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G

G - Variable in class HAL.GridsAndAgents.AgentBase
returns the grid that the agent belongs to (this is a permanent agent property, not a function)
GAMutantToString<T> - Interface in HAL.Interfaces
Created by rafael on 4/8/17.
GAMutationFunction<T> - Interface in HAL.Interfaces
Created by rafael on 4/8/17.
GAScoreFunction<T> - Interface in HAL.Interfaces
Created by rafael on 4/8/17.
Gaussian - Class in HAL.Tools.Internal
Created by Rafael on 11/16/2017.
Gaussian() - Constructor for class HAL.Tools.Internal.Gaussian
 
Gaussian(double, double) - Method in class HAL.Rand
returns a random number from the binomial distribution (number of heads from n weighted coin flips with probability p of heads)
GaussianPDF(double) - Static method in class HAL.Util
 
GaussianPDF(double, double, double) - Static method in class HAL.Util
 
GenCirclePoints(float, int) - Static method in class HAL.Util
returns the evenly spaced coordinates along the edge of a circle in 2D, centered on (0,0)
GenColor(double) - Method in interface HAL.Interfaces.DoubleToColor
 
GenColor(double, double) - Method in interface HAL.Interfaces.DoublesToColor
 
GenColorInt() - Method in interface HAL.Interfaces.ColorIntGenerator
 
GenDouble - Interface in HAL.Interfaces
 
GenDouble() - Method in interface HAL.Interfaces.GenDouble
 
GenDouble(double, double) - Method in interface HAL.Interfaces.Doubles2DDouble
 
GenDouble(double, double, double) - Method in interface HAL.Interfaces.Doubles3DDouble
 
GenDouble(int) - Method in interface HAL.Interfaces.Coords1DDouble
 
GenDouble(int) - Method in interface HAL.Interfaces.IntToDouble
 
GenDouble(int, int) - Method in interface HAL.Interfaces.Coords2DDouble
 
GenDouble(int, int, int) - Method in interface HAL.Interfaces.Coords3DDouble
 
GenDouble(int, int, int, int, int, int) - Method in interface HAL.Interfaces.Coords6DDouble
 
GenDoubles(double) - Method in interface HAL.Interfaces.DoubleToDoubles
 
GenHood1D(int[]) - Static method in class HAL.Util
generates a 1D neighborhood from a set of coordinates, with space for the results of mapping
GenHood2D(int[]) - Static method in class HAL.Util
generates a 2D neighborhood from a set of coordinates, with space for the results of mapping
GenHood3D(int[]) - Static method in class HAL.Util
generates a 3D neighborhood from a set of coordinates, with space for the results of mapping
GenIndicesArray(int) - Static method in class HAL.Util
returns an array of indices starting with 0 and ending with nEntries-1
GenInt(int) - Method in interface HAL.Interfaces.Coords1DInt
 
GenInt(int, int) - Method in interface HAL.Interfaces.Coords2DInt
 
GenInt(int, int, int) - Method in interface HAL.Interfaces.Coords3DInt
 
Genome<T extends Genome> - Class in HAL.Tools.PhylogenyTracker
the genome class is useful for keeping track of shared genetic information and phylogenies.
Genome(T) - Constructor for class HAL.Tools.PhylogenyTracker.Genome
 
Genome(T, boolean) - Constructor for class HAL.Tools.PhylogenyTracker.Genome
´╗┐call this with the parent set to null to create a new phylogeny.
GenomeFn<T extends Genome> - Interface in HAL.Tools.PhylogenyTracker
 
GenomeFn(T) - Method in interface HAL.Tools.PhylogenyTracker.GenomeFn
 
GenomeLineageFn<T extends Genome> - Interface in HAL.Tools.PhylogenyTracker
 
GenomeLineageFn(ArrayList<T>) - Method in interface HAL.Tools.PhylogenyTracker.GenomeLineageFn
 
GenVarSet() - Method in class HAL.Tools.Modularity.VarSetManager
 
Get() - Method in class HAL.Gui.UIBoolInput
returns the current boolean value as a string
Get() - Method in class HAL.Gui.UIComboBoxInput
ignore
Get() - Method in class HAL.Gui.UIDoubleInput
ignore
Get() - Method in class HAL.Gui.UIFileChooserInput
ignore
Get() - Method in class HAL.Gui.UIIntInput
ignore
Get() - Method in class HAL.Gui.UIStringInput
ignore
Get() - Method in interface HAL.Interfaces.MenuItem
 
Get(double) - Method in class HAL.GridsAndAgents.PDEGrid1D
 
Get(double, double) - Method in class HAL.GridsAndAgents.PDEGrid2D
 
Get(double, double[]) - Method in interface HAL.Interfaces.OdeSolution
 
Get(double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
 
Get(int) - Method in class HAL.GridsAndAgents.Grid1Ddouble
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid1Dint
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid1Dlong
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid1Dobject
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid2Ddouble
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid2Dint
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid2Dlong
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid2Dobject
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid3Ddouble
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid3Dint
gets the current field value at the specified coordinates
Get(int) - Method in class HAL.GridsAndAgents.Grid3Dlong
gets the current field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.Grid3Dobject
gets the field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.PDEGrid1D
gets the prev field value at the specified coordinates
Get(int) - Method in class HAL.GridsAndAgents.PDEGrid2D
gets the prev field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.PDEGrid3D
gets the delta field value at the specified index
Get(int) - Method in class HAL.GridsAndAgents.PopulationGridBase
 
Get(int) - Method in class HAL.GridsAndAgents.PopulationGridLongBase
 
Get(int) - Method in class HAL.Tools.BoolSet
 
Get(int, int) - Method in class HAL.GridsAndAgents.Grid2Ddouble
gets the current field value at the specified coordinates
Get(int, int) - Method in class HAL.GridsAndAgents.Grid2Dint
gets the current field value at the specified coordinates
Get(int, int) - Method in class HAL.GridsAndAgents.Grid2Dlong
gets the current field value at the specified coordinates
Get(int, int) - Method in class HAL.GridsAndAgents.Grid2Dobject
gets the current field value at the specified coordinates
Get(int, int) - Method in class HAL.GridsAndAgents.PDEGrid2D
gets the prev field value at the specified coordinates
Get(int, int) - Method in class HAL.GridsAndAgents.PopulationGrid2D
 
Get(int, int) - Method in class HAL.GridsAndAgents.PopulationGrid2DLong
 
Get(int, int, int) - Method in class HAL.GridsAndAgents.Grid3Ddouble
gets the current field value at the specified coordinates
Get(int, int, int) - Method in class HAL.GridsAndAgents.Grid3Dint
gets the current field value at the specified coordinates
Get(int, int, int) - Method in class HAL.GridsAndAgents.Grid3Dlong
gets the current field value at the specified coordinates
Get(int, int, int) - Method in class HAL.GridsAndAgents.Grid3Dobject
gets the field value at the specified coordinates
Get(int, int, int) - Method in class HAL.GridsAndAgents.PDEGrid3D
gets to the current field value at the specified coordinates
Get(int, int, int) - Method in class HAL.GridsAndAgents.PopulationGrid3D
 
Get(int, int, int) - Method in class HAL.GridsAndAgents.PopulationGrid3DLong
 
GetAgent(int) - Method in class HAL.GridsAndAgents.AgentGrid1D
Gets a single agent at the specified grid square, beware using this function with stackable agents, as it will only return one of the stack of agents.
GetAgent(int) - Method in class HAL.GridsAndAgents.AgentGrid2D
Gets a single agent at the specified grid square, beware using this function with stackable agents, as it will only return one of the stack of agents.
GetAgent(int) - Method in class HAL.GridsAndAgents.AgentGrid3D
Gets a single agent at the specified grid square, beware using this function with stackable agents, as it will only return one of the stack of agents.
GetAgent(int, int) - Method in class HAL.GridsAndAgents.AgentGrid2D
Gets a single agent at the specified grid square, beware using this function with stackable agents, as it will only return one of the stack of agents.
GetAgent(int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid3D
Gets a single agent at the specified grid square, beware using this function with stackable agents, as it will only return one of the stack of agents.
GetAgents(ArrayList<T>, int) - Method in class HAL.GridsAndAgents.AgentGrid1D
appends to the provided arraylist all agents on the square at the specified coordinates
GetAgents(ArrayList<T>, int) - Method in class HAL.GridsAndAgents.AgentGrid2D
appends to the provided arraylist all agents on the square at the specified coordinates
GetAgents(ArrayList<T>, int) - Method in class HAL.GridsAndAgents.AgentGrid3D
appends to the provided arraylist all agents on the square at the specified coordinates, will subset only agents for which EvalAgent returns true
GetAgents(ArrayList<T>, int, int) - Method in class HAL.GridsAndAgents.AgentGrid2D
appends to the provided arraylist all agents on the square at the specified coordinates
GetAgents(ArrayList<T>, int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid3D
appends to the provided arraylist all agents on the square at the specified coordinates, will subset only agents for which EvalAgent returns true
GetAgents(ArrayList<T>, int, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
appends to the provided arraylist all agents on the square at the specified coordinates, will subset only agents for which EvalAgent returns true
GetAgents(ArrayList<T>, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
appends to the provided arraylist all agents on the square at the specified coordinates, will subset only agents for which EvalAgent returns true
GetAgents(ArrayList<T>, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
appends to the provided arraylist all agents on the square at the specified coordinates, will subset only agents for which EvalAgent returns true
GetAgents(ArrayList<T>, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
appends to the provided arraylist all agents on the square at the specified coordinates, will subset only agents for which EvalAgent returns true
GetAgents(ArrayList<T>, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
appends to the provided arraylist all agents on the square at the specified coordinates, will subset only agents for which EvalAgent returns true
GetAgentSafe(int) - Method in class HAL.GridsAndAgents.AgentGrid1D
Same as GetAgent above, but if x or y are outside the domain, it will apply wrap around if wrapping is enabled, or return null.
GetAgentSafe(int, int) - Method in class HAL.GridsAndAgents.AgentGrid2D
Same as GetAgent above, but if x or y are outside the domain, it will apply wrap around if wrapping is enabled, or return null.
GetAgentSafe(int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid3D
Same as GetAgent above, but if x or y are outside the domain, it will apply wrap around if wrapping is enabled, or return null.
GetAgentsHood(ArrayList<T>, int[], int) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents within the given neighborhood and adds them to the ArrayList argument
GetAgentsHood(ArrayList<T>, int[], int, int) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents within the given neighborhood and adds them to the ArrayList argument
GetAgentsHood(ArrayList<T>, int[], int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents within the given neighborhood and adds them to the ArrayList argument
GetAgentsHood(ArrayList<T>, int[], int, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents within the given neighborhood forwhich EvalAgent returns true and adds them to the ArrayList argument
GetAgentsHood(ArrayList<T>, int[], int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents within the given neighborhood forwhich EvalAgent returns true and adds them to the ArrayList argument
GetAgentsHood(ArrayList<T>, int[], int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents within the given neighborhood forwhich EvalAgent returns true and adds them to the ArrayList argument
GetAgentsHoodMapped(ArrayList<T>, int[], int) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents in the provided neighborhood, assumes that the neighborhood has already been mapped to a location
GetAgentsHoodMapped(ArrayList<T>, int[], int) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents in the provided neighborhood, assumes that the neighborhood has already been mapped to a location
GetAgentsHoodMapped(ArrayList<T>, int[], int) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents in the provided neighborhood, assumes that the neighborhood has already been mapped to a location
GetAgentsHoodMapped(ArrayList<T>, int[], int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents in the provided neighborhood forwhich EvalAgent returns true, assumes that the neighborhood has already been mapped to a location
GetAgentsHoodMapped(ArrayList<T>, int[], int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents in the provided neighborhood, assumes that the neighborhood has already been mapped to a location
GetAgentsHoodMapped(ArrayList<T>, int[], int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents in the provided neighborhood, assumes that the neighborhood has already been mapped to a location
GetAgentsRad(ArrayList<T>, double, double) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents that are within rad, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, double, double, double) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents that are within rad, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, double, double, double, double) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents that are within rad, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, double, double, double, double, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents that are within rad forwhich EvalAgent returns true, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, double, double, double, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents that are within rad forwhich EvalAgent returns true, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, double, double, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents that are within rad forwhich EvalAgent returns true, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, ArrayList<double[]>, double, double) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents that are within rad, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, ArrayList<double[]>, double, double, double) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents that are within rad, and adds them to the ArrayList, displacementInfo contains the following info for each agent: [dist from point,x disp,y disp]
GetAgentsRad(ArrayList<T>, ArrayList<double[]>, double, double, double, double) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents that are within rad, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, ArrayList<double[]>, double, double, double, double, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents that are within rad forwhich EvalAgent returns true, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, ArrayList<double[]>, double, double, double, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents that are within rad forwhich EvalAgent returns true, and adds them to the ArrayList
GetAgentsRad(ArrayList<T>, ArrayList<double[]>, double, double, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents that are within rad forwhich EvalAgent returns true, and adds them to the ArrayList
GetAgentsRadApprox(ArrayList<T>, double, double) - Method in class HAL.GridsAndAgents.AgentGrid1D
quickly gets all agents that are within rad, but also includes some that are further away than rad, an additional distance check should be used to properly subset this group
GetAgentsRadApprox(ArrayList<T>, double, double, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
quickly gets all agents that are within rad, but also includes some that are further away than rad, an additional distance check should be used to properly subset this group.
GetAgentsRect(ArrayList<T>, int, int) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents within the rectangle argument defined by the bottom corner and the dimension arguments
GetAgentsRect(ArrayList<T>, int, int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents within the rectangle argument defined by the bottom corner and the dimension arguments
GetAgentsRect(ArrayList<T>, int, int, int, int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents within the rectangle argument defined by the bottom corner and the dimension arguments
GetAgentsRect(ArrayList<T>, int, int, int, int, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
gets all agents forwhich evalAgent returns true within the rectangle argument defined by the bottom corner and the dimension arguments
GetAgentsRect(ArrayList<T>, int, int, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
gets all agents forwhich evalAgent returns true within the rectangle argument defined by the bottom corner and the dimension arguments
GetAgentsRect(ArrayList<T>, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
gets all agents forwhich evalAgent returns true within the rectangle argument defined by the bottom corner and the dimension arguments
GetAgentsSafe(ArrayList<T>, int) - Method in class HAL.GridsAndAgents.AgentGrid1D
appends to the provided arraylist all agents on the square at the specified coordinates, will apply wraparound if the coordinates are outside the domain
GetAgentsSafe(ArrayList<T>, int, int) - Method in class HAL.GridsAndAgents.AgentGrid2D
appends to the provided arraylist all agents on the square at the specified coordinates, will apply wraparound if the coordinates are outside the domain
GetAgentsSafe(ArrayList<T>, int, int, int) - Method in class HAL.GridsAndAgents.AgentGrid3D
appends to the provided arraylist all agents on the square at the specified coordinates, will apply wraparound if the coordinates are outside the domain
GetAgentsSafe(ArrayList<T>, int, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid3D
appends to the provided arraylist all agents on the square at the specified coordinates forwhich EvalAgent returns true, will apply wraparound if the coordinates are outside the domain
GetAgentsSafe(ArrayList<T>, int, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid2D
appends to the provided arraylist all agents on the square at the specified coordinates forwhich EvalAgent returns true, will apply wraparound if the coordinates are outside the domain
GetAgentsSafe(ArrayList<T>, int, AgentToBool<T>) - Method in class HAL.GridsAndAgents.AgentGrid1D
appends to the provided arraylist all agents on the square at the specified coordinates, will apply wraparound if the coordinates are outside the domain, will subset only agents for which EvalAgent returns true
GetAllOnSquare(ArrayList<AgentBaseSpatial>) - Method in class HAL.GridsAndAgents.AgentSQ1Dunstackable
 
GetAllOnSquare(ArrayList<AgentBaseSpatial>) - Method in class HAL.GridsAndAgents.AgentSQ2Dunstackable
 
GetAlpha(int) - Static method in class HAL.Util
returns the Alpha component value of the color as an integer from 0 to 1
GetAlpha256(int) - Static method in class HAL.Util
returns the Alpha component value of the color as an integer from 0 to 255
GetAttrs(T) - Method in interface HAL.Interfaces.GetGenomeAttrs
 
GetAvg() - Method in class HAL.GridsAndAgents.Grid1Ddouble
returns the mean value of the grid
GetAvg() - Method in class HAL.GridsAndAgents.Grid1Dint
returns the mean value of the grid
GetAvg() - Method in class HAL.GridsAndAgents.Grid1Dlong
returns the mean value of the grid
GetAvg() - Method in class HAL.GridsAndAgents.Grid2Ddouble
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.Grid2Dint
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.Grid2Dlong
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.Grid3Ddouble
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.Grid3Dint
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.Grid3Dlong
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.PDEGrid1D
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.PDEGrid2D
gets the average value of all squares in the current field
GetAvg() - Method in class HAL.GridsAndAgents.PDEGrid3D
gets the average value of all squares in the current field
GetBit(int, int) - Static method in class HAL.Util
gets the value from a single bit of an int32
GetBit(long, int) - Static method in class HAL.Util
gets the value from a single bit of an long64
GetBlue(int) - Static method in class HAL.Util
returns the Blue component value of the color as an integer from 0 to 1
GetBlue256(int) - Static method in class HAL.Util
returns the Blue component value of the color as an integer from 0 to 255
GetBool(String) - Method in class HAL.Gui.UIWindow
 
GetBool(String) - Method in class HAL.Tools.Internal.ParamSet
gets the boolean value from the set with the specified label
GetChildren(ArrayList<T>) - Method in class HAL.Tools.PhylogenyTracker.Genome
adds all direct descendants of the genome to the arraylist
GetData() - Method in class HAL.Tools.BoolSet
 
GetDeltas() - Method in class HAL.GridsAndAgents.PDEGrid1D
 
GetDeltas() - Method in class HAL.GridsAndAgents.PDEGrid2D
 
GetDeltas() - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GetDouble(String) - Method in class HAL.Gui.UIWindow
 
GetDouble(String) - Method in class HAL.Tools.Internal.ParamSet
gets the double value from the set with the specified label
GetEntry(int) - Method in class HAL.Gui.UIBoolInput
ignore
GetEntry(int) - Method in class HAL.Gui.UIComboBoxInput
ignore
GetEntry(int) - Method in class HAL.Gui.UIDoubleInput
ignore
GetEntry(int) - Method in class HAL.Gui.UIFileChooserInput
ignore
GetEntry(int) - Method in class HAL.Gui.UIIntInput
ignore
GetEntry(int) - Method in class HAL.Gui.UIStringInput
ignore
GetEntry(int) - Method in interface HAL.Interfaces.MenuItem
 
GetField() - Method in class HAL.GridsAndAgents.Grid1Ddouble
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid1Dint
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid1Dlong
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid1Dobject
 
GetField() - Method in class HAL.GridsAndAgents.Grid2Ddouble
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid2Dint
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid2Dlong
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid2Dobject
 
GetField() - Method in class HAL.GridsAndAgents.Grid3Ddouble
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid3Dint
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid3Dlong
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.Grid3Dobject
returns the complete field as an array
GetField() - Method in class HAL.GridsAndAgents.PDEGrid1D
 
GetField() - Method in class HAL.GridsAndAgents.PDEGrid2D
 
GetField() - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GetFirstDivergence(int) - Method in class HAL.Tools.InteractiveModel.InteractiveModel
 
GetGenomeAttrs<T extends Genome> - Interface in HAL.Interfaces
 
GetGreen(int) - Static method in class HAL.Util
returns the Green component value of the color as an integer from 0 to 1
GetGreen256(int) - Static method in class HAL.Util
returns the Green component value of the color as an integer from 0 to 255
GetHoodI(int[], int, int) - Method in interface HAL.Interfaces.Grid1D
gets a specified index from the hood after mapping to the center position
GetHoodI(int[], int, int, int) - Method in interface HAL.Interfaces.Grid2D
gets a specified index from the hood after mapping to the center position
GetHoodI(int[], int, int, int, int) - Method in interface HAL.Interfaces.Grid3D
gets one mapped index from the neighborhood
GetId() - Method in class HAL.Tools.PhylogenyTracker.Genome
gets the ID of the genome, which indicates the order in which it arose
GetInt(String) - Method in class HAL.Gui.UIWindow
 
GetInt(String) - Method in class HAL.Tools.Internal.ParamSet
gets the integer value from the set with the specified label
GetLabel() - Method in class HAL.Gui.UIBoolInput
returns the label associated with the boolean
GetLabel() - Method in class HAL.Gui.UIComboBoxInput
ignore
GetLabel() - Method in class HAL.Gui.UIDoubleInput
ignore
GetLabel() - Method in class HAL.Gui.UIFileChooserInput
ignore
GetLabel() - Method in class HAL.Gui.UIIntInput
ignore
GetLabel() - Method in class HAL.Gui.UIStringInput
ignore
GetLabel() - Method in interface HAL.Interfaces.MenuItem
 
GetLineage(ArrayList<T>) - Method in class HAL.Tools.PhylogenyTracker.Genome
adds all ancestors of the genome ot the arraylist
GetMax() - Method in class HAL.GridsAndAgents.Grid1Ddouble
returns the max value in the grid
GetMax() - Method in class HAL.GridsAndAgents.Grid1Dint
returns the max value in the grid
GetMax() - Method in class HAL.GridsAndAgents.Grid1Dlong
returns the max value in the grid
GetMax() - Method in class HAL.GridsAndAgents.Grid2Ddouble
returns the max value in the grid
GetMax() - Method in class HAL.GridsAndAgents.Grid2Dint
returns the max value in the grid
GetMax() - Method in class HAL.GridsAndAgents.Grid2Dlong
returns the max value in the grid
GetMax() - Method in class HAL.GridsAndAgents.PDEGrid2D
returns the max value in the grid
GetMin() - Method in class HAL.GridsAndAgents.Grid1Ddouble
returns the min value in the grid
GetMin() - Method in class HAL.GridsAndAgents.Grid1Dint
returns the min value in the grid
GetMin() - Method in class HAL.GridsAndAgents.Grid1Dlong
returns the min value in the grid
GetMin() - Method in class HAL.GridsAndAgents.Grid2Ddouble
returns the min value in the grid
GetMin() - Method in class HAL.GridsAndAgents.Grid2Dint
returns the min value in the grid
GetMin() - Method in class HAL.GridsAndAgents.Grid2Dlong
returns the min value in the grid
GetMin() - Method in class HAL.GridsAndAgents.PDEGrid2D
returns the min value in the grid
GetMutationInfo<T> - Interface in HAL.Interfaces
Created by Rafael on 8/3/2017.
GetNumGenomes() - Method in class HAL.Tools.PhylogenyTracker.Genome
returns the total number of genomes that have ever existed in the phylogeny
GetNumIntensities() - Method in interface HAL.Tools.InteractiveModel.TreatableTumor
 
GetNumLivingGenomes() - Method in class HAL.Tools.PhylogenyTracker.Genome
returns the number of currently active unique genomes
GetNumTreeGenomes() - Method in class HAL.Tools.PhylogenyTracker.Genome
returns the number of genomes that exist in the phylogeny (not counting removed leaves)
GetParent() - Method in class HAL.Tools.PhylogenyTracker.Genome
returns the parent genome that was mutated to give rise to this genome
GetPix(int) - Method in class HAL.Gui.UIGrid
returns the pixel color at that location as a colorInt
GetPix(int, int) - Method in class HAL.Gui.UIGrid
returns the pixel color at that location as a colorInt
GetPixColor(T, int, int) - Method in interface HAL.Tools.MultiWellExperiment.DrawWell
 
GetPlotColors() - Method in interface HAL.Tools.InteractiveModel.TreatableTumor
 
GetPlotLegendNames() - Method in interface HAL.Tools.InteractiveModel.TreatableTumor
 
GetPlotVals() - Method in interface HAL.Tools.InteractiveModel.TreatableTumor
 
GetPop() - Method in class HAL.GridsAndAgents.AgentGrid0D
returns the number of agents that are alive in the typeGrid
GetPop() - Method in class HAL.GridsAndAgents.AgentList
returns the size of the AgentList, duplicate agents will be counted multiple times
GetPop() - Method in class HAL.Tools.PhylogenyTracker.Genome
returns the current active population that shares this genome
GetPopRemaining() - Method in class HAL.Tools.MultinomialCalc
 
GetPopRemaining() - Method in class HAL.Tools.MultinomialCalcLong
 
GetProbRemaining() - Method in class HAL.Tools.MultinomialCalc
 
GetProbRemaining() - Method in class HAL.Tools.MultinomialCalcLong
 
GetRed(int) - Static method in class HAL.Util
returns the Red component value of the color as an integer from 0 to 1
GetRed256(int) - Static method in class HAL.Util
returns the Red component value of the color as an integer from 0 to 255
GetRoot() - Method in class HAL.Tools.PhylogenyTracker.Genome
gets the first genome that started the phylogeny
GetSafe(int) - Method in class HAL.Tools.BoolSet
 
GetString(String) - Method in class HAL.Gui.UIWindow
 
GetString(String) - Method in class HAL.Tools.Internal.ParamSet
gets the string value from the set with the specified label
GetText() - Method in class HAL.Gui.UILabel
 
GetTick() - Method in class HAL.GridsAndAgents.AgentGrid0D
 
GetTick() - Method in class HAL.GridsAndAgents.AgentGrid1D
gets the current grid timestep.
GetTick() - Method in class HAL.GridsAndAgents.AgentGrid2D
gets the current grid timestep.
GetTick() - Method in class HAL.GridsAndAgents.AgentGrid3D
gets the current grid timestep.
GetTick() - Method in class HAL.Tools.InteractiveModel.InteractiveModel
 
GetTreatmentColors() - Method in interface HAL.Tools.InteractiveModel.TreatableTumor
 
GetTreatmentNames() - Method in interface HAL.Tools.InteractiveModel.TreatableTumor
 
GetVars() - Method in interface HAL.Tools.Modularity.VarSet
 
GifMaker - Class in HAL.Gui
the GifMaker is used to create gif files by compiling UIGrid states
GifMaker(String, int, boolean) - Constructor for class HAL.Gui.GifMaker
Creates a new GifMaker
gn - Variable in class HAL.Rand
 
GradientX(double, double) - Method in class HAL.GridsAndAgents.PDEGrid2D
 
GradientX(double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid2D
 
GradientX(double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GradientX(double, double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GradientX(int) - Method in class HAL.GridsAndAgents.Grid1Ddouble
returns the gradient of the field in the X direction at the coordinates specified
GradientX(int, double) - Method in class HAL.GridsAndAgents.Grid1Ddouble
returns the gradient of the field in the X direction at the coordinates specified, will use the boundary value provided for gradients that go over the boundary
GradientX(int, int) - Method in class HAL.GridsAndAgents.Grid2Ddouble
returns the gradient of the field in the X direction at the coordinates specified
GradientX(int, int) - Method in class HAL.GridsAndAgents.PDEGrid2D
returns the gradient of the diffusible in the X direction at the coordinates specified
GradientX(int, int, double) - Method in class HAL.GridsAndAgents.Grid2Ddouble
returns the gradient of the field in the X direction at the coordinates specified, will use the boundary value provided for gradients that go over the boundary
GradientX(int, int, double) - Method in class HAL.GridsAndAgents.PDEGrid2D
returns the gradient of the diffusible in the X direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
GradientX(int, int, int) - Method in class HAL.GridsAndAgents.Grid3Ddouble
returns the gradient of the field in the X direction at the coordinates specified
GradientX(int, int, int) - Method in class HAL.GridsAndAgents.PDEGrid3D
returns the gradient of the diffusible in the X direction at the coordinates specified
GradientX(int, int, int, double) - Method in class HAL.GridsAndAgents.Grid3Ddouble
returns the gradient of the field in the X direction at the coordinates specified, will use the boundary value provided for gradients that go over the boundary
GradientX(int, int, int, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
returns the gradient of the diffusible in the X direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
GradientY(double, double) - Method in class HAL.GridsAndAgents.PDEGrid2D
 
GradientY(double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid2D
 
GradientY(double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GradientY(double, double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GradientY(int, int) - Method in class HAL.GridsAndAgents.Grid2Ddouble
returns the gradient of the field in the Y direction at the coordinates specified
GradientY(int, int) - Method in class HAL.GridsAndAgents.PDEGrid2D
returns the gradient of the diffusible in the Y direction at the coordinates specified
GradientY(int, int, double) - Method in class HAL.GridsAndAgents.Grid2Ddouble
returns the gradient of the field in the Y direction at the coordinates specified, will use the boundary value provided for gradients that go over the boundary
GradientY(int, int, double) - Method in class HAL.GridsAndAgents.PDEGrid2D
returns the gradient of the diffusible in the Y direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
GradientY(int, int, int) - Method in class HAL.GridsAndAgents.Grid3Ddouble
returns the gradient of the field in the Y direction at the coordinates specified
GradientY(int, int, int) - Method in class HAL.GridsAndAgents.PDEGrid3D
returns the gradient of the diffusible in the Y direction at the coordinates specified
GradientY(int, int, int, double) - Method in class HAL.GridsAndAgents.Grid3Ddouble
returns the gradient of the field in the Y direction at the coordinates specified, will use the boundary value provided for gradients that go over the boundary
GradientY(int, int, int, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
returns the gradient of the diffusible in the Y direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
GradientZ(double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GradientZ(double, double, double, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
 
GradientZ(int, int, int) - Method in class HAL.GridsAndAgents.Grid3Ddouble
returns the gradient of the field in the Z direction at the coordinates specified
GradientZ(int, int, int) - Method in class HAL.GridsAndAgents.PDEGrid3D
returns the gradient of the diffusible in the Z direction at the coordinates specified
GradientZ(int, int, int, double) - Method in class HAL.GridsAndAgents.Grid3Ddouble
returns the gradient of the field in the Z direction at the coordinates specified, will use the boundary value provided for gradients that go over the boundary
GradientZ(int, int, int, double) - Method in class HAL.GridsAndAgents.PDEGrid3D
returns the gradient of the diffusible in the Z direction at the coordinates specified, will use the boundary condition value if computing the gradient next to the boundary
GREEN - Static variable in class HAL.Util
 
GreyOut(boolean) - Method in class HAL.Gui.UIWindow
Disables or enables all interacton with the UIWindow
grid - Variable in class HAL.Gui.UIPlot
 
Grid1D - Interface in HAL.Interfaces
holds functions that all 1D Grids share
Grid1Ddouble - Class in HAL.GridsAndAgents
a 1D Grid of doubles
Grid1Ddouble(int) - Constructor for class HAL.GridsAndAgents.Grid1Ddouble
creates a new Grid1Ddouble of length xDim without wraparound
Grid1Ddouble(int, boolean) - Constructor for class HAL.GridsAndAgents.Grid1Ddouble
creates a new Grid1Ddouble of length xDim with optional wraparound
Grid1Dint - Class in HAL.GridsAndAgents
a 1D Grid of ints
Grid1Dint(int) - Constructor for class HAL.GridsAndAgents.Grid1Dint
creates a new Grid1Dint of length xDim without wraparound
Grid1Dint(int, boolean) - Constructor for class HAL.GridsAndAgents.Grid1Dint
creates a new Grid1Dint of length xDim with optional wraparound
Grid1Dlong - Class in HAL.GridsAndAgents
a 1D Grid of longs
Grid1Dlong(int) - Constructor for class HAL.GridsAndAgents.Grid1Dlong
creates a new Grid1Dlong of length xDim without wraparound
Grid1Dlong(int, boolean) - Constructor for class HAL.GridsAndAgents.Grid1Dlong
creates a new Grid1Dlong of length xDim with optional wraparound
Grid1Dobject<T> - Class in HAL.GridsAndAgents
a 1D Grid of objects
Grid1Dobject(int) - Constructor for class HAL.GridsAndAgents.Grid1Dobject
creates a new Grid1Dobject of length xDim wtihout wraparound
Grid1Dobject(int, boolean) - Constructor for class HAL.GridsAndAgents.Grid1Dobject
creates a new Grid1Ddouble of length xDim with optional wraparound
Grid2D - Interface in HAL.Interfaces
holds functions that all 2D Grids share
Grid2Ddouble - Class in HAL.GridsAndAgents
a 2D Grid of doubles
Grid2Ddouble(int, int) - Constructor for class HAL.GridsAndAgents.Grid2Ddouble
creates a new Grid2Ddouble of length xDim without wraparound
Grid2Ddouble(int, int, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid2Ddouble
creates a new Grid2Ddouble of length xDim with optional wraparound
Grid2Dint - Class in HAL.GridsAndAgents
a 2D Grid of ints
Grid2Dint(int, int) - Constructor for class HAL.GridsAndAgents.Grid2Dint
creates a new Grid2Dint of dimensions xDim by yDim without wraparound
Grid2Dint(int, int, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid2Dint
creates a new Grid2Dint of dimensions xDim by yDim with optional wraparound
Grid2Dlong - Class in HAL.GridsAndAgents
a 2D Grid of longs
Grid2Dlong(int, int) - Constructor for class HAL.GridsAndAgents.Grid2Dlong
creates a new Grid2Dlong of dimensions xDim by yDim without wraparound
Grid2Dlong(int, int, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid2Dlong
creates a new Grid2Dlong of dimensions xDim by yDim with optional wraparound
Grid2Dobject<T> - Class in HAL.GridsAndAgents
a 2D Grid of objects
Grid2Dobject(int, int) - Constructor for class HAL.GridsAndAgents.Grid2Dobject
creates a new Grid2Dobject of dimensions xDim by yDim without wraparound
Grid2Dobject(int, int, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid2Dobject
creates a new Grid2Dobject of dimensions xDim by yDim with optional wraparound
Grid3D - Interface in HAL.Interfaces
holds functions that all 3D Grids share
Grid3Ddouble - Class in HAL.GridsAndAgents
a 3D Grid of doubles
Grid3Ddouble(int, int, int) - Constructor for class HAL.GridsAndAgents.Grid3Ddouble
creates a new Grid3Ddouble of dimensions xDim by yDim by zDim with optional wraparound
Grid3Ddouble(int, int, int, boolean, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid3Ddouble
creates a new Grid3Ddouble of dimensions xDim by yDim by zDim without wraparound
Grid3Dint - Class in HAL.GridsAndAgents
a 3D Grid of ints
Grid3Dint(int, int, int) - Constructor for class HAL.GridsAndAgents.Grid3Dint
creates a new Grid3Dint of dimensions xDim by yDim by zDim with optional wraparound
Grid3Dint(int, int, int, boolean, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid3Dint
creates a new Grid3Dint of dimensions xDim by yDim by zDim without wraparound
Grid3Dlong - Class in HAL.GridsAndAgents
a 3D Grid of longs
Grid3Dlong(int, int, int) - Constructor for class HAL.GridsAndAgents.Grid3Dlong
creates a new Grid3Dlong of dimensions xDim by yDim by zDim with optional wraparound
Grid3Dlong(int, int, int, boolean, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid3Dlong
creates a new Grid3Dlong of dimensions xDim by yDim by zDim without wraparound
Grid3Dobject<T> - Class in HAL.GridsAndAgents
a 3D Grid of objects
Grid3Dobject(int, int, int) - Constructor for class HAL.GridsAndAgents.Grid3Dobject
creates a new Grid3Dojbect of dimensions xDim by yDim by zDim with optional wraparound
Grid3Dobject(int, int, int, boolean, boolean, boolean) - Constructor for class HAL.GridsAndAgents.Grid3Dobject
creates a new Grid3Dobject of dimensions xDim by yDim by zDim without wraparound
GridDiff2MulitThreadFunction(int, int, int) - Method in interface HAL.Interfaces.GridDiff2MultiThreadFunction
 
GridDiff2MultiThreadFunction - Interface in HAL.Interfaces
Created by rafael on 8/26/17.
GridWindow - Class in HAL.Gui
The GridWindow is a stand-alone window with a UIGrid embedded, it allows drawwing to it by setting pixels
GridWindow(int, int) - Constructor for class HAL.Gui.GridWindow
the below constructors are variants of the above constructor with default values for some of the arguments
GridWindow(int, int, boolean) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(int, int, int) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(int, int, int, boolean) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(int, int, int, boolean, GuiCloseAction) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(int, int, int, boolean, GuiCloseAction, boolean) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(String, int, int) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(String, int, int, boolean) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(String, int, int, int) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(String, int, int, int, boolean) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(String, int, int, int, boolean, GuiCloseAction) - Constructor for class HAL.Gui.GridWindow
 
GridWindow(String, int, int, int, boolean, GuiCloseAction, boolean) - Constructor for class HAL.Gui.GridWindow
Creates a new GridWindow
GuiCloseAction - Interface in HAL.Interfaces
Created by bravorr on 1/30/17.
GuiComp - Interface in HAL.Interfaces
Created by rafael on 1/29/17.
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