Uses of Class
org.primordion.xholon.base.Xholon

Packages that use Xholon
ec.gp   
org.primordion.cellontro.app   
org.primordion.cellontro.app.sbml   
org.primordion.cellontro.base   
org.primordion.ctrnn.app   
org.primordion.ctrnn.base   
org.primordion.dynsys.app   
org.primordion.ealontro.app   
org.primordion.ealontro.ec.app.antforaging   
org.primordion.ealontro.ec.app.cartcentering   
org.primordion.memcomp.app   
org.primordion.memcomp.base   
org.primordion.user.app   
org.primordion.user.app.Epo2   
org.primordion.user.app.WolfSheepGrass   
org.primordion.xholon.app   
org.primordion.xholon.base   
org.primordion.xholon.samples   
org.primordion.xholon.tutorials   
org.primordion.xholon.tutorials.rcs   
org.primordion.xholon.tutorials.StupidModel   
org.primordion.xholon.xmiapps   
org.primordion.xholon.xmiappsArgoUML   
org.primordion.xholon.xmiappsTc   
org.primordion.xholon.xmiappsTcSysML   
 

Uses of Xholon in ec.gp
 

Subclasses of Xholon in ec.gp
 class ec.gp.GPNode
          GPNode is a GPNodeParent which is the abstract superclass of all GP function nodes in trees.
 

Uses of Xholon in org.primordion.cellontro.app
 

Subclasses of Xholon in org.primordion.cellontro.app
 class AppCell
          Cell Model.
 class AppCellAutop
          Cell Model with Autopoiesis.
 class AppLife
          Life.
 class AppSbml
          SBML Application.
 class XhAbstractSbml
          SBML Application.
 class XhCell
          An instance of XhCell represents some biological entity, and exists as a node in a composite structure hierarchy tree.
 class XhCellAutop
          An instance of XhCellAutop represents some biological entity, and exists as a node in a composite structure hierarchy tree.
 class XhLife
          An instance of XhLife represents some biological entity, and exists as a node in a composite structure hierarchy tree.
 

Uses of Xholon in org.primordion.cellontro.app.sbml
 

Subclasses of Xholon in org.primordion.cellontro.app.sbml
 class XhBrusselator
          
 class XhCellModel
          
 class XhCircadianClock
          
 class XhDimericMWCstiff
          

Example of very stiff biochemical model

 class XhGlycolysis
          This model has the same values as RRT model.
 class XhGlycolysis_Test
          
 class XhGlycolysisTESTXML
          This model has the same values as RRT model.
 class XhGlycolysisTESTXML2
          
 class XhGlyHunThouBilayer
          
 class XhGlyHunThouInhibit
          
 class XhGlyMillion
          
 class XhGlyTenThou
          
 class XhYeastGlyPritchardKel
          
 

Uses of Xholon in org.primordion.cellontro.base
 

Subclasses of Xholon in org.primordion.cellontro.base
 class BioXholonClass
          BioXholonClass is an application specific extension of XholonClass.
 

Uses of Xholon in org.primordion.ctrnn.app
 

Subclasses of Xholon in org.primordion.ctrnn.app
 class AppAdapSysLab
          Continuous-Time Recurrent Neural Network (CTRNN).
 class AppCtrnn
          Continuous-Time Recurrent Neural Network (CTRNN).
 class XhAdapSysLab
          Continuous-Time Recurrent Neural Network (CTRNN).
 

Uses of Xholon in org.primordion.ctrnn.base
 

Subclasses of Xholon in org.primordion.ctrnn.base
 class XhAbstractCtrnn
          Continuous-Time Recurrent Neural Network (CTRNN).
 

Uses of Xholon in org.primordion.dynsys.app
 

Subclasses of Xholon in org.primordion.dynsys.app
 class AppFibonacci
          Dynamical Systems - Fibonacci.
 class AppGravity1
          Dynamical Systems - Gravity1.
 class AppInterest
          Dynamical Systems - Interest.
 class AppTrain
          Dynamical Systems - Train.
 class XhFibonacci
          Dynamical Systems - Fibonacci.
 class XhGravity1
          Dynamical Systems - Gravity1.
 class XhInterest
          Dynamical Systems - Interest.
 class XhTrain
          Dynamical Systems - Train.
 

Uses of Xholon in org.primordion.ealontro.app
 

Subclasses of Xholon in org.primordion.ealontro.app
 class AppAntForaging
          Ant System with Genetic Programming.
 class AppAntTrail
          Ant Trail.
 class AppCartCentering
          Cart Centering System with Genetic Programming.
 class AppEcj
          ECJ Application superclass.
 class AppEcjAntTrail
          ECJ Ant Trail.
 class AppEcjTutorial4
          ECJ Tutorial 4.
 class AppTutorial4
          ECJ Tutorial 4.
 class XhAntForaging
          Ant Foraging System WITHOUT Genetic Programming.
 class XhAntTrail
          ECJ Ant Trail.
 class XhCartCentering
          Cart Centering System with Genetic Programming.
 class XhEcjAntTrail
          ECJ Ant.
 class XhEcjTutorial4
          ECJ Tutorial 4.
 class XhTutorial4
          ECJ Tutorial 4.
 

Uses of Xholon in org.primordion.ealontro.ec.app.antforaging
 

Subclasses of Xholon in org.primordion.ealontro.ec.app.antforaging
 class AppEcjAntForaging
          ECJ Ant Foraging.
 class DropPheromone
           
 class IfCarryingFood
           
 class IfFoodHere
           
 class MoveRandom
           
 class MoveToAdjacentFoodElse
           
 class MoveToAdjacentPheromoneElse
           
 class MoveToNest
           
 class PickUp
           
 class XhEcjAntForaging
          Ant Foraging System WITH Genetic Programming.
 

Uses of Xholon in org.primordion.ealontro.ec.app.cartcentering
 

Subclasses of Xholon in org.primordion.ealontro.ec.app.cartcentering
 class ABS
           
 class Add
           
 class AppEcjCartCentering
          ECJ Cart Centering.
 class Divide
           
 class GT
           
 class Multiply
           
 class Subtract
           
 class Velocity
           
 class XhEcjCartCentering
          ECJ Cart Centering.
 class XPosition
           
 

Uses of Xholon in org.primordion.memcomp.app
 

Subclasses of Xholon in org.primordion.memcomp.app
 class AppBraneCalc
          Brane Calculus.
 class AppBraneCalc1
          Brane Calculus.
 class AppCoopPSys00ex0
          Membrane Computing.
 class AppCoopSys02ex32_1
          Membrane Computing.
 class AppCoopSys02ex343_1
          Membrane Computing.
 class AppCoopSys02ex343_2
          Membrane Computing.
 class AppFsm06ex1
          Membrane Computing.
 class AppMemComp
          Membrane Computing.
 class AppSymAnti02ex41
          Membrane Computing.
 class XhBraneCalc1
          Membrane Computing.
 class XhCoopPSys00ex0
          Membrane Computing.
 class XhCoopSys02ex32_1
          Membrane Computing.
 class XhCoopSys02ex343_1
          Membrane Computing.
 class XhCoopSys02ex343_2
          Membrane Computing.
 class XhFsm06ex1
          Membrane Computing.
 class XhSymAnti02ex41
          Membrane Computing.
 

Uses of Xholon in org.primordion.memcomp.base
 

Subclasses of Xholon in org.primordion.memcomp.base
 class XhAbstractBraneCalc
          Brane Calculus.
 class XhAbstractMemComp
          Membrane Computing.
 

Uses of Xholon in org.primordion.user.app
 

Subclasses of Xholon in org.primordion.user.app
 class AppBrenda
          Brenda application - Xholon Java
 class AppTurtleExample1
          TurtleExample1 application - Xholon Java
 class TurtleExample1
           
 class XhBrenda
          Brenda application - Xholon Java
 class XhTurtleExample1
          TurtleExample1 application - Xholon Java
 

Uses of Xholon in org.primordion.user.app.Epo2
 

Subclasses of Xholon in org.primordion.user.app.Epo2
 class Address
          Extended Purchase Order example.
 class AppEpo2
          Extended Purchase Order example.
 class Customer
          Extended Purchase Order example.
 class GlobalAddress
          Extended Purchase Order example.
 class Item
          Extended Purchase Order example.
 class PurchaseOrder
          Extended Purchase Order example.
 class USAddress
          Extended Purchase Order example.
 class XhEpo2
          Extended Purchase Order example.
 

Uses of Xholon in org.primordion.user.app.WolfSheepGrass
 

Subclasses of Xholon in org.primordion.user.app.WolfSheepGrass
 class AppWolfSheepGrass
          Wolf Sheep Grass.
 class Grass
          Wolf Sheep Grass.
 class WolfSheep
          Wolf Sheep Grass.
 class XhWolfSheepGrass
          Wolf Sheep Grass.
 

Uses of Xholon in org.primordion.xholon.app
 

Subclasses of Xholon in org.primordion.xholon.app
 class Application
          This is an abstract class from which all Xholon applications should subclass.
 

Uses of Xholon in org.primordion.xholon.base
 

Subclasses of Xholon in org.primordion.xholon.base
 class AbstractGrid
          AbstractGrid is an abstract class that your detailed behavior class (ex: XhGameOfLife) should extend if it contains a grid superimposed on some portion of the tree.
 class Activity
          An activity is a type of behavior.
 class Attribute
          An Attribute is a passive object.
static class Attribute.Attribute_boolean
           
static class Attribute.Attribute_byte
           
static class Attribute.Attribute_char
           
static class Attribute.Attribute_double
           
static class Attribute.Attribute_float
           
static class Attribute.Attribute_int
           
static class Attribute.Attribute_long
           
static class Attribute.Attribute_Object
           
static class Attribute.Attribute_short
           
static class Attribute.Attribute_String
           
 class ContainmentHierarchy
          A ContainmentHierarchy represents a hierarchy (tree) of Xholon nodes contained within other Xholon nodes.
 class Control
          Control for a Xholon application.
 class GridEntity
          GridEntity is a general instantiable subclass of AbstractGrid.
 class InheritanceHierarchy
          An InheritanceHierarchy represents a hierarchy (tree) of XholonClass nodes that inherit from other XholonClass nodes.
 class Interaction
          UML 2.0 Interaction.
 class Message
          ROOM/UML2 message.
 class ObservableStateMachineEntity
          Observable StateMachineEntity.
 class ObservableXholonWithPorts
          Observable Xholon with ports.
 class Patch
          A patch is an agent in the turtle mechanism.
 class PatchOwner
          PatchOwner owns a collection of Logo Patches.
 class Port
          Port is one type of concrete "port" in a xholon application.
 class PortXhym
          A Port Xhym interacts with an individual port, and with its XhymAgent.
 class Queue
          This is a generic Queue data structure that can be used to store references to any type of data.
 class StateMachineEntity
          A state machine entity is any XholonClass that has to do with state machines.
 class StateMachineXhym
          A State Machine Xhym interacts with an individual xholon StateMachineEntity, and with its XhymAgent.
 class TreeNodeFactoryDynamic
          TreeNodeFactoryDynamic manages concrete instances of TreeNode subclasses.
 class TreeNodeFactoryStatic
          TreeNodeFactoryStatic manages concrete instances of TreeNode subclasses.
 class Turtle
          A turtle is an agent in the turtle mechanism.
 class XholonClass
          A XholonClass is a concrete subclass of Xholon.
 class XholonTime
          Handle time in a Xholon application.
 class XholonWithPorts
          A Xholon with ports, so it can set up lateral connections with peers.
 class XholonXhym
          A Xholon Xhym interacts with an individual xholon, and with its XhymAgent.
 class XhymAgent
          A Xhym Agent exchanges information between local Xhym entities and some process that lives outside of Xholon.
 

Uses of Xholon in org.primordion.xholon.samples
 

Subclasses of Xholon in org.primordion.xholon.samples
 class App09SpatialGames
          This is the detailed behavior of a sample Xholon application.
 class App1dSimple
          1D Cellular Automaton.
 class AppCollisions
          Collisions.
 class AppCombo
          Combo Grid.
 class AppGameOfLife
          Conway's classic Game of Life.
 class AppGeneric
          A generic Xholon application, used for test purposes.
 class AppHex
          Hexagonal Grid.
 class AppPingPong
          Ping Pong.
 class AppTestFsmKW
          Test FSM.
 class AppTestFsmOrthog
          Test FSM.
 class AppTestFsmOrthogKW
          Test FSM.
 class Xh09SpatialGames
          This is the detailed behavior of a sample Xholon application.
 class Xh1dSimple
          1D Cellular Automaton.
 class XhCollisions
          Collisions.
 class XhCombo
          Combo Grid.
 class XhGameOfLife
          Conway's classic Game of Life.
 class XhGeneric
          Used for test purposes.
 class XhHex
          Hexagonal Grid.
 class XhPingPong
          Ping Pong.
 class XhTestFsmKW
          Test FSM.
 class XhTestFsmOrthog
          Test FSM.
 class XhTestFsmOrthogKW
          Test FSM.
 

Uses of Xholon in org.primordion.xholon.tutorials
 

Subclasses of Xholon in org.primordion.xholon.tutorials
 class AppHelloWorld
          Hello World.
 class AppHelloWorld_NoXml
          Hello World.
 class AppHelloWorld_TestTime
          Test XholonTime using Hello World.
 class AppHelloWorld_Vrml
          Hello World with VRML.
 class XhHelloWorld
          Hello World.
 class XhHelloWorld_NoXml
          Hello World.
 class XhHelloWorld_str
          Hello World.
 class XhHelloWorld_TestTime
          Hello World.
 

Uses of Xholon in org.primordion.xholon.tutorials.rcs
 

Subclasses of Xholon in org.primordion.xholon.tutorials.rcs
 class AppRcs1
          Regulated Catalyzing System - Glycogen Phosphorylase (GP) - Symbolic.
 class AppRcs2
          Regulated Catalyzing System, version 2.
 class XhRcs1
          Regulated Catalyzing System - Glycogen Phosphorylase (GP) - Symbolic.
 class XhRcs2
          Regulated Catalyzing System - Glycogen Phosphorylase (GP) - Molecular Machine (MM).
 class XhRcsTemp
          Regulated Catalyzing System Glycogen - Phosphorylase system.
 

Uses of Xholon in org.primordion.xholon.tutorials.StupidModel
 

Subclasses of Xholon in org.primordion.xholon.tutorials.StupidModel
 class AppStupidModel1
          StupidModel1 application - Xholon Java
 class AppStupidModel10
          StupidModel10 application - Xholon Java
 class AppStupidModel11
          StupidModel11 application - Xholon Java
 class AppStupidModel12
          StupidModel12 application - Xholon Java
 class AppStupidModel13
          StupidModel13 application - Xholon Java
 class AppStupidModel14
          StupidModel14 application - Xholon Java
 class AppStupidModel15
          StupidModel15 application - Xholon Java
 class AppStupidModel16
          StupidModel16 application - Xholon Java
 class AppStupidModel16nl
          StupidModel16nl application - Xholon Java
 class AppStupidModel2
          StupidModel2 application - Xholon Java
 class AppStupidModel3
          StupidModel3 application - Xholon Java
 class AppStupidModel4
          StupidModel4 application - Xholon Java
 class AppStupidModel5
          StupidModel5 application - Xholon Java
 class AppStupidModel5tg
          StupidModel5tg application - Xholon Java
 class AppStupidModel6
          StupidModel6 application - Xholon Java
 class AppStupidModel7
          StupidModel7 application - Xholon Java
 class AppStupidModel8
          StupidModel8 application - Xholon Java
 class AppStupidModel9
          StupidModel9 application - Xholon Java
 class BugStupidModel1
          StupidModel1 application - Xholon Java
 class BugStupidModel10
          StupidModel10 application - Xholon Java
 class BugStupidModel11
          StupidModel11 application - Xholon Java
 class BugStupidModel12
          StupidModel12 application - Xholon Java
 class BugStupidModel13
          StupidModel13 application - Xholon Java
 class BugStupidModel14
          StupidModel14 application - Xholon Java
 class BugStupidModel15
          StupidModel15 application - Xholon Java
 class BugStupidModel16
          StupidModel16 application - Xholon Java
 class BugStupidModel16nl
          StupidModel16nl application - Xholon Java
 class BugStupidModel2
          StupidModel2 application - Xholon Java
 class BugStupidModel3
          StupidModel3 application - Xholon Java
 class BugStupidModel4
          StupidModel4 application - Xholon Java
 class BugStupidModel5
          StupidModel5 application - Xholon Java
 class BugStupidModel5tg
          StupidModel5tg application - Xholon Java
 class BugStupidModel6
          StupidModel6 application - Xholon Java
 class BugStupidModel7
          StupidModel7 application - Xholon Java
 class BugStupidModel8
          StupidModel8 application - Xholon Java
 class BugStupidModel9
          StupidModel9 application - Xholon Java
 class HabitatCellStupidModel10
          StupidModel10 application - Xholon Java
 class HabitatCellStupidModel11
          StupidModel11 application - Xholon Java
 class HabitatCellStupidModel12
          StupidModel12 application - Xholon Java
 class HabitatCellStupidModel13
          StupidModel13 application - Xholon Java
 class HabitatCellStupidModel14
          StupidModel14 application - Xholon Java
 class HabitatCellStupidModel15
          StupidModel15 application - Xholon Java
 class HabitatCellStupidModel16
          StupidModel16 application - Xholon Java
 class HabitatCellStupidModel16nl
          StupidModel16nl application - Xholon Java
 class HabitatCellStupidModel3
          StupidModel3 application - Xholon Java
 class HabitatCellStupidModel4
          StupidModel4 application - Xholon Java
 class HabitatCellStupidModel5
          StupidModel5 application - Xholon Java
 class HabitatCellStupidModel5tg
          StupidModel5tg application - Xholon Java
 class HabitatCellStupidModel6
          StupidModel6 application - Xholon Java
 class HabitatCellStupidModel7
          StupidModel7 application - Xholon Java
 class HabitatCellStupidModel8
          StupidModel8 application - Xholon Java
 class HabitatCellStupidModel9
          StupidModel9 application - Xholon Java
 class QueueStupidModel10
          StupidModel10 queue - Xholon Java
 class QueueStupidModel11
          StupidModel11 queue - Xholon Java
 class QueueStupidModel12
          StupidModel12 queue - Xholon Java
 class QueueStupidModel13
          StupidModel13 queue - Xholon Java
 class QueueStupidModel14
          StupidModel14 queue - Xholon Java
 class QueueStupidModel15
          StupidModel15 queue - Xholon Java
 class QueueStupidModel16
          StupidModel16 queue - Xholon Java
 class QueueStupidModel16nl
          StupidModel16nl queue - Xholon Java
 class QueueStupidModel9
          StupidModel9 queue - Xholon Java
 class XhStupidModel1
          StupidModel1 application - Xholon Java
 class XhStupidModel10
          StupidModel10 application - Xholon Java
 class XhStupidModel11
          StupidModel11 application - Xholon Java
 class XhStupidModel12
          StupidModel12 application - Xholon Java
 class XhStupidModel13
          StupidModel13 application - Xholon Java
 class XhStupidModel14
          StupidModel14 application - Xholon Java
 class XhStupidModel15
          StupidModel15 application - Xholon Java
 class XhStupidModel16
          StupidModel16 application - Xholon Java
 class XhStupidModel16nl
          StupidModel16nl application - Xholon Java
 class XhStupidModel2
          StupidModel2 application - Xholon Java
 class XhStupidModel3
          StupidModel3 application - Xholon Java
 class XhStupidModel4
          StupidModel4 application - Xholon Java
 class XhStupidModel5
          StupidModel5 application - Xholon Java
 class XhStupidModel5tg
          StupidModel5tg application - Xholon Java
 class XhStupidModel6
          StupidModel6 application - Xholon Java
 class XhStupidModel7
          StupidModel7 application - Xholon Java
 class XhStupidModel8
          StupidModel8 application - Xholon Java
 class XhStupidModel9
          StupidModel9 application - Xholon Java
 

Uses of Xholon in org.primordion.xholon.xmiapps
 

Subclasses of Xholon in org.primordion.xholon.xmiapps
 class App__XholonTemplate__
          __XholonTemplate__ application - Xholon Java
 class AppElevator
          Elevator application - Xholon Java
 class AppElevator_ShowStates
          Elevator application - Xholon Java
 class AppFsm06ex1_Fsm
          Fsm06ex1_Fsm application - Xholon Java
 class AppHelloWorldTutorial_multiWorld
          HelloWorldTutorial_multiWorld application - Xholon Java
 class AppHelloWorldTutorial_plus
          HelloWorldTutorial_plus application - Xholon Java
 class AppHelloWorldTutorial_universe
          HelloWorldTutorial_universe application - Xholon Java
 class AppProvidedRequiredTest
          ProvidedRequiredTest application - Xholon Java
 class AppRcs_GP_FSM
          Rcs_GP_FSM application - Xholon Java
 class AppRcs_GP_FSM_Grid
          Rcs_GP_FSM_Grid application - Xholon Java
 class AppRcs_GP_MM
          Rcs_GP_MM application - Xholon Java
 class AppRcs_GP_MM_NoSymbols
          Rcs_GP_MM_NoSymbols application - Xholon Java
 class AppStopWatch
          StopWatch application - Xholon Java
 class AppStopWatch_Xhym
          StopWatch application - Xholon Java
 class AppTestFsm
          TestFsm application - Xholon Java
 class AppTestFsmForkJoin
          TestFsmForkJoin application - Xholon Java
 class AppTestFsmHistory
          TestFsmHistory application - Xholon Java
 class AppTestFsmJunction
          TestFsmJunction application - Xholon Java
 class AppTestFsmOrthogonal
          TestFsmOrthogonal application - Xholon Java
 class AppWatch
          Watch application - Inheritance Hierarchy
 class Xh__XholonTemplate__
          __XholonTemplate__ application - Xholon Java
 class XhElevator
          Elevator application - Xholon Java
 class XhFsm06ex1_Fsm
          Fsm06ex1_Fsm application - Xholon Java
 class XhHelloWorldTutorial_multiWorld
          HelloWorldTutorial_multiWorld application - Xholon Java
 class XhHelloWorldTutorial_plus
          HelloWorldTutorial_plus application - Xholon Java
 class XhHelloWorldTutorial_universe
          HelloWorldTutorial_universe application - Xholon Java
 class XhProvidedRequiredTest
          ProvidedRequiredTest application - Xholon Java
 class XhRcs_GP_FSM
          Rcs_GP_FSM application - Xholon Java
 class XhRcs_GP_FSM_Grid
          Rcs_GP_FSM_Grid application - Xholon Java
 class XhRcs_GP_MM
          Rcs_GP_MM application - Xholon Java
 class XhRcs_GP_MM_NoSymbols
          Rcs_GP_MM_NoSymbols application - Xholon Java
 class XhStopWatch
          StopWatch application - Xholon Java
 class XhStopWatch_Xhym
          StopWatch application - Xholon Java
 class XhTestFsm
          TestFsm application - Xholon Java
 class XhTestFsmForkJoin
          TestFsmForkJoin application - Xholon Java
 class XhTestFsmHistory
          TestFsmHistory application - Xholon Java
 class XhTestFsmJunction
          TestFsmJunction application - Xholon Java
 class XhTestFsmOrthogonal
          TestFsmOrthogonal application - Xholon Java
 class XhWatch
          Watch application - Xh Java class
 

Uses of Xholon in org.primordion.xholon.xmiappsArgoUML
 

Subclasses of Xholon in org.primordion.xholon.xmiappsArgoUML
 class AppHelloWorldTutorial
          HelloWorldTutorial application - Inheritance Hierarchy
 class XhHelloWorldTutorial
          HelloWorldTutorial application - Xh Java class
 

Uses of Xholon in org.primordion.xholon.xmiappsTc
 

Subclasses of Xholon in org.primordion.xholon.xmiappsTc
 class AppStateMachineOnly
          StateMachineOnly application - Xholon Java
 class XhStateMachineOnly
          StateMachineOnly application - Xholon Java
 

Uses of Xholon in org.primordion.xholon.xmiappsTcSysML
 

Subclasses of Xholon in org.primordion.xholon.xmiappsTcSysML
 class AppHelloWorldTutorialSysML
          HelloWorldTutorialSysML application - Xholon Java
 class XhHelloWorldTutorialSysML
          HelloWorldTutorialSysML application - Xholon Java