org.ginsim.service.tool.avatar.simulation

Class AvatarSimulation

java.lang.Object

org.ginsim.service.tool.avatar.simulation.Simulation

org.ginsim.service.tool.avatar.simulation.AvatarSimulation

Direct Known Subclasses:

AvatarMDDSimulation

public class AvatarSimulation
extends Simulation

Avatar simulation for the discovery of point and complex attractors.
Class providing all the functionalities to explore STGs, extend and rewire cycles.

Version:

1.0

Author:

Rui Henriques, Pedro T. Monteiro, Nuno Mendes

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AvatarSimulation.AvatarStrategy enum specifying the different behavioral strategies of Avatar

Field Summary

Fields

Modifier and Type	Field and Description
int	approxDepth maximum depth for the approximate rewiring strategy
protected org.colomoto.biolqm.tool.simulation.multiplesuccessor.AsynchronousUpdater	exhaustiveUpdater
boolean	keepOracle whether oracles should be kept between iterations
boolean	keepTransients whether transient cycles should be kept between iterations
int	maxPSize maximum number of visited transitions to stop expansion approximated by #states within the growing cycle times #exits
int	maxRewiringSize maximum number of states within a cycle to be rewired
int	maxSteps maximum depth
int	minCSize minimum cycle size for rewiring
int	minTransientSize minimum size of a transient cycles to be stored
int	runs number of iterations
int	smallStateSpace size of small state spaces for the inflationary mode
AvatarSimulation.AvatarStrategy	strategy Avatar rewiring strategy
int	tauInit cycle expansion rate

Fields inherited from class org.ginsim.service.tool.avatar.simulation.Simulation

chart, exit, isGUI, memory, model, oracle, outputDir, quiet, resultLog, t1

Constructor Summary

Constructors

Constructor and Description
AvatarSimulation() Instantiates an Avatar simulation

Method Summary

Modifier and Type	Method and Description
void	addModel(StatefulLogicalModel _model)
StateSet	calculateComplexAttractor(StateSet Ct, List<StateSet> temporaryTransients, PriorityQueue<StateSet> savedTransients) Calculates a complex attractor based on the knowledge of previous incarnations
void	dynamicUpdateValues() Updates a simulation with parameterizations dynamically fixed based on the properties of the input model
void	extendCycle(State v, StateSet cycle, StateSet exits, StateSet newstates, int i, int tau, Map<String,Integer> time, int originalTime) Method for extending cycles before rewiring
String	getName()
String	parametersToString() Prints the current parameters
void	rewriteGraph(StateSet cycle, StateSet out, FinalPaths pi) Method for rewiring a cycle
Result	runSim() Performs the simulation

Methods inherited from class org.ginsim.service.tool.avatar.simulation.Simulation

exit, output, publish, run, runSimulation, saveOutput, setComponents

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

tauInit

public int tauInit

cycle expansion rate

runs

public int runs

number of iterations

maxSteps

public int maxSteps

maximum depth

maxPSize

public int maxPSize

maximum number of visited transitions to stop expansion approximated by #states within the growing cycle times #exits

maxRewiringSize

public int maxRewiringSize

maximum number of states within a cycle to be rewired

minCSize

public int minCSize

minimum cycle size for rewiring

smallStateSpace

public int smallStateSpace

size of small state spaces for the inflationary mode

minTransientSize

public int minTransientSize

minimum size of a transient cycles to be stored

keepTransients

public boolean keepTransients

whether transient cycles should be kept between iterations

keepOracle

public boolean keepOracle

whether oracles should be kept between iterations

strategy

public AvatarSimulation.AvatarStrategy strategy

Avatar rewiring strategy

approxDepth

public int approxDepth

maximum depth for the approximate rewiring strategy

exhaustiveUpdater

protected org.colomoto.biolqm.tool.simulation.multiplesuccessor.AsynchronousUpdater exhaustiveUpdater

Constructor Detail

AvatarSimulation

public AvatarSimulation()

Instantiates an Avatar simulation

Method Detail

addModel

public void addModel(StatefulLogicalModel _model)

Overrides:

addModel in class Simulation

runSim

public Result runSim()
              throws Exception

Description copied from class: Simulation

Performs the simulation

Specified by:

runSim in class Simulation

Returns:

the discovered attractors, their reachability, and remaining contextual information

Throws:

Exception

calculateComplexAttractor

public StateSet calculateComplexAttractor(StateSet Ct,
                                          List<StateSet> temporaryTransients,
                                          PriorityQueue<StateSet> savedTransients)

Calculates a complex attractor based on the knowledge of previous incarnations

Parameters:

savedTransients -

C - terminal cycles from all incarnations

t - the current time

Returns:

the revised complex attractor

rewriteGraph

public void rewriteGraph(StateSet cycle,
                         StateSet out,
                         FinalPaths pi)
                  throws Exception

Method for rewiring a cycle

Parameters:

cycle - the cycle (state-set) to be rewired

out - the exit states

pi - the transitions between cycle and exit states whose probability is to be adjusted

Throws:

Exception

extendCycle

public void extendCycle(State v,
                        StateSet cycle,
                        StateSet exits,
                        StateSet newstates,
                        int i,
                        int tau,
                        Map<String,Integer> time,
                        int originalTime)

Method for extending cycles before rewiring

Parameters:

v - the state being expanded (null at the start)

cycle - the state-set representing the initial cycle

result - the extended cycle

i - the current time

tau - the expansion rate

time - structure maintaining the time/depth of the included states

originalTime - the original time

dynamicUpdateValues

public void dynamicUpdateValues()

Description copied from class: Simulation

Updates a simulation with parameterizations dynamically fixed based on the properties of the input model

Specified by:

dynamicUpdateValues in class Simulation

parametersToString

public String parametersToString()

Description copied from class: Simulation

Prints the current parameters

Specified by:

parametersToString in class Simulation

Returns:

a String describing the parameters

getName

public String getName()

Specified by:

getName in class Simulation