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R

radius - Variable in class HAL.GridsAndAgents.SphericalAgent2D

radius - Variable in class HAL.GridsAndAgents.SphericalAgent3D

Rand - Class in HAL

contains functions for random value generation and distribution sampling.

Rand() - Constructor for class HAL.Rand

Rand(long) - Constructor for class HAL.Rand

Rand(RNG) - Constructor for class HAL.Rand

creates a Rand object using the RNG argument as its internal generator

RandomAgent(int, int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates

RandomAgent(int, int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true

RandomAgent(int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates

RandomAgent(int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true

RandomAgent(int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the provided coordinates

RandomAgent(int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates

RandomAgent(int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates

RandomAgent(int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true

RandomAgent(int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true

RandomAgent(int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the provided coordinates forwhich EvalAgent returns true

RandomAgent(Rand) - Method in class HAL.GridsAndAgents.AgentGrid0D

gets a random agent from the grid, be careful not to use this during iteration over the grid

RandomAgent(Rand) - Method in class HAL.GridsAndAgents.AgentGrid1D

gets a random agent from the grid, be careful not to use this during iteration over the grid

RandomAgent(Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

gets a random agent from the grid, be careful not to use this during iteration over the grid

RandomAgent(Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

gets a random agent from the grid, be careful not to use this during iteration over the grid

RandomAgent(Rand) - Method in class HAL.GridsAndAgents.AgentList

returns a random agent from the AgentList

RandomAgentHood(int[], int, int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood

RandomAgentHood(int[], int, int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true

RandomAgentHood(int[], int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood

RandomAgentHood(int[], int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true

RandomAgentHood(int[], int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood

RandomAgentHood(int[], int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true

RandomAgentHoodMapped(int[], int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood, assumes the neighborhood has already been mapped

RandomAgentHoodMapped(int[], int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood, assumes the neighborhood has already been mapped

RandomAgentHoodMapped(int[], int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood, assumes the neighborhood has already been mapped

RandomAgentHoodMapped(int[], int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true, assumes the neighborhood has already been mapped

RandomAgentHoodMapped(int[], int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true, assumes the neighborhood has already been mapped

RandomAgentHoodMapped(int[], int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified neighborhood forwhich EvalAgent returns true, assumes the neighborhood has already been mapped

RandomAgentRad(double, double, double, double, Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified radius

RandomAgentRad(double, double, double, double, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified radius

RandomAgentRad(double, double, double, Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified radius

RandomAgentRad(double, double, double, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified radius forwhich EvalAgent returns true

RandomAgentRad(double, double, Rand) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified radius

RandomAgentRad(double, double, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified radius forwhich EvalAgent returns true

RandomAgentRect(int, int, int, int, int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified rectangle

RandomAgentRect(int, int, int, int, int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent from the set of all agents within the specified rectangle forwhich EvalAgent returns true

RandomAgentRect(int, int, int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified rectangle

RandomAgentRect(int, int, int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent from the set of all agents within the specified rectangle forwhich EvalAgent returns true

RandomAgentRect(int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified rectangle

RandomAgentRect(int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent from the set of all agents within the specified rectangle forwhich EvalAgent returns true

RandomAgentSafe(int, int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent, will apply wraparound if the coordiantes are outside of the grid

RandomAgentSafe(int, int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D

returns a single random agent that satisfies EvalAgent, will apply wraparound if the coordiantes are outside of the grid

RandomAgentSafe(int, int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent, will apply wraparound if the coordiantes are outside of the grid

RandomAgentSafe(int, int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D

returns a single random agent that satisfies EvalAgent, will apply wraparound if the coordiantes are outside of the grid

RandomAgentSafe(int, Rand) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent, will apply wraparound if the coordiantes are outside of the grid

RandomAgentSafe(int, Rand, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D

returns a single random agent that satisfies EvalAgent, will apply wraparound if the coordiantes are outside of the grid

RandomDS(double[], double, double) - Method in class HAL.Rand

Fills out with random doubles between min and max inclusive

RandomHoodI(int[], int, int, int, Rand) - Method in interface HAL.Interfaces.Grid3D

gets a random index from the full neighborhood, if the index does not map, returns -1

RandomHoodI(int[], int, int, Rand) - Method in interface HAL.Interfaces.Grid2D

gets a random index from the full neighborhood, if the index does not map, returns -1

RandomHoodI(int[], int, Rand) - Method in interface HAL.Interfaces.Grid1D

gets a random index from the full neighborhood, if the index does not map, returns -1

RandomIS(int[], int, int) - Method in class HAL.Rand

Fills out with random integers between min (inclusive) and max (exclusive)

RandomPointInCircle(double, double[]) - Method in class HAL.Rand

RandomPointInSphere(double, double[]) - Method in class HAL.Rand

RandomPointOnCircleEdge(double, double[]) - Method in class HAL.Rand

gets a random point on the surface of a circle centered at 0,0, with the provided radius.

RandomPointOnSphereEdge(double, double[]) - Method in class HAL.Rand

gets a random point on the surface of a sphere centered at 0,0,0, with the provided radius.

RandomVariable(double[]) - Method in class HAL.Rand

Samples a discrete random variable from the probabilities provided

RandomVariable(double[], double, int, int) - Method in class HAL.Rand

RandomVariable(double[], int, int) - Method in class HAL.Rand

Read() - Method in class HAL.Tools.FileIO

requires read mode ("r") returns an array list of all lines from the file as strings

ReadBinBool() - Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a boolean from the binary file

ReadBinBools(boolean[]) - Method in class HAL.Tools.FileIO

ReadBinDouble() - Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single double from the binary file

ReadBinDoubles(double[]) - Method in class HAL.Tools.FileIO

ReadBinFloat() - Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single float from the binary file

ReadBinFloats(float[]) - Method in class HAL.Tools.FileIO

ReadBinInt() - Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single int from the binary file

ReadBinInts(int[]) - Method in class HAL.Tools.FileIO

ReadBinLong() - Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a single long from the binary file

ReadBinLongs(long[]) - Method in class HAL.Tools.FileIO

ReadBinString() - Method in class HAL.Tools.FileIO

requires readBinary mode ("rb") reads a string from the binary file

ReadDelimit(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of line segments from that line

ReadDoubles(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of doubles from that line

reader - Variable in class HAL.Tools.FileIO

readerBin - Variable in class HAL.Tools.FileIO

ReadInts(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of ints from that line

ReadLine() - Method in class HAL.Tools.FileIO

requires read mode ("r") returns one line from the file as a string

ReadLineDelimit(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimiter, and returns an array of line segments

ReadLineDoubles(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of doubles from that line

ReadLineFloats(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of floats from that line

ReadLineInts(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of integers from that line

ReadLineLongs(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls a line from the file, splits it by the delimeter and returns an array of longs from that line

ReadLongs(String) - Method in class HAL.Tools.FileIO

requires read mode ("r") pulls all lines from the file, splits them by the delimiter, and returns an arraylist, where each entry is an array of longs from that line

ReadObject() - Method in class HAL.Tools.FileIO

ReadWriteAppend - Variable in class HAL.Tools.FileIO

RecordClones(double) - Method in class HAL.Tools.PhylogenyTracker.Genome

RecordClones(String) - Method in class HAL.Tools.PhylogenyTracker.Genome

Rectangle(double, double, double, double, int) - Method in class HAL.Gui.OpenGL2DWindow

draws a rectangle between (x1,y1) and (x2,y2) coded by Jill Gallaher

RectangleAtPoint(double, double, double, double, int) - Method in class HAL.Gui.OpenGL2DWindow

draws a rectangle centered at position x,y

RectangleHood(boolean, int, int) - Static method in class HAL.Util

Returns the coordinates of all squares whose centers lie within a rectangle of the provided radius, centered on (0,0)

RectangleXY(double, double, double, double, double, int) - Method in class HAL.Gui.OpenGL3DWindow

draws a rectangle between (x1,y1,z) and (x2,y2,z)

RectangleXZ(double, double, double, double, double, int) - Method in class HAL.Gui.OpenGL3DWindow

RectangleYZ(double, double, double, double, double, int) - Method in class HAL.Gui.OpenGL3DWindow

RED - Static variable in class HAL.Util

RemoveAgent(T) - Method in class HAL.GridsAndAgents.AgentList

removes all instances of the agent from the AgentList, returns the number of instances removed

Rescale(double, double, double, double, double) - Static method in class HAL.Util

rescales the value from being between oldMin and oldMax to being between newMin and newMax

Reset() - Method in class HAL.GridsAndAgents.AgentGrid0D

calls dispose on all agents in the typeGrid

Reset() - Method in class HAL.GridsAndAgents.AgentGrid1D

calls dispose on all agents, resets the tick timer to 0.

Reset() - Method in class HAL.GridsAndAgents.AgentGrid2D

calls dispose on all agents in the typeGrid, resets the tick timer to 0.

Reset() - Method in class HAL.GridsAndAgents.AgentGrid3D

calls dispose on all agents in the typeGrid, resets the tick timer to 0.

ResetCloneRecord() - Method in class HAL.Tools.PhylogenyTracker.Genome

ResetHard() - Method in class HAL.GridsAndAgents.AgentGrid1D

calls dispose on all agents and completely resets the internal agentlist, also resets the tick timer to 0.

ResetHard() - Method in class HAL.GridsAndAgents.AgentGrid2D

calls dispose on all agents and completely resets the internal agentlist, also resets the tick timer to 0.

ResetHard() - Method in class HAL.GridsAndAgents.AgentGrid3D

calls dispose on all agents and completely resets the internal agentlist, also resets the tick timer to 0.

ResetTick() - Method in class HAL.GridsAndAgents.AgentGrid0D

ResetTick() - Method in class HAL.GridsAndAgents.AgentGrid1D

sets the tick to 0.

ResetTick() - Method in class HAL.GridsAndAgents.AgentGrid2D

sets the tick to 0.

ResetTick() - Method in class HAL.GridsAndAgents.AgentGrid3D

sets the tick to 0.

Response(char, int) - Method in interface HAL.Interfaces.KeyResponse

RGB(double, double, double) - Static method in class HAL.Util

returns a color integer based on the RGB components passed in.

RGB256(int, int, int) - Static method in class HAL.Util

returns a color integer based on the RGB components passed in.

RGBA(double, double, double, double) - Static method in class HAL.Util

returns a color integer based on the RGBA components passed in.

RGBA256(int, int, int, int) - Static method in class HAL.Util

returns a color integer based on the RGB components passed in.

rk_binomial_inversion(int, double, Rand) - Method in class HAL.Tools.Internal.Binomial

rk_binomial_inversion(long, double, Rand) - Method in class HAL.Tools.Internal.Binomial

rn - Variable in class HAL.Rand

RNG - Interface in HAL.Interfaces

run() - Method in class HAL.Tools.Internal.SweepRun

Run(int) - Method in interface HAL.Interfaces.ParallelFunction

Run(int, boolean, int) - Method in class HAL.Tools.MultiWellExperiment.MultiWellExperiment

runs a multiwell experiment for a numTicks duration.

Runge4(Derivative, double[], double[], double, double) - Method in class HAL.Tools.ODESolver.ODESolver

runs 1 round of Runge-Kutta 4 integration, putting the result in the out array

Runge4(Derivative, double[], double, double) - Method in class HAL.Tools.ODESolver.ODESolver

runs 1 round of Runge-Kutta 4 integration, putting the result in the state array

Runge4(Derivative, double[], double, double, double) - Method in class HAL.Tools.ODESolver.ODESolver

runs Runge-Kutta 4 integration from t0 to tf in increments of dt

Runge4(Derivative, ArrayList<double[]>, ArrayList<Double>, double, double, int) - Method in class HAL.Tools.ODESolver.ODESolver

runs Runge-Kutta 4,5 integration from t0 to tf in increments of dt, puts the resulting states in the states array, and the resulting ts in the ts array

Runge45(Derivative, double[], double[], double, double, double, double) - Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, updating the state array until tf.

Runge45(Derivative, double[], double[], double, double, double, double, double, double) - Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, updating the state array until tf.

Runge45(Derivative, double[], double, double, double, double) - Method in class HAL.Tools.ODESolver.ODESolver

Runge45(Derivative, double[], double, double, double, double, double, double) - Method in class HAL.Tools.ODESolver.ODESolver

Runge45(Derivative, ArrayList<double[]>, ArrayList<Double>, double, double, double, int) - Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, putting new states and the times for which those states were computed into the states and ts arraylists.

Runge45(Derivative, ArrayList<double[]>, ArrayList<Double>, double, double, double, int, double, double) - Method in class HAL.Tools.ODESolver.ODESolver

calls runge kutta 4,5 iteratively, putting new states and the times for which those states were computed into the states and ts arraylists.

RunGIF(int, String, int, boolean) - Method in class HAL.Tools.MultiWellExperiment.MultiWellExperiment

runs a multiwell experiment for a numTicks duration.

RunGui() - Method in class HAL.Gui.UIWindow

starts the gui thread and reveals the gui to the user

RunGui() - Method in class HAL.Tools.InteractiveModel.InteractiveModel

RunNextStep() - Method in class HAL.Tools.InteractiveModel.InteractiveModel

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