator

setNumFuncCalls(int) - Method in class parameters.ParameterSet

setNumMatings(int) - Method in class iterators.MatingIterator

setNumSides(int) - Method in class main.CalculatorNode

setNumSides(int) - Method in class main.Node

setNumberOfSubsteps(int) - Method in class integrators.MidpointIntegrator

If one is going to use this object as an integrator in its own right, rather than as a subsidiary of a more sophisticate one, then one has the option of setting how many substeps it uses to cross an interval.

setOutputFile(String) - Method in class iterators.ModelIterator

Called when the output file is changed.

setOutputFile(String) - Method in class iterators.UberIterator

Called when the output file is changed.

setOutputFile(String) - Method in class stat.Stat

setOutputStream(PrintWriter) - Method in class iterators.UberIteratorFunction

setParamRange(String, float, float, String) - Static method in class affectors.Affector

setParamRange(String, float, float, int) - Static method in class affectors.Affector

setParamValue(String, float) - Static method in class affectors.Affector

setParamValue(int, float) - Static method in class affectors.Affector

setParameter(Parameter) - Static method in class affectors.Affector

Use this to set a parameter using a Parameter object.

setParameter(Parameter, int) - Method in class parameters.ParameterSet

setParameterNames(Vector) - Method in class genegui.SuccessList

setParameterNumbers(int[]) - Method in class affectors.Affector

setParameterNumbers(int[]) - Method in class affectors.Affector_Template

setParameterNumbers(int[]) - Method in class affectors.Cleavage2A_ICAff

setParameterNumbers(int[]) - Method in class affectors.Cleavage2B_ICAff

setParameterNumbers(int[]) - Method in class affectors.CleavageA_ECAff

setParameterNumbers(int[]) - Method in class affectors.CleavageA_ICAff

setParameterNumbers(int[]) - Method in class affectors.CleavageA_ICDipAff

setParameterNumbers(int[]) - Method in class affectors.CleavageB_ECAff

setParameterNumbers(int[]) - Method in class affectors.CleavageB_ICAff

setParameterNumbers(int[]) - Method in class affectors.CleavageB_ICDipAff

setParameterNumbers(int[]) - Method in class affectors.CleaveA_Aff

setParameterNumbers(int[]) - Method in class affectors.CleaveB_Aff

setParameterNumbers(int[]) - Method in class affectors.CompAct2Aff

setParameterNumbers(int[]) - Method in class affectors.ConstantInputAff

setParameterNumbers(int[]) - Method in class affectors.ConstantLevelAff

setParameterNumbers(int[]) - Method in class affectors.ConversionEAff

setParameterNumbers(int[]) - Method in class affectors.ConversionIAff

setParameterNumbers(int[]) - Method in class affectors.DecayAff

setParameterNumbers(int[]) - Method in class affectors.DecayRegDownAff

setParameterNumbers(int[]) - Method in class affectors.DecayRegUpAff

setParameterNumbers(int[]) - Method in class affectors.DefinedValuesAff

setParameterNumbers(int[]) - Method in class affectors.DefinedValuesIndicatorAff

setParameterNumbers(int[]) - Method in class affectors.Dephosphor1StepA_ICAff

setParameterNumbers(int[]) - Method in class affectors.Dephosphor1StepB_ICAff

setParameterNumbers(int[]) - Method in class affectors.DephosphorylateA_Aff

setParameterNumbers(int[]) - Method in class affectors.DephosphorylateB_Aff

setParameterNumbers(int[]) - Method in class affectors.DephosphorylationA_ICAff

setParameterNumbers(int[]) - Method in class affectors.DephosphorylationB_ICAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeAllMembrane_AAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeAllMembrane_BAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeCrossMembrane_AAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeCrossMembrane_BAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeCytoMem_AAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeCytoMem_BAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeCytoMem_CAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeMemCyto_AAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeMemCyto_BAff

setParameterNumbers(int[]) - Method in class affectors.DimerizeMemCyto_CAff

setParameterNumbers(int[]) - Method in class affectors.Dimerize_AAff

setParameterNumbers(int[]) - Method in class affectors.Dimerize_BAff

setParameterNumbers(int[]) - Method in class affectors.DissociationA_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationB_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationC_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationCytoMemA_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationCytoMemB_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationCytoMemC_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationEC_Com_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationEC_Lig_Aff

setParameterNumbers(int[]) - Method in class affectors.DissociationEC_Rec_Aff

setParameterNumbers(int[]) - Method in class affectors.EndoEAff

setParameterNumbers(int[]) - Method in class affectors.EndoIAff

setParameterNumbers(int[]) - Method in class affectors.EnhancerRegionAff

setParameterNumbers(int[]) - Method in class affectors.EnzymeConversionEC_Pro_Aff

setParameterNumbers(int[]) - Method in class affectors.EnzymeConversionEC_Sub_Aff

setParameterNumbers(int[]) - Method in class affectors.ExoEAff

setParameterNumbers(int[]) - Method in class affectors.ExoIAff

setParameterNumbers(int[]) - Method in class affectors.Formula1Aff

setParameterNumbers(int[]) - Method in class affectors.HeatShockAff

setParameterNumbers(int[]) - Method in class affectors.LMxferEAff

setParameterNumbers(int[]) - Method in class affectors.LMxferIAff

setParameterNumbers(int[]) - Method in class affectors.MultiEnhancerAff

setParameterNumbers(int[]) - Method in class affectors.MxferInAff

setParameterNumbers(int[]) - Method in class affectors.MxferOutAff

setParameterNumbers(int[]) - Method in class affectors.NoChangeAff

setParameterNumbers(int[]) - Method in class affectors.Phosphor1StepA_ICAff

setParameterNumbers(int[]) - Method in class affectors.Phosphor1StepB_ICAff

setParameterNumbers(int[]) - Method in class affectors.PhosphorylateA_Aff

setParameterNumbers(int[]) - Method in class affectors.PhosphorylateB_Aff

setParameterNumbers(int[]) - Method in class affectors.PhosphorylationA_ICAff

setParameterNumbers(int[]) - Method in class affectors.PhosphorylationB_ICAff

setParameterNumbers(int[]) - Method in class affectors.PlaceHolderAff

setParameterNumbers(int[]) - Method in class affectors.Product

setParameterNumbers(int[]) - Method in class affectors.ProductAff

setParameterNumbers(int[]) - Method in class affectors.PsiAff

setParameterNumbers(int[]) - Method in class affectors.PsiECAff

setParameterNumbers(int[]) - Method in class affectors.RecycleAAff

setParameterNumbers(int[]) - Method in class affectors.RecycleBAff

setParameterNumbers(int[]) - Method in class affectors.SaturationEnhancerAff

setParameterNumbers(int[]) - Method in class affectors.SumAff

setParameterNumbers(int[]) - Method in class affectors.TlnAff

setParameterNumbers(int[]) - Method in class affectors.TlnRegUpAff

setParameterNumbers(int[]) - Method in class affectors.Txn1Aff

setParameterNumbers(int[]) - Method in class affectors.Txn1ECAff

setParameterNumbers(int[]) - Method in class affectors.Txn2aAff

setParameterNumbers(int[]) - Method in class affectors.Txn2aDipAff

setParameterNumbers(int[]) - Method in class affectors.Txn2bAff

setParameterNumbers(int[]) - Method in class affectors.Txn2bDipAff

setParameterNumbers(int[]) - Method in class affectors.Txn3aAff

setParameterNumbers(int[]) - Method in class affectors.Txn3bAff

setParameterNumbers(int[]) - Method in class affectors.Txn4Aff

setParameterNumbers(int[]) - Method in class affectors.Txn4DipAff

setParameterNumbers(int[]) - Method in class affectors.Txn5Aff

setParameterNumbers(int[]) - Method in class affectors.Txn6aAff

setParameterNumbers(int[]) - Method in class affectors.Txn6bAff

setParameterNumbers(int[]) - Method in class affectors.TxnLeakyCyceAff

setParameterNumbers(int[]) - Method in class affectors.TxnSiteActInhibit2Aff

setParameterNumbers(int[]) - Method in class affectors.TxnSiteActInhibit3Aff

setParameterNumbers(int[]) - Method in class affectors.TxnSiteActInhibitAff

setParameterNumbers(int[]) - Method in class affectors.TxnSiteActivatorAff

setParameterNumbers(int[]) - Method in class affectors.TxnSiteAddInhibitorAff

setParameterNumbers(int[]) - Method in class affectors.TxnSiteInhibitorAff

setParameterNumbers(int[]) - Method in class affectors.VonForresterA_Aff

setParameterNumbers(int[]) - Method in class affectors.VonForresterA_ECAff

setParameterNumbers(int[]) - Method in class affectors.VonForresterA_ICAff

setParameterNumbers(int[]) - Method in class affectors.VonForresterB_Aff

setParameterNumbers(int[]) - Method in class affectors.VonForresterB_ECAff

setParameterNumbers(int[]) - Method in class affectors.VonForresterB_ICAff

setParameterNumbers(int[]) - Method in class affectors.WhiteNoiseAff

setParameterNumbers(int[]) - Method in class affectors.XferInAff

setParameterNumbers(int[]) - Method in class affectors.XferOutAff

setParameterSet(ParameterSet) - Method in class genegui.ParameterViewer

Resets the ParameterSet

setParameterSet(ParameterSet) - Method in class main.Model

setPass(boolean) - Method in class parameters.ParameterSet

setPrint(boolean) - Method in class iterators.ModelIterator

setPrintStream(PrintWriter) - Method in class iterators.ModelIterator

setRandomSeed(int) - Static method in class main.MoreMath

setRangeOn(boolean) - Method in interface genegui.OptionsPanelInterface

Turns range display on or off.

setRangeOn(boolean) - Method in class genegui.TimeGraph

Turns range display on or off.

setRunMode(int) - Method in class iterators.UberIteratorFunction

setRunMode(String) - Method in class main.ModelRunner

setRunTime(float) - Static method in class main.Globals

setSaveMatings(boolean) - Method in class iterators.MatingIterator

setScaleAndTranslation(double, Point) - Method in class genegui.CellSurfaceViewer

Sets scale and translation for CellShapeArray used in painting operations.

setScaleAndTranslation(double, Point) - Method in class genegui.ModelStateView

Sets scale and translation for CellShapeArray used in painting operations.

setScore(float) - Method in class parameters.ParameterSet

setScores(Vector) - Method in class genegui.SuccessList

setScriptRunning(boolean) - Static method in class main.Globals

setSecondWheel(ParameterSetArray) - Method in class iterators.MatingIterator

setSelected(boolean) - Method in class genegui.ModelStateView

Sets this ModelStateView as being selected.

setSelectedCellState(CellState) - Method in class genegui.NetworkPaintPanel

Sets the CellState for a selected cell.

setSelectedCells(boolean[]) - Method in class genegui.ModelState

Accepts a list of cells that are selected in a ModelStateView and updates the ActiveModelStateNodePalette.

setSelectedNodes(boolean[]) - Method in class genegui.ModelStateNodePalette

Sets those nodes that are selected.

setShow(boolean) - Method in class main.NodeTemplate

setSide(int) - Method in class affectors.Affector

setSide(int) - Method in class affectors.EnhancerRegionAff

setSide(int) - Method in class affectors.LMxferIAff

setSided(boolean, int[]) - Method in class affectors.Affector

setState(ParameterSet) - Method in class iterators.ModelIterator

setStepSize(float) - Method in class integrators.HuenIntegrator

Deprecated. HuenIntegrator overrides Integrator.setStepSize(float) to enforce the minimum time step.

setStepSize(float) - Method in class integrators.Integrator

Set the size of the timestep used by the integrator for the next (and subsequent) calls to IntegrateOneStep.

setStopTime(float) - Method in class stoppers.MetaStop

setStopTime(float) - Method in class stoppers.MetaStopTwo

setStopTime(float) - Method in class stoppers.SimpleStop

setStopper(SimpleStop) - Method in class iterators.Function

setStopper(SimpleStop) - Method in class iterators.ICSamplingFunction

setStopper(SimpleStop) - Method in class iterators.ICVaryingFunction

setStopper(SimpleStop) - Method in class iterators.ModelIterator

setStopper(SimpleStop) - Method in class main.ModelRunner

setTag(String) - Method in class parameters.ParameterSet

setTime(float) - Method in class genegui.ModelState

Sets the time.

setTimestep(float) - Method in class integrators.CashKarpIntegrator

setToolBox(ModelStateToolBox) - Method in class genegui.ModelState

Sets the one and only ModelStateToolBox attached to this ModelState.

setType(int) - Method in class main.CalculatorNode

setType(int) - Method in class main.NodeTemplate

setURL(String) - Method in class genegui.HTMLViewer

Sets the page contents according to the URL

setURL(URL) - Method in class genegui.HTMLViewer

Sets the page contents according to the URL

setUpperBound(int, float) - Method in class parameters.ParameterSet

setUsingGUI(boolean) - Static method in class main.Globals

setValue(float) - Method in class initialconditions.InitialCondition

setValue(float) - Method in class main.CalculatorNode

setValue(int, float) - Method in class main.Cell

setValue(String, float) - Method in class main.Cell

setValue(float) - Method in class main.Node

setValue(int, float) - Method in class main.Node

setValue(NodeValues) - Method in class main.Node

setValue(float) - Method in class parameters.Parameter

setValue(int, float) - Method in class parameters.ParameterSet

setValues(float[]) - Method in class genegui.ModelStateNodePalette

Sets the values being displayed by all the NodePalettes.

setVariationMode(int) - Method in class parameters.Parameter

setVariationMode(String) - Method in class parameters.Parameter

setVariationMode(int, int) - Method in class parameters.ParameterSet

setXPos(int) - Method in class main.NodeTemplate

setXScale(float) - Method in interface genegui.OptionsPanelInterface

Set scale of X axis

setXScale(float) - Method in class genegui.TimeGraph

Resets the XScale for all panels

setYPos(int) - Method in class main.NodeTemplate

setYScale(float) - Method in interface genegui.OptionsPanelInterface

Set scale of Y axis

setYScale(float) - Method in class genegui.TimeGraph

Resets the YScale for all panels

setYScale(float) - Method in class main.NodeTemplate

setupOutput() - Method in class main.Model

setupTokenizer(BetterTokenizer) - Static method in class main.GeneralInput

show(boolean) - Method in class genegui.Console

showInOpenViewers(int) - Method in class genegui.IteratorViewer

showInternalFrame(JInternalFrame) - Method in class genegui.MainGui

Verifies that a JInternalFrame is visible.

size() - Method in class genegui.SuccessList

Returns the number of pairs in the list.

slashSlashComments(boolean) - Method in class main.BetterTokenizer

* Determines whether or not the tokenizer recognizes C++-style comments.

slashStarComments(boolean) - Method in class main.BetterTokenizer

* Determines whether or not the tokenizer recognizes C-style comments.

sort(Object[], MoreMath.Comparer) - Static method in class main.MoreMath

sort(Object[], Object[], int, int, boolean, MoreMath.Comparer) - Static method in class main.MoreMath

Sort a and b, using a as the reference - stolen from somewhere on internet

sqr(double) - Static method in class main.MoreMath

Returns num * num

sqr(float) - Static method in class main.MoreMath

startExperiment() - Method in class main.Experiment

startRun() - Method in class iterators.ModelIterator

startRun() - Method in class iterators.UberIterator

startRun() - Method in class main.ModelRunner

These next functions wrap the running of a model inside a thread.

stat - package stat

stop(float) - Method in class stoppers.CellSurround2Stop

stop(float) - Method in class stoppers.CellSurroundStop

stop(float) - Method in class stoppers.CellThresholdStop

stop(float) - Method in class stoppers.FPStripeStop

stop(float) - Method in class stoppers.FindMaxRatioStop

stop(float) - Method in class stoppers.MetaFPStripeStop

stop(float) - Method in class stoppers.MetaStop

stop(float) - Method in class stoppers.MetaStopTwo

stop(float) - Method in class stoppers.MetaStripeStop

stop(float) - Method in class stoppers.MultiNodeThresholdStop

stop(float) - Method in class stoppers.NeuroNoiseStop

stop(float) - Method in class stoppers.NeuroTest2Stop

stop(float) - Method in class stoppers.NeuroTest3Stop

stop(float) - Method in class stoppers.NoChangeStop

stop(float) - Method in class stoppers.OscillatingStripeStop

stop(float) - Method in class stoppers.OscillatorStop

stop(float) - Method in class stoppers.OscillatorStopSpecial

stop(float) - Method in class stoppers.PulseStop

stop(float) - Method in class stoppers.SimpleStop

stop(float) - Method in class stoppers.StripeStop

stop(float) - Method in class stoppers.ThresholdStop

stop(float) - Method in class stoppers.TwoCellDifferenceStop

stopRun() - Method in class iterators.Function

Called by the iterator when it stops running.

stopRun() - Method in class iterators.ModelIterator

stopRun() - Method in class iterators.UberIteratorFunction

This is here to gracefully stop processing when the user stops the iterator before its finished.

stopRun() - Method in class main.ModelRunner

Call stopRun() to stop a model that's currently running.

stopper - Variable in class main.Experiment

stopper - Variable in class main.ModelRunner

stoppers - package stoppers

storeFinalValues() - Method in class main.CalculatorNode

sval - Variable in class main.BetterTokenizer

If the current token is a word token, this field contains a * string giving the characters of the word token.

T

TERMTYPE - Static variable in class affectors.Affector

Position meanings for Type[].

TT - Static variable in class affectors.Affector

Type.[MATHTYPE] values; FF refers to a nonlinear function of only *other* nodes, GG is a nonlinear function of other nodes times the target node, HH is a constant times the target node, KK is a constant times some other nodes, CC is a constant, TT is a function only of time.

TT_EOF - Static variable in class main.BetterTokenizer

* A constant indicating that the end of the stream has been read.

TT_EOL - Static variable in class main.BetterTokenizer

* A constant indicating that the end of the line has been read.

TT_NUMBER - Static variable in class main.BetterTokenizer

* A constant indicating that a number token has been read.

TT_WORD - Static variable in class main.BetterTokenizer

* A constant indicating that a word token has been read.

TheGeneNet - Static variable in class main.GeneNet

TheIteratorViewer - Variable in class iterators.ModelIterator

Pointer the the viewer that displays results for this iterator

TheMainGui - Static variable in class main.GeneNet

The main Graphical User Interface

TheModel - Static variable in class main.GeneNet

ThresholdStop - class stoppers.ThresholdStop.

ThresholdStop() - Constructor for class stoppers.ThresholdStop

ThresholdStop(float) - Constructor for class stoppers.ThresholdStop

TimeGraph - class genegui.TimeGraph.

TimeGraph.java A spanking new GUI component for collection and displaying time vs concentration graphs.

TimeGraph(Model, MainGui) - Constructor for class genegui.TimeGraph

Main Constructor

TlnAff - class affectors.TlnAff.

Translation of an mRNA into protein.

TlnAff() - Constructor for class affectors.TlnAff

TlnRegUpAff - class affectors.TlnRegUpAff.

Translation of an mRNA into protein.

TlnRegUpAff() - Constructor for class affectors.TlnRegUpAff

TransectIterator - class iterators.TransectIterator.

This performs a sensitivity analysis on a model.

TransectIterator() - Constructor for class iterators.TransectIterator

TwoCellDifferenceStop - class stoppers.TwoCellDifferenceStop.

TwoCellDifferenceStop() - Constructor for class stoppers.TwoCellDifferenceStop

TwoCellDifferenceStop(float) - Constructor for class stoppers.TwoCellDifferenceStop

Txn1Aff - class affectors.Txn1Aff.

The simplest regulated transcription affector.

Txn1Aff() - Constructor for class affectors.Txn1Aff

Txn1ECAff - class affectors.Txn1ECAff.

A variant of Txn1Aff that integrates an external influence from a neighboring cell (e.g.

Txn1ECAff() - Constructor for class affectors.Txn1ECAff

Txn2aAff - class affectors.Txn2aAff.

Txn2a implements transcriptional activation under the control of one activator and one inhibitor, the latter of which competetively inhibits the activator.

Txn2aAff() - Constructor for class affectors.Txn2aAff

Txn2aDipAff - class affectors.Txn2aDipAff.

Diploid version of Txn2bAff.

Txn2aDipAff() - Constructor for class affectors.Txn2aDipAff

Txn2bAff - class affectors.Txn2bAff.

Txn2b implements transcriptional activation under the control of one extracellular activator expressed on neighboring cells and one cytoplasmic inhibitor, the latter of which competetively inhibits the activator.

Txn2bAff() - Constructor for class affectors.Txn2bAff

Txn2bDipAff - class affectors.Txn2bDipAff.

Diploid version of Txn2bAff.

Txn2bDipAff() - Constructor for class affectors.Txn2bDipAff

Txn3aAff - class affectors.Txn3aAff.

Txn3a takes two activators which synergize such that only in the presence of both can the target achieve full activity.

Txn3aAff() - Constructor for class affectors.Txn3aAff

Txn3bAff - class affectors.Txn3bAff.

Txn3b takes two activators which synergize such that the second makes the first more potent.

Txn3bAff() - Constructor for class affectors.Txn3bAff

Txn4Aff - class affectors.Txn4Aff.

Txn4 takes two activators and one inhibitor which titrates away the *second* activator.

Txn4Aff() - Constructor for class affectors.Txn4Aff

Txn4DipAff - class affectors.Txn4DipAff.

Diploid version of Txn4Aff.

Txn4DipAff() - Constructor for class affectors.Txn4DipAff

Txn5Aff - class affectors.Txn5Aff.

Txn5 takes two activators and one inhibitor that suppresses both activators equally.

Txn5Aff() - Constructor for class affectors.Txn5Aff

Txn6aAff - class affectors.Txn6aAff.

Txn6a takes two activators which synergize such that only in the presence of both can the target achieve full activity, and one inhibitor which reduces the effective concentration of the SECOND of these.

Txn6aAff() - Constructor for class affectors.Txn6aAff

Txn6bAff - class affectors.Txn6bAff.

Txn6b takes two activators which synergize such that only in the presence of both can the target achieve full activity, and one inhibitor which reduces the effective concentration of the FIRST of these.

Txn6bAff() - Constructor for class affectors.Txn6bAff

TxnLeakyCyceAff - class affectors.TxnLeakyCyceAff.

TxnLeakyCyce implements leaky transcriptional activation under the control of two equivalent activators and one inhibitor.

TxnLeakyCyceAff() - Constructor for class affectors.TxnLeakyCyceAff

TxnSiteActInhibit2Aff - class affectors.TxnSiteActInhibit2Aff.

Use for activation + inhibition of transcription.

TxnSiteActInhibit2Aff() - Constructor for class affectors.TxnSiteActInhibit2Aff

TxnSiteActInhibit3Aff - class affectors.TxnSiteActInhibit3Aff.

Use for activation + inhibition of transcription.

TxnSiteActInhibit3Aff() - Constructor for class affectors.TxnSiteActInhibit3Aff

TxnSiteActInhibitAff - class affectors.TxnSiteActInhibitAff.

Use for activation + inhibition of transcription.

TxnSiteActInhibitAff() - Constructor for class affectors.TxnSiteActInhibitAff

TxnSiteActivator1Aff - class affectors.TxnSiteActivator1Aff.

An old name for TxnSiteActivator

TxnSiteActivator1Aff() - Constructor for class affectors.TxnSiteActivator1Aff

TxnSiteActivatorAff - class affectors.TxnSiteActivatorAff.

Use for activation of transcription.

TxnSiteActivatorAff() - Constructor for class affectors.TxnSiteActivatorAff

TxnSiteAddInhibitorAff - class affectors.TxnSiteAddInhibitorAff.

Use for inhibitor that is additive.

TxnSiteAddInhibitorAff() - Constructor for class affectors.TxnSiteAddInhibitorAff

TxnSiteInhibitorAff - class affectors.TxnSiteInhibitorAff.

Use for multiplicative inhibition of transcription.

TxnSiteInhibitorAff() - Constructor for class affectors.TxnSiteInhibitorAff

Type - Variable in class affectors.Affector

The Type array is public only so it can be read without the cost of a method call...

tag - Variable in class parameters.ParameterSet

tagNames - Variable in class parameters.ParameterSetArray

takeFPStep() - Method in class main.CalculatorNode

theFunction - Variable in class iterators.ModelIterator

this_debug_num - Variable in class main.Node

time - Static variable in class main.Globals

The current time in the integration

timeGraphFrame - Variable in class genegui.InspectorList

toFront() - Method in class genegui.Console

toString(PrintWriter, String) - Method in class initialconditions.CellIC

toString(PrintWriter, String) - Method in class initialconditions.CenterIC

toString(PrintWriter, String) - Method in class initialconditions.ColumnIC

toString(PrintWriter, String) - Method in class initialconditions.IncrementingACSC1

toString(PrintWriter, String) - Method in class initialconditions.IncrementingIC

toString(PrintWriter, String) - Method in class initialconditions.InitialCondition

toString(PrintWriter, String) - Method in class initialconditions.InitialConditionSet

toString(PrintWriter, String) - Method in class initialconditions.NeuroNoiseIC

toString(PrintWriter, String) - Method in class initialconditions.RowIC

toString(PrintWriter, String) - Method in class initialconditions.SequenceACSC1

toString(PrintWriter, String) - Method in class main.AffectorTemplate

toString() - Method in class main.BetterTokenizer

Returns the string representation of the current stream token.

toString(PrintWriter, String) - Method in class main.NodeTemplate

toString() - Method in class parameters.Parameter

toString(boolean) - Method in class parameters.Parameter

toString() - Method in class parameters.ParameterSet

toString(PrintWriter, String) - Method in class parameters.ParameterSet

totNumSets - Variable in class parameters.ParameterSetArray

ttype - Variable in class main.BetterTokenizer

* After a call to the nextToken method, this field * contains the type of the token just read.

U

UNIFORM - Static variable in class main.MoreMath

UNSPECIFIED - Static variable in class affectors.Affector

Type.[] default value.

UPDATE_CELLS - Static variable in class main.Model

UPDATE_MODEL - Static variable in class genegui.GeneNetInterface

UPDATE_MODEL - Static variable in class genegui.InspectorList

UberIterator - class iterators.UberIterator.

UberIterator() - Constructor for class iterators.UberIterator

UberIteratorFunction - class iterators.UberIteratorFunction.

UberIteratorFunction(ModelRunner, PrintWriter) - Constructor for class iterators.UberIteratorFunction

updateAll() - Method in class genegui.CellSurfaceViewer

Implementation of ModelStateChangeListener Causes entire display to be repainted.

updateAll() - Method in class genegui.MainGui

Indicates that the entire ModelState has been updated This method slows things down a LOT because of the constant repainting of the time display.

updateAll() - Method in interface genegui.ModelStateChangeListener

Indicates that the entire ModelState has been updated

updateAll() - Method in class genegui.NetworkViewer2

Implementation of ModelStateChangeListener Causes entire display to be repainted.

updateAll() - Method in class genegui.NodeStateViewer

Implementation of ModelStateChangeListener Causes entire display to be repainted.

updateAll() - Method in class genegui.TimeGraph

Implementation of ModelStateChangeListener

updateAll() - Method in class main.Model

Indicates that the entire ModelState has been updated

updateAllCells() - Method in class genegui.ModelStateView

Updates the colors of all cells whether they are selected or not.

updateCell(int) - Method in class genegui.ModelState

Udates the values for a cell and notifies all node listeners that a change has occurred so the cell may be repainted were needed.

updateCell(int) - Method in class genegui.ModelStateView

Repaints a single cell.

updateCell(int) - Method in interface genegui.NodeStateChangeListener

Repaints a single cell.

updateCells(boolean[]) - Method in class genegui.ModelStateView

Updates the colors for all the selected cells.

updateCells(boolean[]) - Method in interface genegui.NodeStateChangeListener

Causes all cells in the selectedCell array to be repainted.

updateDisplays() - Method in class genegui.ParameterViewer

Updates Displayed values for all parameters

updateFPStep() - Method in class main.CalculatorNode

updateModel(Model, float) - Method in class genegui.ModelState

Called to completely update the values of the ModelState based upon a passed Model.

updateNode(int, int, float) - Method in class genegui.CellSurfaceViewer

Updates only the indicated node.

updateNode(int, int, float) - Method in class genegui.MainGui

Updates only the indicated node.

updateNode(int, int, float) - Method in interface genegui.ModelStateChangeListener

Updates only the indicated node.

updateNode(int, int, float) - Method in class genegui.NetworkViewer2

Updates only the indicated node.

updateNode(int, int, float) - Method in class genegui.NodeStateViewer

Updates only the indicated node.

updateNode(int, int, float) - Method in class genegui.TimeGraph

Updates only the indicated node.

updateNode(int, int, float) - Method in class main.Model

Updates only the indicated node.

updateNodeValue(int, float) - Method in class genegui.ModelState

Updates all the value for a node for all the selected cells in the currently active ModelStateView.

updateNodeValue(int, int, float, ModelStateChangeListener) - Method in class genegui.ModelState

Updates the value in a node for a state

updateOutput(int) - Method in class main.Model

updateOutput(String) - Method in class parameters.ParameterSetArray

updateParameter(int) - Method in class genegui.ParameterViewer

Updates a single Parameter

updateParameterSet(ParameterSet) - Method in class genegui.ParameterViewer

Changes out the parameter set and updates the display.

updateParameters() - Method in class genegui.ParameterViewer

Updates all the Parameters

updateTemplate() - Method in class genegui.AffectorViewPanel

Updates all the affector display sub panels.

updateTemplate() - Method in class genegui.NodeViewPanel

Updates the node display values based upon the current values in its NodeTemplate.

upperBound - Variable in class parameters.Parameter

The lowest value this parameter can every have.

usingGUI - Static variable in class main.Globals

Set to true if GeneNet is being run with gui, false otherwise

V

ValueFieldHistogramStat - class stat.ValueFieldHistogramStat.

Makes a histogram of the values of one of the Value Fields across all the parameter sets.

ValueFieldHistogramStat() - Constructor for class stat.ValueFieldHistogramStat

VonForresterA_Aff - class affectors.VonForresterA_Aff.

This affector implements one half of a constant delay through a von Forrester equation.

VonForresterA_Aff() - Constructor for class affectors.VonForresterA_Aff

VonForresterA_ECAff - class affectors.VonForresterA_ECAff.

This affector implements one half of a constant delay through a von Forrester equation.

VonForresterA_ECAff() - Constructor for class affectors.VonForresterA_ECAff

VonForresterA_ICAff - class affectors.VonForresterA_ICAff.

This affector implements one half of a constant delay through a von Forrester equation.

VonForresterA_ICAff() - Constructor for class affectors.VonForresterA_ICAff

VonForresterB_Aff - class affectors.VonForresterB_Aff.

This affector implements one half of a constant delay through a von Forrester equation.

VonForresterB_Aff() - Constructor for class affectors.VonForresterB_Aff

VonForresterB_ECAff - class affectors.VonForresterB_ECAff.

This affector implements one half of a constant delay through a von Forrester equation.

VonForresterB_ECAff() - Constructor for class affectors.VonForresterB_ECAff

VonForresterB_ICAff - class affectors.VonForresterB_ICAff.

This affector implements one half of a constant delay through a von Forrester equation.

VonForresterB_ICAff() - Constructor for class affectors.VonForresterB_ICAff

VulvaClassifyIterator - class iterators.VulvaClassifyIterator.

VulvaClassifyIterator() - Constructor for class iterators.VulvaClassifyIterator

value - Variable in class parameters.Parameter

The value of the parameter.

values - Variable in class integrators.NodeValues

variationMode - Variable in class parameters.Parameter

Can be either LINEAR or LOGARITHMIC

verbose - Variable in class iterators.ModelIterator

This is here to say whether the iterator should be saving stuff out to a file or not.

W

WEIGHTEDSUM - Static variable in class main.NodeTemplate

WhiteNoiseAff - class affectors.WhiteNoiseAff.

Adds white noise to the concentration of a node.

WhiteNoiseAff() - Constructor for class affectors.WhiteNoiseAff

whitespaceChars(int, int) - Method in class main.BetterTokenizer

* Specifies that all characters c in the range * low <= c <= high * are white space characters.

wordChars(int, int) - Method in class main.BetterTokenizer

* Specifies that all characters c in the range * low <= c <= high * are word constituents.

write(byte[], int, int) - Method in class genegui.Console

write(int) - Method in class genegui.Console

X

XferInAff - class affectors.XferInAff.

This is one half of a pair of Affectors that moves things from one cell to neighboring cells.

XferInAff() - Constructor for class affectors.XferInAff

XferOutAff - class affectors.XferOutAff.

This is one half of a pair of Affectors that moves things from one cell to neighboring cells.

XferOutAff() - Constructor for class affectors.XferOutAff

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