Class Simulation

java.lang.Object
  Simulation

public class Simulation

extends java.lang.Object

Simulation holds all Assembly information and actually runs the queue-based discrete-assembly algorightm

Constructor Summary

Simulation(Solution s, java.util.Vector initial_Assemblies, double ct, java.util.HashMap bondTimes, java.util.HashMap confTimes, java.util.HashMap bindingPartner)
Creates a Simulation with specified Solution s, Vector of Assemblies a, double current time, and HashMap of bonding times (detailed in private variable definitions), and HashMap of conformation changing times (detailed in private variable definitions)

Method Summary

java.util.Vector	getAssemblies() todo future never used Returns a Vector of all the Assemblies in this Simulation
double	getRand() Returns a random double within [0 , 1)
int	numberOfSize(int size) gets the number of assemblies in the simulation of a certain size
void	printQ()
void	run() Runs this simulation by calling step() repeatedly until a certain number of events have been processed.
SimulatorGraphic	startGraphic() Creates a SimulatorGraphic based on this Simulation and returns it.
void	step()
java.lang.String	toString() Returns a String version of this Simulation
void	updateMonomerCount() Updates the JLabel showing the number of monomers

Methods inherited from class java.lang.Object

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

Constructor Detail

Simulation

public Simulation(Solution s,
                  java.util.Vector initial_Assemblies,
                  double ct,
                  java.util.HashMap bondTimes,
                  java.util.HashMap confTimes,
                  java.util.HashMap bindingPartner)

Creates a Simulation with specified Solution s, Vector of Assemblies a, double current time, and HashMap of bonding times (detailed in private variable definitions), and HashMap of conformation changing times (detailed in private variable definitions)

Parameters:

s - Solution the properities of environment in which the simulation occurs

initial_Assemblies - Vector of Assemblies to be assembled

ct - double current time

bondTimes - HashMap of HashMaps String bstNames | | | | | | | | | |-> double times[3]. (times[0]-->bindingTime, | | times[1]-->breakingTime, | | times[2]-->intraAssemblyBindingTime) | | | | |__| (Another HashMap, keys are also String bstNames)

confTimes - HashMap of HashMaps String confNames | | | | | | | | | |-> double times[1]. (times[0]-->confChangeTime) | | | | | | | | |__| (Another HashMap, keys are also String confNames)

bindingPartner - HashMap of BindingSite type and corresponding compatable BindingSite types

Method Detail

run

public void run()

Runs this simulation by calling step() repeatedly until a certain number of events have been processed. User can hardcode his number here and print the intermediate result to files

step

public void step()

getRand

public double getRand()

Returns a random double within [0 , 1)

Returns:

double

toString

public java.lang.String toString()

Returns a String version of this Simulation

Returns:

String

getAssemblies

public java.util.Vector getAssemblies()

todo future never used Returns a Vector of all the Assemblies in this Simulation

Returns:

Vector of Assemblies

startGraphic

public SimulatorGraphic startGraphic()

Creates a SimulatorGraphic based on this Simulation and returns it.

Returns:

SimulatorGraphic

printQ

public void printQ()

numberOfSize

public int numberOfSize(int size)

gets the number of assemblies in the simulation of a certain size

Parameters:

size - - int

Returns:

num - int

updateMonomerCount

public void updateMonomerCount()

Updates the JLabel showing the number of monomers