tenua.simulator
Class Mechanism

java.lang.Object
  tenua.simulator.AbstractDataGenerator
      tenua.simulator.Mechanism

All Implemented Interfaces:

java.lang.Runnable, DataGenerator

public class Mechanism
extends AbstractDataGenerator

a class that simulates a set of chemical reactions

Author:

Daniel Wachsstock

Nested Class Summary

Nested classes/interfaces inherited from interface tenua.simulator.DataGenerator

DataGenerator.Listener

Field Summary

static java.lang.String	CHEMICAL_RATES
static java.lang.String	OUTPUTS
static java.lang.String	PARAMETERS
static java.lang.String	RATE_CONSTANTS
static java.lang.String	SPECIES
static java.lang.String	TIME_CONSTANTS

Constructor Summary

Mechanism(java.util.Hashtable variableNames, Expression calculations, Expression derivativeCalculations, SymbolTable st, bsh.Interpreter interpreter)
Creates a new instance of Mechanism

Method Summary

DoubleBean	doubleBean(java.lang.String name) creates a #util.DoubleBean for a variable
java.lang.Object	eval(java.lang.String s) executes a string in the mechanism's interpreter.
java.lang.Object	get(java.lang.String name) returns the value of a variable in this mechanism or its script interpreter.
int	getCount() Get the number of times the simulation has been run with goSimulate() since creation.
double	getInitial(java.lang.String name) returns the initial value of a variable in this mechanism.
double	getLatest(java.lang.String name) returns the most recently determined value of a variable in this mechanism.
java.lang.Object	getMemento() returns the current state of the simulation.
java.lang.String	getMinimizer() returns the name of the current minimization algorithm.
java.lang.String	getSolver() returns the name of the current ODE solver.
void	goSimulate() actually runs the simulation; called by the interpreter
void	goVarying(int n, java.lang.String[] names) runs the simulation while varying a given list of variables, multiple times.
void	goVarying(java.lang.String[] names) runs the simulation while varying a given list of variables.
void	put(java.lang.String name, double d) assigns a value to a variable
void	put(java.lang.String name, java.lang.Object o) assigns a value to a variable
void	putInitial(java.lang.String name, double d) assigns a value to use for the initial value for a variable.
void	putLatest(java.lang.String name, double d) assigns a value to a variable.
void	renameOutput(int i, java.lang.String newName) Renames an output datum.
void	resetVariables() Resets all the variables' initial values to their default values.
void	setMinimizer(java.lang.String name) Set the minimization algorithm.
void	setSolver(java.lang.String name) set the ODE solver to use.
void	start(java.lang.Object memento) generates data by calling script() in the interpreter, which generally calls goSimulate().
java.util.List	variableNames(java.lang.String listName) returns a List of the names of all the variables defined of a given type.

Methods inherited from class tenua.simulator.AbstractDataGenerator

addListener, getNames, removeListener, run

Methods inherited from class java.lang.Object

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

Field Detail

TIME_CONSTANTS

public static final java.lang.String TIME_CONSTANTS

SPECIES

public static final java.lang.String SPECIES

RATE_CONSTANTS

public static final java.lang.String RATE_CONSTANTS

CHEMICAL_RATES

public static final java.lang.String CHEMICAL_RATES

PARAMETERS

public static final java.lang.String PARAMETERS

OUTPUTS

public static final java.lang.String OUTPUTS

Constructor Detail

Mechanism

public Mechanism(java.util.Hashtable variableNames,
                 Expression calculations,
                 Expression derivativeCalculations,
                 SymbolTable st,
                 bsh.Interpreter interpreter)

Creates a new instance of Mechanism

Method Detail

start

public void start(java.lang.Object memento)

generates data by calling script() in the interpreter, which generally calls goSimulate().

Specified by:

start in interface DataGenerator

Overrides:

start in class AbstractDataGenerator

Parameters:

memento - the VariableMemento to use. If null, ignored

goSimulate

public void goSimulate()
                throws java.lang.InterruptedException,
                       java.lang.NoSuchMethodException,
                       java.lang.InstantiationException,
                       java.lang.IllegalAccessException

actually runs the simulation; called by the interpreter

Throws:

java.lang.InterruptedException

java.lang.NoSuchMethodException

java.lang.InstantiationException

java.lang.IllegalAccessException

goVarying

public void goVarying(java.lang.String[] names)

runs the simulation while varying a given list of variables.

Parameters:

names - the array of variable names to vary On return, the initial variables will be set such that the variables named minimize the script function called fitFunction(), which should return a double.

goVarying

public void goVarying(int n,
                      java.lang.String[] names)
               throws bsh.EvalError

runs the simulation while varying a given list of variables, multiple times.

Parameters:

names - the array of variable names to vary On return, the initial variables will be set such that the variables named minimize the script function called fitFunction(), which should return a double. Also, a double array parameters is created in the interpreter such that parameters[i][j] is the value of the jth variable after the ith run. Also, double arrays mean, stddev and stddev1 are created, such than mean[j] is the mean of the jth variable in all the runs, stddev[j] is the standard deviation, and stddev1[j] is the standard deviation assuming that parameters[0] is the true value of the variables. This would be the case if the first run fit to the actual data and the other runs fit to simulated or selected data.

Throws:

bsh.EvalError

renameOutput

public void renameOutput(int i,
                         java.lang.String newName)

Renames an output datum.

Parameters:

i - the index of the output to change

newName - the name to change to Does nothing if the name is not found

getMemento

public java.lang.Object getMemento()

returns the current state of the simulation.

Specified by:

getMemento in interface DataGenerator

Overrides:

getMemento in class AbstractDataGenerator

Returns:

a memento of the simulation's state

getSolver

public java.lang.String getSolver()

returns the name of the current ODE solver.

Returns:

the name

setSolver

public void setSolver(java.lang.String name)

set the ODE solver to use. The names "fast", "normal" and "stiff" are guaranteed to be defined

Parameters:

name - the name of the ODE solver

Throws:

java.lang.IllegalArgumentException - if the name is undefined

getMinimizer

public java.lang.String getMinimizer()

returns the name of the current minimization algorithm.

Returns:

the name

setMinimizer

public void setMinimizer(java.lang.String name)

Set the minimization algorithm. Does no error checking now; it will throw IllegalArgumentException when we call goVarying if the name is invalid.

Parameters:

name - the name of the minimizer

doubleBean

public DoubleBean doubleBean(java.lang.String name)

creates a #util.DoubleBean for a variable

Parameters:

name - the name of the variable

Throws:

java.lang.IllegalArgumentException - if name is not a variable

java.lang.ClassCastException - if name does not evaluate to a number

get

public java.lang.Object get(java.lang.String name)
                     throws java.lang.IllegalArgumentException

returns the value of a variable in this mechanism or its script interpreter.

Parameters:

name - the name of the variable to search for

Returns:

the value. For mechanism variables, returns the value in the current run if we are running; otherwise the initial value.

Throws:

java.lang.IllegalArgumentException - if name is not found

getInitial

public double getInitial(java.lang.String name)
                  throws java.lang.IllegalArgumentException

returns the initial value of a variable in this mechanism.

Parameters:

name - the name of the variable to search for

Returns:

the value in the initial memento

Throws:

java.lang.IllegalArgumentException - if name is not found

getLatest

public double getLatest(java.lang.String name)
                 throws java.lang.IllegalArgumentException

returns the most recently determined value of a variable in this mechanism.

Parameters:

name - the name of the variable to search for

Returns:

the value in the most recent memento if we are running

Throws:

java.lang.IllegalArgumentException - if name is not found

put

public void put(java.lang.String name,
                double d)

assigns a value to a variable

Parameters:

name - the name of the variable to seach for

d - the value to assign. For mechanism variables, uses the most recent memento if we are running; otherwise the initial memento. Any name not defined in the mechanism is assumed to be defined in the script interpreter.

Throws:

java.lang.IllegalArgumentException - if name is not found

put

public void put(java.lang.String name,
                java.lang.Object o)

assigns a value to a variable

Parameters:

name - the name of the variable to seach for

o - the value to assign. For mechanism variables, uses the most recent memento if we are running; otherwise the initial memento. Any name not defined in the mechanism is assumed to be defined in the script interpreter.

Throws:

java.lang.IllegalArgumentException - if name is not found, or a non-number is assigned to a mechanism variable.

putInitial

public void putInitial(java.lang.String name,
                       double d)

assigns a value to use for the initial value for a variable.

Parameters:

name - the name of the variable to seach for

d - the value to assign. Uses the initial memento.

Throws:

java.lang.IllegalArgumentException - if name is not found

putLatest

public void putLatest(java.lang.String name,
                      double d)

assigns a value to a variable.

Parameters:

name - the name of the variable to seach for

d - the value to assign. Uses the most recent memento

Throws:

java.lang.IllegalArgumentException - if name is not found

resetVariables

public void resetVariables()

Resets all the variables' initial values to their default values.

variableNames

public java.util.List variableNames(java.lang.String listName)

returns a List of the names of all the variables defined of a given type.

Parameters:

listName - the type of variable to return

Returns:

the List of Strings. Returns an empty List (not null) if the type is not defined or is empty This should be entirely read-only; but that's not enforceable in Java

eval

public java.lang.Object eval(java.lang.String s)

executes a string in the mechanism's interpreter.

Parameters:

s - the String to evaluate

Returns:

the result of the evaluation

getCount

public int getCount()

Get the number of times the simulation has been run with goSimulate() since creation.