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P
 panel  Variable in class HAL.Gui.UIWindow
 ParallelFunction  Interface in HAL.Interfaces
 ParamSet  Class in HAL.Tools.Internal

the ParamSet class is used to keep track of all of the items in a menu it can be queried to get the current values of the menu values and labels can also be loaded as arrays of strings, allowing for the menuset to be used without a gui
 ParamSet()  Constructor for class HAL.Tools.Internal.ParamSet
 ParamSet(String[], String[])  Constructor for class HAL.Tools.Internal.ParamSet
 ParamSetChangeAction  Interface in HAL.Interfaces

Created by Rafael on 10/26/2017.
 PDEequations  Class in HAL.Tools.Internal

Created by Rafael on 10/14/2017.
 PDEequations()  Constructor for class HAL.Tools.Internal.PDEequations
 PDEGrid1D  Class in HAL.GridsAndAgents

a 1D
 PDEGrid1D(int)  Constructor for class HAL.GridsAndAgents.PDEGrid1D
 PDEGrid1D(int, boolean)  Constructor for class HAL.GridsAndAgents.PDEGrid1D
 PDEGrid2D  Class in HAL.GridsAndAgents

PDEGrid2D class facilitates 2D diffusion with two arrays of doubles called fields the intended usage is that during a diffusion tick, the current values will be read, and the prev values will be written to after updates, Update is called to set the prev field as the current field.
 PDEGrid2D(int, int)  Constructor for class HAL.GridsAndAgents.PDEGrid2D
 PDEGrid2D(int, int, boolean, boolean)  Constructor for class HAL.GridsAndAgents.PDEGrid2D
 PDEGrid3D  Class in HAL.GridsAndAgents

PDEGrid3D class facilitates 3D diffusion with two arrays of doubles called fields the intended usage is that during a diffusion tick, the current values will be read, and the next values will be written to after updates, Update is called to set the delta field as the current field.
 PDEGrid3D(int, int, int)  Constructor for class HAL.GridsAndAgents.PDEGrid3D
 PDEGrid3D(int, int, int, boolean, boolean, boolean)  Constructor for class HAL.GridsAndAgents.PDEGrid3D
 PhToProtons(double)  Static method in class HAL.Util

converts pH to proton concentration
 PhylogenyPop()  Method in class HAL.Tools.PhylogenyTracker.Genome

returns the total population of all living members of the phylogeny
 PlanToHistory(int)  Method in class HAL.Tools.InteractiveModel.InteractiveModel
 PlotLine  Class in HAL.Gui

this class is used to add segments one at a time to a PlotLine on a UIPlot/PlotWindow
 PlotLine(UIPlot, int)  Constructor for class HAL.Gui.PlotLine

establishes the UIPlot that will contain the PlotLine, and the color of the segment lines
 PlotLine(double[], double[], int)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs from the xs and ys array with the provided color
 PlotLine(double[], double[], int, double)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs from the xs and ys array with the provided color.
 PlotLine(double[], double[], int, int, int)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs with the provided color.
 PlotLine(double[], double[], int, int, int, double)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs with the provided color.
 PlotLine(double[], double[], int, int, int, double, double)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the x,y pairs with the provided color.
 PlotLine(double[], int)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...
 PlotLine(double[], int, double)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...
 PlotLine(double[], int, int, int)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...
 PlotLine(double[], int, int, int, double)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...
 PlotLine(double[], int, int, int, double, double)  Method in class HAL.Gui.UIGrid

plots a line, connecting all pixels between the points defined by the list of x,y,x,y...
 PlotSegment(double, double, double, double, int)  Method in class HAL.Gui.UIGrid

plots a line segment, connecting all pixels between the points defined by (x1,y1) and (x2,y2) with the provided color.
 PlotSegment(double, double, double, double, int, double)  Method in class HAL.Gui.UIGrid

plots a line segment, connecting all pixels between the points defined by (x1,y1) and (x2,y2) with the provided color.
 PlotSegment(double, double, double, double, int, double, double)  Method in class HAL.Gui.UIGrid

plots a line segment, connecting all pixels between the points defined by (x1,y1) and (x2,y2) with the provided color.
 PlotWindow  Class in HAL.Gui
 PlotWindow(int, int)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, double, double, double, double)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, double, double, double, double, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int, boolean, GuiCloseAction)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int, boolean, GuiCloseAction, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int, double, double, double, double)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int, double, double, double, double, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int, double, double, double, double, boolean, GuiCloseAction)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(int, int, int, double, double, double, double, boolean, GuiCloseAction, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, double, double, double, double)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, double, double, double, double, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, int)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, int, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, int, boolean, GuiCloseAction)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, int, boolean, GuiCloseAction, boolean)  Constructor for class HAL.Gui.PlotWindow

the PlotWindow object component is similar to the GridWindow object but specifically for generating plots.
 PlotWindow(String, int, int, int, double, double, double, double)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, int, double, double, double, double, boolean)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, int, double, double, double, double, boolean, GuiCloseAction)  Constructor for class HAL.Gui.PlotWindow
 PlotWindow(String, int, int, int, double, double, double, double, boolean, GuiCloseAction, boolean)  Constructor for class HAL.Gui.PlotWindow
 Point1DBool  Interface in HAL.Interfaces
 Point2DBool  Interface in HAL.Interfaces
 Point3DBool  Interface in HAL.Interfaces
 PoissonProb(int, double)  Static method in class HAL.Util

Samples a Poisson distribution
 Pop()  Method in class HAL.GridsAndAgents.AgentGrid1D

returns the number of agents that are alive in the grid
 Pop()  Method in class HAL.GridsAndAgents.AgentGrid2D

returns the number of agents that are alive in the grid
 Pop()  Method in class HAL.GridsAndAgents.AgentGrid3D

returns the number of agents that are alive in the grid
 Pop()  Method in class HAL.GridsAndAgents.PopulationGridBase
 Pop()  Method in class HAL.GridsAndAgents.PopulationGridLongBase
 Pop()  Method in class HAL.Tools.PhylogenyTracker.Genome

returns the current population size that shares this genome
 PopAt(int)  Method in class HAL.GridsAndAgents.AgentGrid1D

gets the population at a specific location
 PopAt(int)  Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location
 PopAt(int)  Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location
 PopAt(int, int)  Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location
 PopAt(int, int, int)  Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location
 PopAt(int, int, int, AgentToBool)  Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true
 PopAt(int, int, AgentToBool)  Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true
 PopAt(int, AgentToBool)  Method in class HAL.GridsAndAgents.AgentGrid1D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true
 PopAt(int, AgentToBool)  Method in class HAL.GridsAndAgents.AgentGrid2D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true
 PopAt(int, AgentToBool)  Method in class HAL.GridsAndAgents.AgentGrid3D

gets the population at a specific location, subsetting to only those for which EvalAgent returns true
 popRemaining  Variable in class HAL.Tools.MultinomialCalc
 popRemaining  Variable in class HAL.Tools.MultinomialCalcLong
 PopulationGrid1D  Class in HAL.GridsAndAgents
 PopulationGrid1D(int)  Constructor for class HAL.GridsAndAgents.PopulationGrid1D
 PopulationGrid1D(int, boolean)  Constructor for class HAL.GridsAndAgents.PopulationGrid1D
 PopulationGrid1DLong  Class in HAL.GridsAndAgents
 PopulationGrid1DLong(int)  Constructor for class HAL.GridsAndAgents.PopulationGrid1DLong
 PopulationGrid1DLong(int, boolean)  Constructor for class HAL.GridsAndAgents.PopulationGrid1DLong
 PopulationGrid2D  Class in HAL.GridsAndAgents
 PopulationGrid2D(int, int)  Constructor for class HAL.GridsAndAgents.PopulationGrid2D
 PopulationGrid2D(int, int, boolean, boolean)  Constructor for class HAL.GridsAndAgents.PopulationGrid2D
 PopulationGrid2DLong  Class in HAL.GridsAndAgents
 PopulationGrid2DLong(int, int)  Constructor for class HAL.GridsAndAgents.PopulationGrid2DLong
 PopulationGrid2DLong(int, int, boolean, boolean)  Constructor for class HAL.GridsAndAgents.PopulationGrid2DLong
 PopulationGrid3D  Class in HAL.GridsAndAgents
 PopulationGrid3D(int, int, int)  Constructor for class HAL.GridsAndAgents.PopulationGrid3D
 PopulationGrid3D(int, int, int, boolean, boolean, boolean)  Constructor for class HAL.GridsAndAgents.PopulationGrid3D
 PopulationGrid3DLong  Class in HAL.GridsAndAgents
 PopulationGrid3DLong(int, int, int)  Constructor for class HAL.GridsAndAgents.PopulationGrid3DLong
 PopulationGrid3DLong(int, int, int, boolean, boolean, boolean)  Constructor for class HAL.GridsAndAgents.PopulationGrid3DLong
 PopulationGridBase  Class in HAL.GridsAndAgents
 PopulationGridBase(int)  Constructor for class HAL.GridsAndAgents.PopulationGridBase
 PopulationGridLongBase  Class in HAL.GridsAndAgents
 PopulationGridLongBase(int)  Constructor for class HAL.GridsAndAgents.PopulationGridLongBase
 PopulationGridPDEequations  Class in HAL.Tools.Internal
 PopulationGridPDEequations()  Constructor for class HAL.Tools.Internal.PopulationGridPDEequations
 probRemaining  Variable in class HAL.Tools.MultinomialCalc
 probRemaining  Variable in class HAL.Tools.MultinomialCalcLong
 ProbScale(double, double)  Static method in class HAL.Util

adjusts probability that an event will occur in 1 unit of time to the probability that the event will occur at least once over the duration
 ProtonsToPh(double)  Static method in class HAL.Util

converts proton concentration to pH
 PWD()  Static method in class HAL.Util

gets the current working directory as a string
 Py4jDoublesIn(byte[])  Static method in class HAL.Util
 Py4jDoublesIn(byte[], int)  Static method in class HAL.Util
 Py4jDoublesInAsArrayList(byte[], int)  Static method in class HAL.Util
 Py4jDoublesOut(double[])  Static method in class HAL.Util
 Py4jDoublesOut(double[][])  Static method in class HAL.Util
 Py4jDoublesOut(ArrayList<double[]>)  Static method in class HAL.Util
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