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M
 MAGENTA  Static variable in class HAL.Util
 main(String[])  Static method in class HAL.Tools.BoolSet
 MakeDirs(String)  Static method in class HAL.Util

creates directories to ensure that the path argument exists
 MapEmptyHood(int[])  Method in class HAL.GridsAndAgents.Agent1DBase

These functions are similar to the the MapHood function, but they will only include valid empty or occupied indices, and skip the others.
 MapEmptyHood(int[])  Method in class HAL.GridsAndAgents.Agent2DBase

These functions are similar to the the MapHood function, but they will only include valid empty or occupied indices, and skip the others.
 MapEmptyHood(int[])  Method in class HAL.GridsAndAgents.Agent3DBase

These functions are similar to the the MapHood function, but they will only include valid empty or occupied indices, and skip the others.
 MapEmptyHood(int[], int)  Method in class HAL.GridsAndAgents.AgentGrid1D

similar to the MapHood function, but will only include indices of locations that are empty
 MapEmptyHood(int[], int)  Method in class HAL.GridsAndAgents.AgentGrid2D

similar to the MapHood function, but will only include indices of locations that are empty
 MapEmptyHood(int[], int)  Method in class HAL.GridsAndAgents.AgentGrid3D

similar to the MapHood function, but will only include indices of locations that are empty
 MapEmptyHood(int[], int, int)  Method in class HAL.GridsAndAgents.AgentGrid2D

similar to the MapHood function, but will only include indices of locations that are empty
 MapEmptyHood(int[], int, int, int)  Method in class HAL.GridsAndAgents.AgentGrid3D

similar to the MapHood function, but will only include indices of locations that are empty
 MapHood(int[])  Method in class HAL.GridsAndAgents.Agent1DBase

This function takes a neighborhood (As generated by the neighborhood Util functions, or using GenHood2D/GenHood3D), translates the neighborhood coordinates to be centered around the agent, and computes the set of indices that the translated coordinates map to.
 MapHood(int[])  Method in class HAL.GridsAndAgents.Agent2DBase

This function takes a neighborhood (As generated by the neighborhood Util functions, or using GenHood2D/GenHood3D), translates the neighborhood coordinates to be centered around the agent, and computes the set of indices that the translated coordinates map to.
 MapHood(int[])  Method in class HAL.GridsAndAgents.Agent3DBase

This function takes a neighborhood (As generated by the neighborhood Util functions, or using GenHood2D/GenHood3D), translates the neighborhood coordinates to be centered around the agent, and computes the set of indices that the translated coordinates map to.
 MapHood(int[], int)  Method in interface HAL.Interfaces.Grid1D

This function takes a neighborhood centered around the origin, translates the set of coordinates to be centered around a particular central location, and computes which indices the translated coordinates map to.
 MapHood(int[], int)  Method in interface HAL.Interfaces.Grid2D

This function takes a neighborhood centered around the origin, translates the set of coordinates to be centered around a particular central location, and computes which indices the translated coordinates map to.
 MapHood(int[], int)  Method in interface HAL.Interfaces.Grid3D

This function is very similar to the previous definition of MapHood, only it additionally takes as argument an EvaluationFunctoin.
 MapHood(int[], int, int)  Method in interface HAL.Interfaces.Grid2D

This function takes a neighborhood centered around the origin, translates the set of coordinates to be centered around a particular central location, and computes which indices the translated coordinates map to.
 MapHood(int[], int, int, int)  Method in interface HAL.Interfaces.Grid3D

This function is very similar to the previous definition of MapHood, only it additionally takes as argument an EvaluationFunctoin.
 MapHood(int[], int, int, int, IndexCoords3DBool)  Method in interface HAL.Interfaces.Grid3D

This function is very similar to the previous definition of MapHood, only it additionally takes as argument an EvaluationFunctoin.
 MapHood(int[], int, int, IndexCoords2DBool)  Method in interface HAL.Interfaces.Grid2D

This function is very similar to the previous definition of MapHood, only it additionally takes as argument an EvaluationFunctoin.
 MapHood(int[], int, Coords1DBool)  Method in interface HAL.Interfaces.Grid1D

This function is very similar to the previous definition of MapHood, only it additionally takes as argument an EvaluationFunctoin.
 MapHood(int[], int, IndexCoords2DBool)  Method in interface HAL.Interfaces.Grid2D

This function is very similar to the previous definition of MapHood, only it additionally takes as argument an EvaluationFunctoin.
 MapHood(int[], int, IndexCoords3DBool)  Method in interface HAL.Interfaces.Grid3D

This function takes a neighborhood centered around the origin, translates the set of coordinates to be centered around a particular central location, and computes which indices the translated coordinates map to.
 MapHood(int[], Coords1DBool)  Method in class HAL.GridsAndAgents.Agent1DBase

This function takes a neighborhood and another mapping function as argument, the mapping function should return a boolean that specifies whether coordinates map to a valid location.
 MapHood(int[], IndexCoords2DBool)  Method in class HAL.GridsAndAgents.Agent2DBase

This function takes a neighborhood and another mapping function as argument, the mapping function should return a boolean that specifies whether coordinates map to a valid location.
 MapHood(int[], IndexCoords3DBool)  Method in class HAL.GridsAndAgents.Agent3DBase

This function takes a neighborhood and another mapping function as argument, the mapping function should return a boolean that specifies whether coordinates map to a valid location.
 MapI(int, Grid2D)  Method in interface HAL.Interfaces.Grid2D

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapI(Grid1D)  Method in class HAL.GridsAndAgents.Agent1DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapI(Grid2D)  Method in class HAL.GridsAndAgents.Agent2DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapI(Grid3D)  Method in class HAL.GridsAndAgents.Agent3DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapOccupiedHood(int[])  Method in class HAL.GridsAndAgents.Agent1DBase

These functions are similar to the the MapHood function, but they will only include valid empty or occupied indices, and skip the others.
 MapOccupiedHood(int[])  Method in class HAL.GridsAndAgents.Agent2DBase

These functions are similar to the the MapHood function, but they will only include valid empty or occupied indices, and skip the others.
 MapOccupiedHood(int[])  Method in class HAL.GridsAndAgents.Agent3DBase

These functions are similar to the the MapHood function, but they will only include valid empty or occupied indices, and skip the others.
 MapOccupiedHood(int[], int)  Method in class HAL.GridsAndAgents.AgentGrid1D

similar to the MapHood function, but will only include indices of locations that are occupied
 MapOccupiedHood(int[], int)  Method in class HAL.GridsAndAgents.AgentGrid2D

similar to the MapHood function, but will only include indices of locations that are occupied
 MapOccupiedHood(int[], int)  Method in class HAL.GridsAndAgents.AgentGrid3D

similar to the MapHood function, but will only include indices of locations that are occupied
 MapOccupiedHood(int[], int, int)  Method in class HAL.GridsAndAgents.AgentGrid2D

similar to the MapHood function, but will only include indices of locations that are occupied
 MapOccupiedHood(int[], int, int, int)  Method in class HAL.GridsAndAgents.AgentGrid3D

similar to the MapHood function, but will only include indices of locations that are occupied
 MapXpt(double, Grid1D)  Method in interface HAL.Interfaces.Grid1D

returns the position that x rescales to in the other grid
 MapXpt(double, Grid2D)  Method in interface HAL.Interfaces.Grid2D

returns the position that x rescales to in the other grid
 MapXpt(Grid1D)  Method in class HAL.GridsAndAgents.Agent1DBase

returns the provided coordinate scaled to the dimensions of the otherGrid.
 MapXpt(Grid2D)  Method in class HAL.GridsAndAgents.Agent2DBase

returns the provided coordinate scaled to the dimensions of the otherGrid.
 MapXpt(Grid3D)  Method in class HAL.GridsAndAgents.Agent3DBase

returns the provided coordinate scaled to the dimensions of the otherGrid.
 MapXsq(int, Grid1D)  Method in interface HAL.Interfaces.Grid1D

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapXsq(int, Grid2D)  Method in interface HAL.Interfaces.Grid2D

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapXsq(Grid1D)  Method in class HAL.GridsAndAgents.Agent1DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapXsq(Grid2D)  Method in class HAL.GridsAndAgents.Agent2DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapXsq(Grid3D)  Method in class HAL.GridsAndAgents.Agent3DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapYpt(double, Grid2D)  Method in interface HAL.Interfaces.Grid2D

returns the position that y rescales to in the other grid
 MapYpt(Grid2D)  Method in class HAL.GridsAndAgents.Agent2DBase

returns the provided coordinate scaled to the dimensions of the otherGrid.
 MapYpt(Grid3D)  Method in class HAL.GridsAndAgents.Agent3DBase

returns the provided coordinate scaled to the dimensions of the otherGrid.
 MapYsq(int, Grid2D)  Method in interface HAL.Interfaces.Grid2D

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapYsq(Grid2D)  Method in class HAL.GridsAndAgents.Agent2DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapYsq(Grid3D)  Method in class HAL.GridsAndAgents.Agent3DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MapZpt(Grid3D)  Method in class HAL.GridsAndAgents.Agent3DBase

returns the provided coordinate scaled to the dimensions of the otherGrid.
 MapZsq(Grid3D)  Method in class HAL.GridsAndAgents.Agent3DBase

returns the index of the center of the square in otherGrid that the coordinate maps to.
 MatrixToCSV(double[][], String)  Static method in class HAL.Util
 MatrixToCSV(int[][], String)  Static method in class HAL.Util
 MatrixToCSV(long[][], String)  Static method in class HAL.Util
 MatVecMul(double[], double[], double[])  Static method in class HAL.Util
 MaxDelta()  Method in class HAL.GridsAndAgents.PDEGrid1D

returns the maximum difference as stored on the delta field, call right before calling Update()
 MaxDelta()  Method in class HAL.GridsAndAgents.PDEGrid2D

returns the maximum difference as stored on the delta field, call right before calling Update()
 MaxDelta()  Method in class HAL.GridsAndAgents.PDEGrid3D

returns the maximum difference as stored on the delta field, call right before calling Update()
 MaxDeltaScaled(double)  Method in class HAL.GridsAndAgents.PDEGrid1D

like MaxDelta only the differences are scaled relative to the value in the current field.
 MaxDeltaScaled(double)  Method in class HAL.GridsAndAgents.PDEGrid2D

like MaxDelta only the differences are scaled relative to the value in the current field.
 MaxDeltaScaled(double)  Method in class HAL.GridsAndAgents.PDEGrid3D

like MaxDelta only the differences are scaled relative to the value in the current field.
 MaxDifInternal()  Method in class HAL.GridsAndAgents.PDEGrid3D

returns the maximum difference between the field passed in and the current field.
 maxDifscratch  Variable in class HAL.GridsAndAgents.PDEGrid3D
 MemoryUsageInfo(long[])  Static method in class HAL.Util
 MemoryUsageStr()  Static method in class HAL.Util

gets information about the memory usage and max memory allocated for the program
 MenuItem  Interface in HAL.Interfaces

Created by rafael on 11/25/16.
 methodNames  Variable in class HAL.Tools.Modularity.ModuleSetManager
 MichaelisMenten(double, double, double)  Static method in class HAL.Util

uses the Michaelis Menten equation to compute the reaction rate for a given substrate concentration
 mode  Variable in class HAL.Tools.FileIO
 moduleLists  Variable in class HAL.Tools.Modularity.ModuleSetManager
 modules  Variable in class HAL.Tools.Modularity.ModuleSetManager
 ModuleSetManager<baseModule>  Class in HAL.Tools.Modularity

the ModuleSetManager class is used to store and use module objects.
 ModuleSetManager(Class<baseModule>)  Constructor for class HAL.Tools.Modularity.ModuleSetManager

the module base class object should define all of the method hooks that modules can use, the behavior of the base class object will be ignored
 MooreHood(boolean)  Static method in class HAL.Util

Returns the coordinates defining the Moore neighborhood centered on (0,0)
 MooreHood3D(boolean)  Static method in class HAL.Util
 MovePT(double)  Method in class HAL.GridsAndAgents.AgentPT1D

Moves the agent to the specified coordinates
 MovePT(double, double)  Method in class HAL.GridsAndAgents.AgentPT2D

Moves the agent to the specified coordinates
 MovePT(double, double, double)  Method in class HAL.GridsAndAgents.AgentPT3D

Moves the agent to the specified coordinates
 MoveSafePT(double)  Method in class HAL.GridsAndAgents.AgentPT1D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafePT(double, double)  Method in class HAL.GridsAndAgents.AgentPT2D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafePT(double, double, double)  Method in class HAL.GridsAndAgents.AgentPT3D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafePT(double, double, double, Point3DBool)  Method in class HAL.GridsAndAgents.AgentPT3D
 MoveSafePT(double, double, Point2DBool)  Method in class HAL.GridsAndAgents.AgentPT2D
 MoveSafePT(double, Point1DBool)  Method in class HAL.GridsAndAgents.AgentPT1D
 MoveSafeSQ(int)  Method in class HAL.GridsAndAgents.AgentPT1D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafeSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ1D

Moves the agent to the specified square, will apply wraparound if it is enabled
 MoveSafeSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ1Dunstackable

Moves the agent to the specified square, will apply wraparound if it is enabled
 MoveSafeSQ(int, int)  Method in class HAL.GridsAndAgents.AgentPT2D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafeSQ(int, int)  Method in class HAL.GridsAndAgents.AgentSQ2D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafeSQ(int, int)  Method in class HAL.GridsAndAgents.AgentSQ2Dunstackable

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafeSQ(int, int, int)  Method in class HAL.GridsAndAgents.AgentPT3D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafeSQ(int, int, int)  Method in class HAL.GridsAndAgents.AgentSQ3D

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafeSQ(int, int, int)  Method in class HAL.GridsAndAgents.AgentSQ3Dunstackable

Similar to the move functions, only it will automatically either apply wraparound, or prevent moving along a partiular axis if movement would cause the agent to go out of bounds.
 MoveSafeSQ(int, int, int, Coords3DBool)  Method in class HAL.GridsAndAgents.AgentPT3D
 MoveSafeSQ(int, int, Coords2DBool)  Method in class HAL.GridsAndAgents.AgentPT2D
 MoveSafeSQ(int, Coords1DBool)  Method in class HAL.GridsAndAgents.AgentPT1D
 MoveSafeSQ(int, Coords1DBool)  Method in class HAL.GridsAndAgents.AgentSQ1D
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentBaseSpatial

moves the agent to the middle of the square at the indices/index specified
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentPT1D

Moves the agent to the center of the square at the specified coordinates
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentPT2D

Moves the agent to the center of the square at the specified coordinates
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentPT3D

Moves the agent to the specified coordinates
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ1D

Moves the agent to the specified square
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ1Dunstackable

Moves the agent to the square with the specified index
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ2D

Moves the agent to the specified square
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ2Dunstackable

Moves the agent to the square with the specified index
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ3D
 MoveSQ(int)  Method in class HAL.GridsAndAgents.AgentSQ3Dunstackable

Moves the agent to the specified coordinates
 MoveSQ(int, int)  Method in class HAL.GridsAndAgents.AgentPT2D

Moves the agent to the center of the square at the specified coordinates
 MoveSQ(int, int)  Method in class HAL.GridsAndAgents.AgentSQ2D

Moves the agent to the specified square
 MoveSQ(int, int)  Method in class HAL.GridsAndAgents.AgentSQ2Dunstackable

Moves the agent to the square at the specified coordinates
 MoveSQ(int, int, int)  Method in class HAL.GridsAndAgents.AgentPT3D

Moves the agent to the specified coordinates
 MoveSQ(int, int, int)  Method in class HAL.GridsAndAgents.AgentSQ3D

Moves the agent to the specified coordinates
 MoveSQ(int, int, int)  Method in class HAL.GridsAndAgents.AgentSQ3Dunstackable

Moves the agent to the specified coordinates
 Mul(double, double)  Method in class HAL.GridsAndAgents.PDEGrid1D
 Mul(double, double, double)  Method in class HAL.GridsAndAgents.PDEGrid2D
 Mul(double, double, double, double)  Method in class HAL.GridsAndAgents.PDEGrid3D
 Mul(int, double)  Method in class HAL.GridsAndAgents.PDEGrid1D

multiplies a value in the “current field” and adds the change to the “delta field”
 Mul(int, double)  Method in class HAL.GridsAndAgents.PDEGrid2D

multiplies a value in the “current field” and adds the change to the “delta field”
 Mul(int, double)  Method in class HAL.GridsAndAgents.PDEGrid3D

multiplies a value in the “current field” and adds the change to the “delta field”
 Mul(int, int, double)  Method in class HAL.GridsAndAgents.PDEGrid2D

multiplies a value in the “current field” and adds the change to the “delta field”
 Mul(int, int, int, double)  Method in class HAL.GridsAndAgents.PDEGrid3D

multiplies a value in the “current field” and adds the change to the “delta field”
 MulAll(double)  Method in class HAL.GridsAndAgents.Grid2Ddouble

multiplies all entries in the field by the value
 MulAll(double)  Method in class HAL.GridsAndAgents.Grid2Dint

adds specified value to all entries of the curr field
 MulAll(double)  Method in class HAL.GridsAndAgents.PDEGrid1D

multiplies all values in the “current field” and puts the results into the “delta field”
 MulAll(double)  Method in class HAL.GridsAndAgents.PDEGrid2D

multiplies all values in the “current field” and puts the results into the “delta field”
 MulAll(double)  Method in class HAL.GridsAndAgents.PDEGrid3D

multiplies all values in the “current field” and puts the results into the “delta field”
 Multinomial(double[], int, int[])  Method in class HAL.Rand
 Multinomial(double[], long, long[])  Method in class HAL.Rand
 MultinomialCalc  Class in HAL.Tools
 MultinomialCalc(Rand)  Constructor for class HAL.Tools.MultinomialCalc
 MultinomialCalcLong  Class in HAL.Tools
 MultinomialCalcLong(Rand)  Constructor for class HAL.Tools.MultinomialCalcLong
 MultiThread(int, int, ParallelFunction)  Static method in class HAL.Util

Creates a thread pool and launches a total of nRun threads, with nThreads running simultaneously at a time.
 MultiThread(int, ParallelFunction)  Static method in class HAL.Util

does the same thing as MultiThread above, but generates a number of threads equal to the number of available processors
 MultiWellExperiment<T>  Class in HAL.Tools.MultiWellExperiment

MultiWellExperiments allow the user to visualize many models in a single GridWindow, and can be easily multithreaded for faster execution
 MultiWellExperiment(int, int, T[], int, int, int, int, StepWell<T>, DrawWell<T>)  Constructor for class HAL.Tools.MultiWellExperiment.MultiWellExperiment

generates a MultiWellExperiment.
 MutantToString(T)  Method in interface HAL.Interfaces.GAMutantToString
 MutantToString(T)  Method in interface HAL.Interfaces.GetMutationInfo
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