M-Index

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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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