| ADIequations |
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| Agent0D<T extends AgentGrid0D> |
An agent type without any spatial representation
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| Agent1DBase<T extends AgentGrid1D> |
Agent1DBase functions are shared amongst all 1D agent types
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| Agent2DBase<T extends AgentGrid2D> |
Agent2DBase functions are shared amongst all 2D agent types
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| Agent3DBase<T extends AgentGrid3D> |
Agent3DBase functions are shared amongst all 3D agent types
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| AgentAction<T extends AgentBase> |
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| AgentBase<T> |
AgentBase functions are shared amongst all agent types
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| AgentBaseSpatial<T> |
AgentBaseSpatial functions are shared amongst all spatial agent types
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| AgentGrid0D<T extends Agent0D> |
AgentGrid0Ds can only hold Agent0Ds
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| AgentGrid1D<T extends AgentBaseSpatial> |
AgentGrid1Ds can hold any type of 1D agent
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| AgentGrid2D<T extends AgentBaseSpatial> |
AgentGrid2Ds can hold any type of 2D Agent
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| AgentGrid3D<T extends AgentBaseSpatial> |
AgentGrid3Ds can hold any type of 3D Agent
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| AgentList<T> |
AgentLists can hold any type of agent
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| AgentPT1D<T extends AgentGrid1D> |
extend the AgentPT2D class if you want agents that exist on a 2D continuous lattice
with the possibility of stacking multiple agents on the same typeGrid square
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| AgentPT2D<T extends AgentGrid2D> |
extend the AgentPT2D class if you want agents that exist on a 2D continuous lattice
with the possibility of stacking multiple agents on the same typeGrid square
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| AgentPT3D<T extends AgentGrid3D> |
extend the AgentPT3D class if you want agents that exist on a 3D continuous lattice
with the possibility of stacking multiple agents on the same typeGrid square
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| AgentRadDispToAction1D<T extends AgentBase> |
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| AgentRadDispToAction2D<T extends AgentBase> |
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| AgentRadDispToAction3D<T extends AgentBase> |
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| AgentSQ1D<T extends AgentGrid1D> |
extend the AgentSQ2D class if you want agents that exist on a 2D discrete lattice with the possibility of stacking
multiple agents on the same typeGrid square
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| AgentSQ1Dunstackable<T extends AgentGrid1D> |
extend the AgentSQ2Dunstackable class if you want agents that exist on a 2D discrete lattice
without the possibility of stacking multiple agents on the same typeGrid square
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| AgentSQ2D<T extends AgentGrid2D> |
extend the AgentSQ2D class if you want agents that exist on a 2D discrete lattice
with the possibility of stacking multiple agents on the same typeGrid square
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| AgentSQ2Dunstackable<T extends AgentGrid2D> |
extend the AgentSQ2Dunstackable class if you want agents that exist on a 2D discrete lattice
without the possibility of stacking multiple agents on the same typeGrid square
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| AgentSQ3D<T extends AgentGrid3D> |
extend the AgentSQ3D class if you want agents that exist on a 3D discrete lattice
with the possibility of stacking multiple agents on the same typeGrid square
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| AgentSQ3Dunstackable<T extends AgentGrid3D> |
extend the AgentSQ3D class if you want agents that exist on a 3D discrete lattice
with the possibility of stacking multiple agents on the same typeGrid square
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| AgentStepFunction<T> |
Created by rafael on 8/26/17.
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| AgentToBool<T extends AgentBase> |
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| AgentToColorInt<T> |
Created by bravorr on 7/18/17.
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| AgentToDouble<T extends AgentBase> |
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| AgentToInts<T> |
Created by rafael on 9/7/17.
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| AgentToString<T extends AgentBase> |
Created by rafael on 8/19/17.
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| Binomial |
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| BoolSet |
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| ButtonAction |
Created by bravorr on 1/30/17.
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| ColorIntGenerator |
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| Coords1DBool |
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| Coords1DDouble |
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| Coords1DInt |
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| Coords2DAction |
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| Coords2DBool |
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| Coords2DColor |
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| Coords2DDouble |
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| Coords2DInt |
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| Coords2DSetArray |
Created by Rafael on 10/20/2017.
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| Coords3DAction |
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| Coords3DBool |
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| Coords3DDouble |
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| Coords3DInt |
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| Coords3DSetArray |
Created by Rafael on 10/20/2017.
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| Coords6DDouble |
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| CustomSerialization |
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| Derivative |
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| DistToForceMap |
Created by bravorr on 5/31/17.
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| DoubleArrayToDouble |
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| DoubleArrayToVoid |
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| Doubles2DDouble |
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| Doubles3DDouble |
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| DoublesToColor |
Created by Rafael on 10/13/2017.
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| DoubleToAction |
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| DoubleToColor |
Created by Rafael on 10/13/2017.
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| DoubleToDouble |
Created by Rafael on 9/18/2017.
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| DoubleToDoubles |
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| DoubleToInt |
Created by Rafael on 7/24/2017.
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| DrawFunction |
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| DrawWell<T> |
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| FileIO |
used to read from and write to files, can open a file in "read" "write", "readBinary" and "writeBinary" modes.
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| GAMutantToString<T> |
Created by rafael on 4/8/17.
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| GAMutationFunction<T> |
Created by rafael on 4/8/17.
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| GAScoreFunction<T> |
Created by rafael on 4/8/17.
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| Gaussian |
Created by Rafael on 11/16/2017.
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| GenDouble |
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| Genome<T extends Genome> |
the genome class is useful for keeping track of shared genetic information and phylogenies.
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| GenomeFn<T extends Genome> |
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| GenomeLineageFn<T extends Genome> |
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| GetGenomeAttrs<T extends Genome> |
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| GetMutationInfo<T> |
Created by Rafael on 8/3/2017.
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| GifMaker |
the GifMaker is used to create gif files by compiling UIGrid states
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| Grid1D |
holds functions that all 1D Grids share
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| Grid1Ddouble |
a 1D Grid of doubles
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| Grid1Dint |
a 1D Grid of ints
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| Grid1Dlong |
a 1D Grid of longs
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| Grid1Dobject<T> |
a 1D Grid of objects
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| Grid2D |
holds functions that all 2D Grids share
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| Grid2Ddouble |
a 2D Grid of doubles
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| Grid2Dint |
a 2D Grid of ints
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| Grid2Dlong |
a 2D Grid of longs
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| Grid2Dobject<T> |
a 2D Grid of objects
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| Grid3D |
holds functions that all 3D Grids share
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| Grid3Ddouble |
a 3D Grid of doubles
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| Grid3Dint |
a 3D Grid of ints
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| Grid3Dlong |
a 3D Grid of longs
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| Grid3Dobject<T> |
a 3D Grid of objects
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| GridDiff2MultiThreadFunction |
Created by rafael on 8/26/17.
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| GridWindow |
The GridWindow is a stand-alone window with a UIGrid embedded, it allows drawwing to it by setting pixels
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| GuiCloseAction |
Created by bravorr on 1/30/17.
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| GuiComp |
Created by rafael on 1/29/17.
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| IndexAction |
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| IndexBool |
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| IndexCoords2DAction |
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| IndexCoords2DBool |
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| IndexCoords2DDouble |
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| IndexCoords3DAction |
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| IndexCoords3DBool |
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| IndexIntAction |
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| IndexIntToAction |
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| IndexLongAction |
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| IntDoubleToVoid |
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| InteractiveModel |
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| IntToBool |
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| IntToDouble |
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| IntToInt |
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| IsEntry1Before2 |
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| KeyRecorder |
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| KeyResponse |
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| LocalIndexAction |
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| MenuItem |
Created by rafael on 11/25/16.
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| ModuleSetManager<baseModule> |
the ModuleSetManager class is used to store and use module objects.
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| MultinomialCalc |
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| MultinomialCalcLong |
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| MultiWellExperiment<T> |
MultiWellExperiments allow the user to visualize many models in a single GridWindow, and can be easily multithreaded for faster execution
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| OdeSolution |
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| ODESolver |
use this class to solve any ODE system.
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| OpenGL2DWindow |
Created by rafael on 5/28/17.
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| OpenGL3DWindow |
Created by rafael on 5/28/17.
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| OverlapForceResponse2D<T extends SphericalAgent2D> |
Created by philipaxelrod on 7/11/17.
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| OverlapForceResponse3D<T extends SphericalAgent3D> |
Created by philipaxelrod on 7/11/17.
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| ParallelFunction |
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| ParamSet |
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
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| ParamSetChangeAction |
Created by Rafael on 10/26/2017.
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| PDEequations |
Created by Rafael on 10/14/2017.
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| PDEGrid1D |
a 1D
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| PDEGrid2D |
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.
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| PDEGrid3D |
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.
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| PlotLine |
this class is used to add segments one at a time to a PlotLine on a UIPlot/PlotWindow
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| PlotWindow |
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| Point1DBool |
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| Point2DBool |
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| Point3DBool |
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| PopulationGrid1D |
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| PopulationGrid1DLong |
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| PopulationGrid2D |
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| PopulationGrid2DLong |
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| PopulationGrid3D |
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| PopulationGrid3DLong |
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| PopulationGridBase |
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| PopulationGridLongBase |
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| PopulationGridPDEequations |
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| Rand |
contains functions for random value generation and distribution sampling.
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| RNG |
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| SerializableModel |
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| Sortable |
allows for the QuickSort function to be used to sort the object
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| SphericalAgent2D<A extends SphericalAgent2D,G extends AgentGrid2D<A>> |
Spherical cow model of 2D cells
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| SphericalAgent3D<A extends SphericalAgent3D,G extends AgentGrid3D<A>> |
Spherical cow model of 3D cells
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| SplittableRN |
A generator of uniform pseudorandom values applicable for use in
(among other contexts) isolated parallel computations that may
generate subtasks.
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| StepWell<T> |
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| SwapEntries |
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| SweepRun<T> |
Created by rafael on 4/15/17.
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| TdmaSolver |
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| TickTimer |
class used to impose a frame rate on the running of a model
call TickPause every timestep to impose a framerate
usually used within a window of some kind, but can also be used by itself
Created by rafael on 2/16/17.
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| TreatableTumor |
Created by Rafael on 9/26/2017.
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| UIBoolInput |
a menu item that can be toggled to true or false
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| UIButton |
a gui item that when clicked executes the myAction function
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| UIComboBoxInput |
a menu item that facilitates choosing from a set of options
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| UIDoubleInput |
a menu item that takes double input
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| UIFileChooserInput |
a gui item that allows the user to select an existing file, or create a new file
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| UIGrid |
a gui item that is used to efficiently visualize a grid in 2 dimensions
uses an array of pixels whose color values are individually set
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| UIIntInput |
a menu item that takes int input
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| UILabel |
a gui item that presents text
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| UIPlot |
the UIPlot gui component is similar to the UIGrid but is specifically for generating plots.
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| UIStringInput |
a menu item that takes string input
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| UIWindow |
a JFrame wrapper that holds menu and gui items
the window that the other gui items sit in
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| Util |
A collection of helpful static utility functions
recommended import: import static Util.*
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| VarSet |
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| VarSetManager |
the VarSetManager class maintains a count of parameters that are requested for an agent class that implements the
VarSet interface.
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| VoidFunction |
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